Agilent MassHunter

Workstation Software
Quantitative Analysis

Quantitation DataSet

Agilent Technologies
Contents
Quantitation DataSet Overview 4
Results 5
Data Types 9

Quantitation DataSet schema 11

Globals 11
Batch Table 34

Outliers Overview 177

Outliers Enabled by Default 177

Outliers 186
Peak Result 186
Qualifier 199
ISTD 204
Sample 205
Blank 207
Calibration 208
QC 216
CC 218
Matrix 223
Surrogate 229
Response Check 231
Mass 231
Custom 236

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Quantitation DataSet Overview

The Quantitation DataSet is an in-memory relational database which stores all the
quantitation information and the relationships between sample, compound(s),
qualifier(s), and calibration. A one to many (1:n) relationship exists between the
following tables:
• Each Batch (sample) has one or more TargetCompounds.
• Each TargetCompound (method) has one or more TargetQualifiers (method).
• Each TargetCompound (method) has one or more Peaks (results).
• Each Peak (results) has one or more QualifierPeaks (result).
• Each TargetCompound has one Calibration.
As a general rule, Target tables hold the method, and Peak tables hold the results.
• The TargetCompound and TargetQualifier tables store the method information
for the compounds and their qualifiers, respectively.
• The Peak and PeakQualifier tables store the result information for the
compounds and their qualifiers, respectively.

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Results
Differentiates analysis and reporting results.

Analysis
Analysis results are stored in an XML document in a relational database format.
Analysis results are stored when you save a batch.
Note that only the columns that assigned values are persisted in the results. Column
assigned NULL are not persisted in the XML document.

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Results 1: Analysis results are stored in QuantResults directory.

Note that the analysis results are stored in DrugsOfAbuseDemo.batch.bin binary file for
reasons of size and speed.

Reporting
Reporting results are stored in an XML document in a hierarchical database format.
Reporting results are stored when you generate a report. Reporting results are then
delivered to the Excel reporting subsystem.
Reporting results serve as the input to an upload to an external database. Typically,
the external database parses out the summary results using XML XPath technology
and maps those results into the customers existing database.

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Results 2: Reporting results stored in QuantReports directory under the BatchName.

Note the Excel 2007 workbook as

QuantReport_LIMsExport_summary_B_03_01.xlsx

Note the results XML document as report.results.xml

Note the directories which contain the graphics files as .emf

Globalization
Below are reference tables designed to use XPath expressions to find and replace
Enum Names (string values in the reporting results) with UI Names (localized string
values in the reporting results). Additional enum-related tables are located with their
respective column definitions.
The approach is to translate the reporting results to the local strings. The reporting
results are then imported into a localized template producing a localized Excel report.
Note that the underlying schema does not change, only the reporting result values.

Enum Name UI Name XPath expression

false false *//@*[.='true']

true true *//@*[.='false']

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Enum Name UI Name XPath expression

true true *//*[.='true']

false false *//*[.='false']

High High *//*[.='High']

Low Low *//*[.='Low']

Enum Name UI Name Example XPath expression

High High *//OutlierAccuracy[.='High']

Low Low *//OutlierAccuracy[.='Low']

Relationships
A one to many (1:n) relationship exists between the following tables:
Each Batch (sample) has one or more TargetCompounds.
Each TargetCompound (method) has one or more TargetQualifiers (method).
Each TargetCompound (method) has one or more Peaks (results).
Each Peak (results) has one or more QualifierPeaks (result).
Each TargetCompound has one Calibration.
As a general rule, “Target” tables hold the method, and “Peak” tables hold the results.
Specifically, the TargetCompound and TargetQualifier tables store the method
information to the compounds and their qualifiers, respectively.
The Peak and PeakQualifier tables store the result information for the compounds and
their qualifiers, respectively.

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Data Types
Below are definitions of the data types used in the Quantitation DataSet.

Boolean
Boolean represents “True” or “False”.

Double
Double represents a 64 bit floating point number. The number ranges from ±4.9E-324
to ±1.7976931348623157E+308.

Integer
Integer represents a 32 bit signed integer. The number ranges from -2147483648 to
2147483647.

Short
Integer represent a 16 bit signed integer. The number ranges from -32768 to 32767.

Byte
Byte represents an 8 bit signed integer. The number ranges from -128 to 127.

DateTime
Date-Time format follows ISO 8601 XML-compliant representation of dates and times.
All timezoned times are Coordinated Universal Time (UTC, sometimes called
“Greenwich Mean Time”). The presentation shows the “Local” or untimezoned times.
Example:
The Date-Time string 2008-01-20T19:00:00.

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DateTimeOffset
Date-Time Offset represents a point in time, typically expressed as a date and time of
day, relative to Coordinated Universal Time (UTC). The DateTimeOffset structure
includes a DateTime value, together with an Offset property that defines the difference
between the current DateTimeOffset instance’s date and time and UTC.

String
String represents a set of characters.
String values are often enumerations representing different categories.
Example:
The following set:

Categories: Choices for Sample Type.

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Quantitation DataSet schema

Below are the details of each column (XML attributes and elements) organized by the
hierarchy of tables in the DataSet.

DataSet 1: The Quantitation DataSet is an in-memory relational database which stores all the
quantitation information and the relationships between sample, compound(s), qualifier(s), and
calibration.

Globals
Below are the definitions of the globals (XML attributes) that pertain to the entire
batch.

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DataSet 2: Shows the globals from the Excel XML mapping.

AnalyzeQuantVersion
AnalyzeQuantVersion designates the version of Quantitation software when batch is
saved.

AnalysisTimeStamp
AnalysisTimeStamp is the date and time for last change to the results.
AnalysisTimeStamp is set whenever re-calculation occurs in Batch-at-a-Glance.

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DateTime 1: Records the datetime in XML format.

AnalystName
AnalystName is the name of person logged on who generated these results. The name
is fetch from the environment which reflects the user’s logon information.
AnalystName is set when reports are generated.

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Name 1: Records user name.

ApplyMultiplierISTD
ApplyMultiplierISTD represents the selection to apply the sample Multiplier. The
sample multiplier is a multiplicative operation on the FinalConcentration. A sample
multiplier of "2" will double the reported concentration of the affected compound
types.

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ApplyMultiplierISTD may be useful in adjusting samples that were prepared with

different ISTD concentrations.

ApplyMultiplierMatrixSpike
ApplyMultiplierMatrixSpike represents the selection to apply the sample Multiplier.
The sample multiplier is a multiplicative operation on the FinalConcentration. A
sample multiplier of "2" will double the reported concentration of the affected
compound types.

ApplyMultiplierSurrogate
ApplyMultiplierSurrogate represents the selection to apply the sample Multiplier. The
sample multiplier is a multiplicative operation on the FinalConcentration. A sample
multiplier of "2" will double the reported concentration of the affected compound
types.

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ApplyMultiplierTarget
ApplyMultiplierTarget represents the selection to apply the sample Multiplier. The
sample multiplier is a multiplicative operation on the FinalConcentration. A sample
multiplier of "2" will double the reported concentration of the affected compound
types.

AppSchemaVersion
AppSchemaVersion designates the Quantitation DataSet schema version used by the
currently running Quant application instance.

AuditTrail
AuditTrail records the state of audit trail for this batch.

BatchDataPathFileName
BatchDataPathFileName is the file system path and file name to the batch analysis
results. Saving the batch sets the BatchDataPathFileName.

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BatchName
BatchName is the user-defined name for the collection of samples analyzed together.

BatchState
BatchState is an internal quantitation state that records the synchronization of the
analysis.

BatchState 1: "Processed" when analysis completed.

Enum Name UI Name XPath expression

Initial Initial *//@BatchState[.='Initial']

Processed Processed *//@BatchState[.='Processed'

]
ResultsCleaned ResultsCleaned *//@BatchState[.='ResultsCle
aned']

ResultsDirty ResultsDirty *//@BatchState[.='ResultsDir

ty']

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BracketingType
BracketingType changes the association between samples and their calibration
samples. The purpose of bracketing is to reduce uncertainty of the calibration curve
applied to a particular sample.
By default, all the calibration samples grouped in a batch to create the calibration
curve. In other words, the position of the calibration samples with respect to a
sample block does not affect the sample’s calibration curve. All samples share the
same calibration curve regardless.
BracketingType set to Overlapped groups the set of Calibration and QCs above the
below a set of samples and averages that group of Calibration and QCs to generate a
calibration curve that is applied to those “bracketed” samples. In this manner, the
“bracketed” samples receive a calibration curve created from calibration samples
whose variation is minimized.

Bracketing 1: In this example, the first sample block [Positions 11,12,13,14,15,] use the
calibration curve created from the CAL1, CAL2, CAL3 samples above and below that sample
block. Similarly, the next sample block [Positions 16,17,18,19,20] uses the CAL1, CAL2, CAL3

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(overlapped) above and the CAL1, CAL2, CAL3 sample below. Hence, the name overlapped
averaged bracketing.

BracketingType set to “SampleGroup”, for each compound in each sample, only the calibration
samples that share the same Sample Group attribute as the sample in question are used to
compute the compound calibration table.

Enum Name UI Name XPath expression

None None *//@BracketingType[.='None']

Overlapped Overlapped *//@BracketingType[.='Overla

pped']

SampleGroup SampleGroup *//@BracketingType[.='Sample

Group']

CalibrationLastUpdatedTimeStamp
CalibrationLastUpdatedTimeStamp is the date and time for last change to the
calibration table. Set whenever the Calibration information is recalculated. For
example, re-analyzing the batch re-builds the calibration table that resets this
timestamp.

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DateTime 2: Records DateTime in XML format.

CCMaximumElapsedTimeInHours
CCMaximumElapsedTimeInHours records the maxium allowed difference in time
between any sample and the CC sample type in that batch.

ComplianceName
ComplianceName records the compliance module name. e.g. ECM.

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ComplianceServer
ComplianceServer records the server path that contains the batch file.

ComplianceVersion
ComplianceVersion records the compliance module version.

CorrelationWindow
CorrelationWindow represents the size of the correlation window.
CorrelationWindow is used in processing the current data file to determine if peaks
found during integration of the target and qualifier signals are due to the same
chromatographic elution (i.e., have the same retention time). The units are minutes.
Example:
Change the RT correlation window from 1 minute to 2 minutes helps the quantitation
algorithm to associate the qualifier peak with the quantifier from same compound.

DAMethodLastAppliedTimeStamp
DAMethodLastAppliedTimeStamp records the date and time for last change to the
method. Set whenever the method is edited in the Method Editor and then applied to
Batch.

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DateTime 3: Records DateTime in XML format.

Note that DateTime recorded in XML standard DateTime format.

DAMethodPathFileNameOrigin
DAMethodPathFileNameOrigin designates the path and file name where the method
originally was opened and applied. When a user opens a method from an existing file
and applies that method to the batch, Batch-at-a-Glance records the
DAMethodPathFileNameOrigin.
If the user opens a method from an existing batch, the DAMethodPathFileNameOrigin
remains with its original setting. Note that if a user creates a method manually, the
DAMethodPathFileNameOrigin is not set.

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DataVersion
DataVersion represents the version of the software used to generate the reporting
results.

DynamicBackgroundSubtraction
DynamicBackgroundSubtraction “flattens” the chromatogram.
DynamicBackgroundSubtraction activates an algorithm which processes the raw
chromatogram by removing “noise” ions. “Noise” ions, which are evaluated by
deconvolution technique, do not group together forming a peak shape and are
therefore considered part of the background.

DBS 1: Quant Method globals allows DynamicBackgroundSubtraction which affects all chromatograms in
batch.

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DBS 2: Enabled DynamicBackgroundSubtraction "flattens" the chromatogram. Compare before and after.

Note that DynamicBackgroundSubtraction requires computer time to execute the

algorithm so enabling DynamicBackgroundSubtraction will slow down the Quant
Analysis time.

FeatureDection
FeatureDetection changes the data access being used in quantitation. If it is true,
feature data access (marketing name “SureMass”) is used. It only applies to accurate
mass data.

HashCode
HashCode is a checksum calculated and stored with the results.

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Hashcode 1: Unique string stored in XML document identifies any changes to the document if the
hash code does not match.

IgnorePeaksNotFound
IgnorePeaksNotFound is a global flag that affects the Quantitation Message. The
purpose is avoid flagging target compounds that are normally absent in target samples,
such as pesticides in food samples.
If the IgnorePeaksNotFound global flag is false, the software will flag all errors of type
“Peak not found” with a Quantitation Message. If IgnorePeaksNotFound is true (the
box is checked), the “Peak not found” quantitation message errors are ignored for
target compounds in target samples (Sample) and blank samples (Blank, DoubleBlank,
and MatrixBlank). Failed manual integrations, ISTD compounds, MatrixSpike

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compounds, Surrogate compounds and non-target samples are still flagged. ISTD
compound in DoubleBlank sample is not flagged since it is not expected to be present.

IgnorePeaksNotFound: With this sample, analysis informs you with a quantitation message that
for this particular compound, no peak has been found. If you do not want to see messages informing
you that no peaks are found, you can turn on this batch global setting.

LibraryMethodPathFileName
LibraryMethodPathFileName is the file system path and file name to the library
method that contains parameter settings for deconvolution, library search and
compound identification.

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LibraryPathFileName
LibraryPathFileName is the file system path and file name to the Agilent formatted
compound library used during Library Search features. Library search features are
disabled if the LibrarySearchPathFileName is NULL. This field is obsolete now.

NonReferenceWindow
NonReferenceWindow is used to determine if the peak specified in the Quantitation
DataSet is present in the data file currently being processed.
Example:
A window of 5% means that the peak group (quantifier and qualifier peaks) processed
must have an average retention time within +/-2.5% of the time in the quantitation
database.
The reference window applies to internal standards that are designated as time
reference peaks. The non-reference window applies to all other compounds.
The NonReferenceWindow size is based on the
NonReferenceWindowPercentOrMinutes.
Example:
Changing the non-reference RT window from 40 percent to 200 percent increases the
range around the expected RT that is used to identify quantifier peaks. The wider
window helps with retention times that wander around from sample to sample.
Recognition window is the RT range around the adjusted expected Retention Time RT’.
The RT range is determined from the ReferenceWindow size or NonReferenceWindow
size depending on if the compound has a time reference compound or not. Adjusted
expected Retention Time is equal expected Retention Time if the compound does not
have a time reference ISTD; and is adjusted by the ratio of the actual-to-expected
retention time of reference ISTD’s primary hit peak if it has a time reference ISTD. i.e.,
Recognition window = [ RT’- 0.5* ReferenceWindow Size, RT’ + 0.5 *
ReferenceWindow Size] or
Recognition window = [ RT’- 0.5* NonReferenceWindow Size, RT’ + 0.5 *
NonReferenceWindow Size]

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Note: If the ReferenceWindow size is smaller that the Correlation Window it is possible
to see a target or qualifier peak that falls outside the ReferenceWindow.

NonReferenceWindowPercentOrMinutes
NonReferenceWindowPercentOrMinutes represents the setting in percent or minutes
for the non-reference window.

Enum Name UI Name XPath expression

Minutes Minutes *//@NonReferenceWindowPercentOrMinutes[.=

'Minutes']

Percent Percent *//@NonReferenceWindowPercentOrMinutes[.=

'Percent']

ReferenceWindow
ReferenceWindow is used to determine if the peak specified in the Quantitation
DataSet is present in the data file currently being processed.
Example:
A window of 5% means that the peak group (quantifier and qualifier peaks) being
processed must have an average retention time within +/-2.5% of the time in the
quantitation database.
The reference window is used for internal standards that are designated as time
reference peaks. The non-reference window is used for all other compounds.
The ReferenceWindow size is based on the ReferenceWindowPercentOrMinutes.
Recognition window is the RT range around the adjusted expected Retention Time RT’.
The RT range is determined from the ReferenceWindow size or NonReferenceWindow
size depending on if the compound has a time reference compound or not. Adjusted
expected Retention Time is equal expected Retention Time if the compound does not
have a time reference ISTD; and is adjusted by the ratio of the actual-to-expected
retention time of reference ISTD’s primary hit peak if it has a time reference ISTD. i.e.,

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Recognition window = [ RT’- 0.5* ReferenceWindow Size, RT’ + 0.5 *

ReferenceWindow Size] or
Recognition window = [ RT’- 0.5* NonReferenceWindow Size, RT’ + 0.5 *
NonReferenceWindow Size]
Note: If the ReferenceWindow size is smaller that the Correlation Window it is possible
to see a target or quialifier peak that falls outside the ReferenceWindow

ReferenceWindowPercentOrMinutes
ReferenceWindowPercentOrMinutes represents the setting in percent or minutes for
the reference window.

Enum Name UI Name XPath expression

Minutes Minutes *//@ReferenceWindowPercentOrMinutes[.='Mi

nutes']

Percent Percent *//@ReferenceWindowPercentOrMinutes[.='Pe

rcent']

RefLibraryPathFileName
RefLibraryPathFileName is the file system path and file name to the Reference Library
created from high level calibration sample or from existing library in the .L or
.mslibray.xml format. Reference Library Match score features are disabled if the
RefLibrarySearchPathFileName is NULL.

RefLibraryPatternPathFileName
RefLibraryPatternPathFileName is the file system path and file name to the Pattern
Reference Library. The Pattern Reference Library is typically synthesized from the
MolecularFormula and associated adducts and stores a “spectral” entry for each
pattern.

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More than one pattern is likely for each compound. For example, with the
monoisotopic mass M, the isotopic patterns that corresponds to the (M+H)+ and
(M+Na)+ and (M+K)+ adducts.
Note: Mass Match score features are disabled if the RefLibraryPatternPathFileName is
NULL.

RelativeISTD
RelativeISTD represents a mechanism to analyze using the ISTD as the reference
calibration amount - instead of the typically ISTD correction.
In the following example, the amount of [Phe] is determined by calculating the area
ratio against the heavy isotoped analog and then multiplying by the known ISTD
amount of [D5Phe].
Intensity of Phe
[ Phe] = x [ D 5 Phe]
Intensity of D 5 Phe
Note that the RelativeISTD mechanism can adjust the Response Factor of the target
versus ISTD using the RelativeISTDMultiplier.

ReportGenerationStartedTimeStamp
ReportGeneratedStartedTimeStamp is the date and time for initiation of reporting
results generation. Value is updated in report.results.xml, instead of global.

ReportGeneratorName
ReportGeneratorName records the user name that generated the reporting results.

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Name 2: Records user name.

ReportQuantVersion
ReportQuantVersion designates the version of Quantitation software when report is
generated.

ReportResultsPathFileName
ReportResultsPathFileName is the file system path and file name to the reporting
results generated. Uploading the reporting results sets the
ReportResultsPathFileName so the location of the reporting results is known.

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RepositoryRevisionNumber
RepositoryRevisionNumber is the ECM batch revision number for Quant batch report.

SchemaVersion
SchemaVersion designates the revision of the XML schema used with this particular
Quantitation DataSet. The SchemaVersion is read from the batch XML file as an
attribute and is compared to AppSchemaVersion.

StandardAddition
StandardAddition changes the association between samples and their “calibration”
samples. The purpose of standard addition is to quantitate whenever the matrix of a
sample changes the analytical sensitivity of the method.
StandardAddition is a technique that introduces a standard of your target compound
directly into the analytical sample. After estimating the amount of target analyte
present in the sample, samples are then spiked with known concentrations. By
extrapolating the curve from the spiked samples, the original amount present in the

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sample can be determined. This technique assumes that the response for that
particular analyte is linear in the concentration range of the sample.
The purpose of the spiked standards is to establish an analytical curve and determine
the response factor for the target analyte. With the responses obtained from the target
analyte in both the original sample and the spiked samples, the responses are used to
calculate the method specific response factor for the target analyte. That response
factor is subsequently used to determine the concentration of the unknown based on
the responses of the unknown and the “standards”.

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Batch Table

Primary Key
{BatchID, SampleID} serves as the primary key. The composite of the BatchID and
SampleID unique identify each row in this table. The keys in the Quantitation DataSet
are not show in the user interface.
A primary key value must be unique with in the table. A composite key is a primary
key that incorporates more than one column.

BatchID
BatchID uniquely identifies the batch. BatchID is part of the composite primary key.
The BatchID is typically set to -1 because Batch-at-a-Glance analyzes one batch.

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SampleID
SampleID uniquely identifies the sample in the batch. SampleID is part of the
composite primary key. Thus, each sample in the batch is assigned a unique
SampleID.

AcqDateTime
AcqDateTime stores the date and time that the sample’s raw data was acquired. It
shows the date time where the Quant program is running.

AcqDateTimeLocal
AcqDateTimeLocal records the acquisition date time in time zone where data is
acquired.

AcqMethodFileName
AcqMethodFileName stores the short filename of the acquisition method used to
acquire the sample’s raw data.

AcqMethodPathName
AcqMethodPathName stores the path to the AcqMethodFileName used during
acquisition.

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AcqOperator
AcqOperator stores the user that ran this sample.

BalanceOverride
BalanceOverride stores sample information concerning the balance adjustments used
during acquisition.

Barcode
Barcode stores the sample information related to a Barcode identifier used during
acquisition.
Barcode is a machine-readable representation of a string. Barcodes are typically used
to labeled samples containers and scanned by optical scanners to "type" in the
SampleName.

CalibrationReferenceSampleID
CalibrationReferenceSampleID internally identifies the SampleID that contains the
calibration table information.

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Figure 1: Show calibration table stored in QuantitationDataSet for a particular compound.

Note that the calibration table is stored in only one sample in the batch.
The only exceptions are cases where the calibration table is different for different
sample such as StandardAddition or BracketingType.

Comment
Comment stores user entered information about this sample.

Completed
Completed stores whether the sample was successfully finished acquisition.

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DADateTime
DADateTime stores the date and time that the sample’s data was last processed.

DAMethodFileName
DAMethodFileName stores the data analysis method name used to analyze this
sample. If the method was not saved using a name, then DAMethodFileName is NULL.

DAMethodPathName
DAMethodPathName stores the path to the Data Analysis Method name. If the method
was not saved using a name, then DAMethodPathName is NULL.

DAMethodPathName: This DAMethodPathName is C:\Data\THC_in_Oral_Fluids\.

DataFileName
DataFileName stores the name of the data file directory (.d) that collects this sample’s
files.

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DataFileName: The DataFileName for this sample is OF_THC_01.d.

DataPathName
DataPathName stores the path to the DataFileName. It’s the location of data when
samples were originally added to the batch. If the data set has been moved to a
different location from when the batch was created, DataPathName will update to
reflect the new location after sample is analyzed.

DataPathName: This DataPathName is C:\Data\THC_in_Oral_Fluids\.

Dilution
Dilution stores the Dilution Factor.
Multiplier = Dilution
FinalConcentration = CalculatedConcentration × Multiplier

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Example:
If the sample is diluted by a factor of 2, the Dilution Factor is 2. Hence, the
CalculatedConcentration is multiplied by 2 to adjust the FinalConcentration.

DualInjector
DualInjector declares that another vial is injected in the other injector port during the
sample run. The dual injection expects an acquired signal used for confirmation. The
dual signal is stored in the same .d as the sample acquired.
Since one sample is organized as one .d directory, analysis typically treats the signal
as acquired from the same sample.

DualInjectorAcqDateTime
DualInjectorAcqDateTime stores the date and time that the sample’s raw data was
acquired from the dual injector. It shows the date time where the Quant program is
running.

DualInjectorBarcode
DualInjectorBarcode stores the sample information related to the Barcode identifier
used during acquisition for the dual injector.
Barcode is a machine-readable representation of a string. Barcodes are typically used
to labeled samples containers and scanned by optical scanners to “type” in the
SampleName.

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DualInjectorExpectedBarcode
DualInjectorExpectedBarcode stores the sample information related to a Barcode
identifier used during acquisition. The DualInjector typically refers to the rear GC
injector as opposed to the front GC injector i.e. ExpectedBarcode.

DualInjectorVial
DualInjectorVial stores the number of the vial used to create the dual injection.

DualInjectorVolume
DualInjectorVolume stores the volume of the dual injection for this sample.

EquilibrationTime
EquilibrationTime stores the time used to equilibrate the column before injection.

ExpectedBarcode
ExpectedBarcode stores the sample information related to a Barcode identifier used
during acquisition.
ExpectedBarcode stores the barcode recorded during sample login which typically
matches the BarCode.
ExpectedBarcode is a machine-readable representation of a string. Barcodes are
typically used to label samples containers and are scanned by optical scanners to
"type" in the SampleName.

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GraphicSampleChromatogram
GraphicSampleChromatogram represents a relative path and filename to a graphic
(.emf) file used in reporting.

Graphic 1: Graphic file reference.

InjectionsPerPosition
InjectionsPerPosition stores the number of injections from that particular position in
that container. A typical container is a vial.
Not necessarily support in all acquisition subsystems.

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InjectorVolume
InjectorVolume stores the volume of the injection for this sample.

InstrumentName
InstrumentName stores the name of the instrument that acquired this sample.
InstrumentName is useful to relate back to the instrument used to answer questions
about the acquired data origins.

InstrumentType
InstrumentType stores kind of instrument. Typical instruments are QQQ, qTOF, and
TOF.
Different InstrumentTypes required different presentations. For example, MS/MS
instruments have additional scan types.

ISTDDilution
ISTDDilution stores a per sample ISTDConcentration correction.
ISTDConcentration = ISTDDilution *ISTDConcentration (ISTD compound)
ISTDDilution is useful when you are weighing out the ISTD for each sample and the
amount varies slightly.
ISTDDilution is also useful to correct for (mistakenly) adding twice as much ISTD as
needed.
ISTDDilution updates the ISTDConcentration stored with the target compound that
uses that ISTD compound.
ISTDDilution works independently from the Multiplier or ApplyMultipliertoISTD
adjustments.

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MatrixSpikeDilution
MatrixSpikeDilution stores a per sample MatrixSpike Concentration correction. It
only affects MatrixSpike expected concentration and MatrixSpike recovery. The
CalculatedConcentration and FinalConcentration of MatrixSpike compound are not
affected.
MatrixSpike Concentration = MatrixSpike Dilution *MatrixSpike Concentration (MatrixSpike
Compound)
MatrixSpikeDilution is useful when you are weighing out the MatrixSpike for each
sample and the amount varies slightly.
MatrixSpikeDilution updates the MatrixSpike Concentration stored with the matrix
spike compound.

MatrixSpikeGroup
MatrixSpikeGroup represents a user-defined name that enables a set of samples to
associate together in order to accomplish the Matrix Spike Percent Recovery
calculations.
If MatrixSpikeGroup is assigned for any sample only this recovery outline is
calculated.

MatrixType
MatrixType is a user-defined name that enables association with MatrixTypeOverride
to define different outlier limits at a per sample base.

LevelName
LevelName stores the calibration level name used to identify the compound’s
concentrations into a group. LevelName(s) are used to identify Calibration and QC
(Quality Control) samples that are used to construct the calibration curve for each
compound. Different compounds can have different calibration levels with one
restriction: Any internal standards must have the same number of levels, level names,
and concentrations as the target compound.

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The LevelName and the compound’s ExpectedConcentration work together to

establish the calibration curve.
LevelName(s) are established either during:
• Acquisition Sequence (Worklist) Setup
• Analysis time
LevelName is editable in Batch-at-a-Glance.

Locked
Locked stores the “Locked” state of the Worklist during acquisition. If Locked is true
then this sample was acquired under “Locked” acquisition Worklist conditions.

PlateCode
PlateCode stores the code that identifies that plate (container).
PlateCode is sample information entered in acquisition.

PlatePosition
PlatePosition stores the position that identifies to location on the plate (container).

QuantitationMessage
QuantitationMessage stores problems associate with the analysis of that particular
sample.

RackCode
RackCode stores the code that identifies the rack (container).
RackCode is sample information entered in acquisition.

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RackPosition
RackPosition stores the position in the rack (container).
RackCode is sample information entered in acquisition.

RunStartValvePositionDescription
RunStartValvePositionDescription stores the LC column switching valve position at
the start of the chromatographic run. Valve position determines which LC column is
being used for chromatographic separation. Refer to the instrument LC comlumn
configuration for more information on this parameter.

RunStartValvePositionNumber
RunStartValvePositionNumber stores the LC column switching valve position
description at the start of the chromatographic run. Valve position determines which
LC column is being used for chromatographic separation. Refer to the instrument LC
column configuration for more information on this parameter.

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RunStopValvePositionDescription
RunStopValvePositionDescription stores the LC column switching valve position at the
end of the chromatographic run. Valve position determines which LC column is being
used for chromatographic separation. Refer to the instrument LC column
configurqation for more information on this parameter.

RunStopValvePositionNumber
RunStopValvePositionNumber stores the LC column switching valve position
description at the end of the chromatographic run. Valve position determines which
LC column is being used for chromatographic separation. Refer to the instrument LC
column configuration for more information on this parameter.

SampleAmount
SampleAmount stores the amount of sample actually used in analysis. The
SampleAmount along with the TotalSampleAmount computes the Multiplier. The
Multiplier then converts the CalculatedConcentration to the FinalConcentration.
Multiplier = TotalSampleAmount ÷ SampleAmount
FinalConcentration = CalculatedConcentration × Multiplier
In this scenario, FinalConcentration adjusts as an amount.
Example:
If your sample preparation needs to adjust the FinalConcentration for a volume, use
the SampleAmount as the Volume adjustment and set TotalSampleAmount to “1”.
Multiplier = 1 ÷ SampleAmount
Note that both SampleAmount and TotalSampleAmount must have values for the
calculation to occur.
Example:
If you need to adjust the FinalConcentration using several sample preparation factors,
note that Dilution can work in concert with the TotalSampleAmount/SampleAmount
adjustment.

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Multiplier = (TotalSampleAmount ÷ SampleAmount )*Dilution

SampleApproved
SampleApproved records the user’s decision on the status of the sample. For example,
the user sets the SampleApproved status to True, meaning the sample is considered
approved.
SampleApproved is initialized to NULL and editable by the user in Batch-at-a-Glance.

SampleGroup
SampleGroup represents a user-defined name that enables a set of samples to
associate together.
For example, if you create a sequence with a set of samples designated with the same
SampleGroup name, then you could group those samples in reporting.
Another example, if you queued several different sequences together, yet with
different SampleGroup names, then you could later search for those sequences using
the SampleGroup column.
The quantiation software does not assign any particular behavior to the SampleGroup
column so its purpose is user-defined.

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SampleGroup 1: Labeling samples with a SampleGroup name enables customizable filtering.

SampleInformation
SampleInformation stores the information about the sample.
SampleInformation is sample information entered in acquisition.

SampleName
SampleName stores the name of the sample.
SampleName is sample information entered in acquisition.

SamplePosition
SamplePosition stores the position of the sample.
In LC-MS acquisition, the SamplePosition typically stores the position of the sample in
the container.
SamplePosition is sample information entered in acquisition.

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SamplePrepFileName
SamplePrepFileName stores the filename of the sample preparation method used
when running this particular sample.

SamplePrepPathName
SamplePrepFileName stores the path i.e. directory of the sample preparation method
used when running this particular sample.

SampleState
SampleState stores the state of the sample.
Typical definitions are as follows:
Entered— Sample entered in a sample tracking
Analyzed— Sample analyzed by Quantitative Analysis

SampleType
SampleType stores the type of sample.
Typical definitions are as follows:
Sample—the actual matrix (i.e. water, soil, food, etc.) which possibly
contains the compound(s) of interest in unknown quantities as prepared for
analysis (i.e. sample preparation). For Drug mode workflow, this sample type
is referred to as a “Specimen”.

Blank—usually an amount of the solvent(s) used for preparation of the

sample that is analyzed in order to detect possible contamination.ISTD is
added to this sample to allow proper quantitation. For Drug mode workflow,
this sample type is referred to as a “Negative”.

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Double Blank—identical to a blank above except the Internal Standard is not

added to it. For Drug mode workflow, this sample type is referred to as a
“Blank”.

Calibration Sample (aka Standard)—an amount of solvent(s) that contains a

known quantity of the compound(s) of interest. Calibration Samples are
injected at different levels to construct a Calibration Curve.

QC Sample — an amount of solvent(s) that contains a known quantity of the

compound(s) of interest (just like a Calibration Sample). The QC Sample is
injected and quantitated like a regular Sample in order to validate the
Calibration Curve.

CC Sample — an amount of solvent(s) that contains a known quantity of the

compound(s) of interest (just like a QC Sample). The CC Sample is injected
and quantitated like a regular Sample in order to validate the initial
Calibration Curve. If the initial Calibration Curve is acceptable, then the
Calibration Curve is considered satisfactory and re-running the Calibration
sample is not considered necessary.

Matrix Blank—an amount of the matrix (i.e. water, soil, food, etc.) which is
known to not have any of the compound(s) of interest that is prepared for
analysis (i.e. sample preparation).

Matrix QC (aka Matrix Spike) —an amount of the matrix (i.e. water, soil,
food, etc.) which is “spiked” with a known amount of the compound(s) of
interest and then prepared for analysis (i.e. sample preparation). A
parameter called the “Recovery” is calculated from the Matrix QC to measure
the accuracy of the analysis.

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Matrix QC Duplicate (aka Matrix Spike Duplicate) —identical to a Matrix QC,

the term is used when two Matrix QC of the same concentration are
quantitated to validate the precision of the analysis (i.e. that you can inject
the identical amount twice and get the same results).

ISTD (“Internal Standard”)—a compound with similar chemical characteristics

but different physical characteristics (e.g. m/z) than the compound(s) of
interest that is “spiked” into all the Sample Types. The ISTD is then used to
correct concentrations for all Sample Types based on its concentration. It
may also be used to adjust the retention times of the compound(s) of
interest if its retention time shifts during a set of analyses.

Surrogate—identical to an ISTD except it is not used to correct

concentrations for all Sample Types based on its concentration.
SampleType is editable in Batch-at-a-Glance.

Enum Name XPath expression

Sample *//SampleType[.='Sample']

Blank *//SampleType[.='Blank']

Calibration *//SampleType[.='Calibration']

QC *//SampleType[.='QC']

CC *//SampleType[.='CC']

DoubleBlank *//SampleType[.='DoubleBlank']

Matrix *//SampleType[.='Matrix']

MatrixDup *//SampleType[.='MatrixDup']

MatrixBlank *//SampleType[.='MatrixBlank']

TuneCheck *//SampleType[.='TuneCheck']

ResponseCheck *//SampleType[.='ResponseCheck']

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SamplingDateTime
SamplingDateTime holds the date and time that enables a time relationship between
samples in the batch.
Certain time series experiments involve sampling at time intervals to monitor changes
in analytes. Recording the SamplingDateTime enables the organization of the samples
in a time-oriented sequence.
For example, in biological systems, a time series study involves monitoring the
metabolite concentration levels over time after administration of an antagonist.

SamplingTime
SamplingTime stores time measured as a number in arbitrary units.
For example, seconds since the initiation of an experiment.
Recording SamplingTime is useful in a time-series sampling.

SurrogateDilution
SurrogateDilution stores a per sample Surrogate Concentration correction. It only
affects Surrogate expected concentration and surrogate recovery. The
CalculatedConcentration and FinalConcentration of surrogate compound are not
affected.
Surrogate Concentration = Surrogate Dilution *Surrogate Concentration (Surrogate
Compound)
SurrogateDilution is useful when you are weighing out the surrogate for each sample
and the amount varies slightly.
SurrogateDilution updates the Surrogate Concentration stored with the surrogate
compound.
SurrogateDilution works independently from the Multiplier or
ApplyMultipliertoSurrogate adjustments.

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TrayName
TrayName stores the tray name.
Typical the trayname refers to the CTC PAL injector tray.

TotalSampleAmount
TotalSampleAmount stores the total amount of the sample. The SampleAmount in
conjunction with the TotalSampleAmount adjusts the FinalConcentration.
Multiplier = TotalSampleAmount ÷ SampleAmount
FinalConcentration = CalculatedConcentration × Multiplier
In this scenario, FinalConcentration adjusts as an amount.

TuneFileLastTimeStamp
TuneFileLastTimeStamp stores the last tune time of the instrument that was used to
acquire the sample’s raw data. It’s the time stamp of the tune file whose file name is
TuneFileName.

TuneFileName
TuneFileName stores the tune filename that was used to tune the instrument when
acquire the sample’s raw data.

TunePathName
TunePathName stores the path name of the tune file that was used to tune the
instrument when acquire the sample’s raw data.

UserDefined
UserDefined stores an arbitrary user-defined string.
UserDefined is editable in Batch-at-a-Glance.

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UserDefined1
UserDefined1 stores an arbitrary user-defined string.

UserDefined2
UserDefined2 stores an arbitrary user-defined string.

UserDefined3
UserDefined3 stores an arbitrary user-defined string.

UserDefined4
UserDefined4 stores an arbitrary user-defined string.

UserDefined5
UserDefined5 stores an arbitrary user-defined string.

UserDefined6
UserDefined6 stores an arbitrary user-defined string.

UserDefined7
UserDefined7 stores an arbitrary user-defined string.

UserDefined8
UserDefined8 stores an arbitrary user-defined string.

UserDefined9
UserDefined9 stores an arbitrary user-defined string.

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Vial
Vial stores the number or designator that identifies the vial used to create the
injection.
In GC-MS acquisition, the Vial typically stores the sample vial number for the
container.

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TargetCompound Table

Primary Key
{BatchID, SampleID, CompoundID} serves as the primary key. The composite of the
BatchID and SampleID and CompoundID unique identify each row in this table. The
keys in the Quantitation DataSet are not show in the user interface.
A primary key value must be unique with in the table. A composite key is a primary
key that incorporates more than one column.

BatchID
BatchID uniquely identifies the batch. BatchID is part of the composite primary key.
The BatchID is typically set to -1 because Batch-at-a-Glance analyzes one batch.

SampleID
SampleID uniquely identifies the sample in the batch. SampleID is part of the
composite primary key. Thus, each sample in the batch is assigned a unique
SampleID.

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CompoundID
CompoundID uniquely identifies the sample in the batch. CompoundID is part of the
composite primary key. Thus, each compound in the batch is assigned a unique
CompoundID.

AccuracyLimitMultiplierLOQ
AccuracyLimitMultiplierLOQ represents an adjustment to lowest enabled calibration
level Accuracy limit.
Example:
If AccuracyMaximumPercentDeviation is set at 20% and AccuracyLimitMultiplierLOQ
is set at 1.5, the lowest enabled calibration level Accuracy is evaluated with the limit of
30%.

AccuracyMaximumPercentDeviation
AccuracyMaximumPercentDeviation represents the limit for the Accuracy outlier.
OutlierAccuracy is set too High if this compound’s CalculatedConcentration exceeds
ExpectedConcentration by more than AccuracyMaximumPercentDeviation percent.

AgilentID
AgilentID represents an identifier in Agilent database.

AlternativePeakCriteria
AlternativePeakCriteria represents a standard, e.g., deconvoluted library match score,
to evaluate the quality of an alternative peak against the primary peak selected by
Quant engine.

AlternativePeakID
AlternativePeakID represents the peak ID of an alternative peak that has better score
based on the AlternativePeakCriteria selected.

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AreaCorrectionFactor
AreaCorrectionFactor represents a scale factor. AreaCorrectionFactor is applied to the
integrator-determined area of an Area Correction signal specified by
AreaCorrectionMZ. The resulting product is subtracted from the integrator-determined
area of the signal specified by MZ (and SelectedMZ in the case of tandem mass spectral
experiments). The resulting difference is used for target signal response quantitation.
If QuantitateByHeight is true, area correction is based on peak height.

AreaCorrectionMZ
AreaCorrectionMZ represents a mass-to-charge measurement, in units of daltons per
unit charge, which specifies a signal to extract from the quantitation data source. Once
extracted, this signal is integrated and the resulting area is subtracted from the target
signal area. The resulting difference is used for quantitation instead of the unmodified
target signal area. If the value of AreaCorrectionMZ is 0, no area-correction signal is
extracted, and no area correction is brought to bear on the target signal response. If
QuantitateByHeight is true, area correction is based on peak height.

AreaCorrectionSelectedMZ
AreaCorrectionSelectedMZ together with AreaCorrectionMZ defines a MRM signal to
extract from the quantitation data source. Once extracted, this signal is integrated and
the resulting area is subtracted from the target signal area. The resulting difference is
used for quantitation instead of the unmodified target signal area. If the value of
AreaCorrectionMZ is 0, no area-correction signal is extracted, and no area correction
is brought to bear on the target signal response. If QuantitateByHeight is true, area
correction is based on peak height.

AverageRelativeRetentionTime
AverageRelativeRetentionTime represents the average of the relative retention time
values of all the peaks that provide the responses for this compound’s enabled
Calibration and QC points. A relative retention time is defined as the ratio of the
retention time of the primary peak for the target compound to the retention time of
the primary peak of the related internal standard. AverageRelativeRetentionTime is
computed only for those compounds that have an internal standard.
AverageRelativeRetentionTime is used to evaluate the Relative Retention Time outlier
condition.

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AverageResponseFactor
AverageResponseFactor represents the average of the response factors of all the
enabled calibration points for this compound. The response factor of a calibration
point is defined as the ratio of the calibration peak’s response to the concentration of
this point’s calibration level. AverageResponseFactor is used to evaluate to the
Average Response Factor outlier condition.

AverageResponseFactorRSD
AverageResponseFactorRSD represents the relative standard deviation of the level
response factors of a target compound across the calibration levels.
AverageResponseFactor RSD is used to evaluate to the Average Response Factor RSD
outlier condition.

BlankResponseOffset
BlankResponseOffset stores the average of the TargetResponse values for the same
compound in all the samples of type Blank. If there are no blank samples in the batch,
the column stays NULL.

CalibrationRangeFilter
CalibrationRangeFilter is an enum {HighOnly, LowOnly, HighLow} that controls what flag
to show for Calibration range outlier.

CapacityFactorLimit
CapacityFactorLimit is the outlier limit for the capacity factor outlier.

CASNumber
CASNumber stores the Chemical Abstracts Service registry number.
Example:
The CAS number of cocaine (CAS 50-36-2) serves as an index into the NIST Library.
The NIST Library contains substantial about of compound information:

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A CAS registry number is separated by hyphens into three parts, the first consisting of
up to six digits, the second consisting of two digits, and the third consisting of a single
digit serving as a check digit. The numbers are assigned in increasing order and do not
have any inherent meaning. The checksum is calculated by taking the last digit times 1,
the next digit times 2, the next digit times 3 etc., adding all these up and computing the
sum modulo 10.
Example:
The CAS number of water is 7732-18-5: the checksum is calculated as (8×1 + 1×2 + 2×3
+ 3×4 + 7×5 + 7×6) = 105; 105 mod 10 = 5.

CCISTDResponseRatioLimitHigh
CCISTDResponseRatioLimitHigh represents the high limit for the continuing
calibration ISTD response ratio involved in the CCISTDResponseRatio outlier.

CCISTDResponseRatioLimitLow
CCISTDResponseRatioLimitLow represents the low limit for the continuing calibration
ISTD response ratio involved in the CCISTDResponseRatio outlier.

CCResponseRatioLimitHigh
CCResponseRatioLimitHigh represents the high limit for the continuing calibration
response ratio involved in the CCResponseRatio outlier.

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CCResponseRatioLimitLow
CCResponseRatioLimitLow represents the low limit for the continuing calibration
response ratio involved in the CCResponseRatio outlier.

CellAcceleratorVoltage
CellAcceleratorVoltage represents a meta data from LCQQQ acquisition.

CoelutionScoreLimit
CoelutionScoreLimit represents the outlier limit for the Coelution Score outlier.

CollisionEnergy
CollisionEnergy represents the amount of collision-induced dissociation (CID)
occurring in the triple (QQQ) collision cell. CID is a mechanism to fragment molecular
ions in the gas phase. The molecular ions are accelerated by this electrical potential
too high kinetic energy in the vacuum of a mass spectrometer and to collide in the
higher pressure collision cell with neutral gas molecules (nitrogen). In the collision
some of the kinetic energy is converted into internal energy which results in bond
breakage and the fragmentation of the molecular ion into smaller fragments.

CollisionEnergyDelta
CollisionEnergyDelta defines the one-sided extend of the chromatograms/spectra
extraction range of the CollisionEnergy. If this value is set, the actual extraction range
of chromatograms and spectra is given by the following formula:
CE range = [CollisionEnergy – CollisionEnergyDelta, CollisionEnergy
+ CollisionEnergyDelta]
The quantifier and each of the qualifier ions can be assigned independent CE
extraction ranges.

ColumnVoidTime
ColumnVoidTime is the retention time of unretained compound.

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CompoundApproved
CompoundApproved records the user’s decision on the status of the compound in a
sample. For example, the user sets the CompoundApproved status to True, meaning
the compound in this sample is considered approved.
CompoundApproved is initialized to NULL and editable by the user in Batch-at-a-
Glance.

CompoundName
CompoundName represents a human-readable, non-unique identifier for a
TargetCompound row. Typically it will be a standard structural or generic chemical
name for the compound.

CompoundGroup
CompoundGroup allows a classification of a particular compound with other similarly
recorded compounds.
This association of individual compounds enables grouping of compounds as a unit.
For example, the chemical group of PCBs (plychlorinated biphenyls) is composed of a
numerous compounds (congeners) which make up total PCBs. Each individual
compound makes a percent contribution to the total PCBs in the mixture.

CompoundMath
CompoundMath allows aggregation of compounds in the same CompoundGroup for
the math calculations in the following table.

Enum Name UI Name

ResponseSum Response Sum
ResponseAverage Response Average
ConcentrationSum Concentration Sum
ConcentrationAverage Concentration Average
TPHResponseSubtraction TPH Subtraction

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Setup:
1) Set up individual compounds

In the “CompoundGroup” column, compounds aggregated together need to be assigned to the

same group. Sublist is supported in Compound Group Math, i.e., if a compound is assigned in
multiple groups (separated by comma), all assigned groups will contain the contribution from
this compound.

2) Set up aggregate compounds

Add a new compound as the aggregate compound, and assign a single “Compound Group”.
Sublist should only be used for the individual compound. In the
TargetCompound/CompoundGroupMath column, select a value from the pulldown menu
{ConcentrationSum, ConcentrationAverage, ResponseSum, ResponseAverage}.

If a compound is assigned “ResponseSum” or “ResponseAverage”, the responses of all the

individual compounds from the same compound group will be aggregated (summed or
averaged), for both calibration and quantitation.

If a compound is assigned “ConcentrationSum” or “ConcentrationAverage”, the calculated

concentrations and final concentrations will be aggregated (summed or averaged). Responses
and Calibration curves are meaningless for concentration aggregated compounds.

3) For TPH Subtraction, no compound group set up is needed, only “TPH Subtraction”
needs to be selected for the TPH compounds. The algorithm will find the surrogate/ISTD
compounds that are within TPH integration range and subtract responses of them from
TPH compound.

Note:

1) If an individual participating compound is manually integrated, peak results of a

corresponding aggregate compound will be updated. For response-based compound
math, area/height/targetResponse will be updated, as well as concentrations. For
concentration-based compound math, only concentrations will be updated. The “MI”
(manual integration) flag will be checked too.
2) Manual integration of the aggregate compound is cleared only if manual integration is
cleared for all compounds in the same group.

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3) If the aggregate compound is set as Response Average or Concentration Average, and

the individual participating compound is zero peaked, the zero peaked compound will
not contribute to the average.

CompoundType
CompoundType represents a human-readable classification tag relating to the user the
function of this compound within the chemical analysis represented by this
Quantitation DataSet class instance. Possible values (in English) would include
"Target", "ISTD", "Surrogate", and "Matrix Spike". This string is subject to localization in
other supported languages.

Enum Name UI Name XPath expression

Target Target *//CompoundType[.='Target']

ISTD ISTD *//CompoundType[.='ISTD']

Surrogate Surrogate *//CompoundType[.='Surrogate']

MatrixSpike Matrix Spike *//CompoundType[.='MatrixSpike']

ConcentrationUnits
ConcentrationUnits represents a human readable string which defines the units of
measurement for all measured and nominal concentration values associated with the
quantitation of this TargetCompound row.
Default value is "µg/ml".

CurveFit
CurveFit is a human-readable string that represents the curve-fitting mathematical
model applied to the set of (response, concentration) calibration data points
associated with any chemical analysis experiment run for the represented target
compound against this Quantitation DataSet class instance. In English, its possible
values include "Linear", "Quadratic", "Power", "First order ln", “Second order ln”, and
"Average of Response Factors". This string is subject to localization in other supported
languages.

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CurveFitFormula
CurveFitFormula represents an equation of the curve-fit model applied to the
calibration data for this compound.
Example:
The equation: 𝑦𝑦 = 0.0603 𝑥𝑥 2 + 0.3520 ∗ 𝑥𝑥 + 00033
CurveFitFormula represents a quadratic calibration curve fit, where y is the response
and x is the concentration.

CurveFitLimitHigh
CurveFitLimitHigh represents the highest concentration in the set of enabled
calibration points for this compound. CurveFitLimitHigh is computed internally by the
system and is used to evaluate the Calibration Range outlier condition. QC points and
Continuing Calibration points are ignored when calculating CurveFitLimitHigh.

CurveFitLimitLow
CurveFitLimitLow represents the lowest concentration in the set of enabled
calibration points for this compound. CurveFitLimitLow is computed internally by the
system and is used to evaluate the Calibration Range outlier condition. QC points and
Continuing Calibration points are ignored when calculating CurveFitLimitLow.

CurveFitMinimumR2
CurveFitMinimumR2 represents the limit for the Curve Fit R2 outlier.
OutlierMinimumCurveFitR2 is set too Low if the value of CurveFitR2 for this
compound is less than CurveFitMinimumR2.

CurveFitOrigin
CurveFitOrigin is a human-readable string that represents the treatment of the point
(0, 0) with respect to the set of (response, concentration) calibration data points
regressed using the curve-fitting mathematical model represented by the CurveFit
column. In English, its possible values include "Ignore", "Include", and "Force". This
string is subject to localization in other supported languages. To Ignore the point (0, 0)
means that no (0, 0) point is added to the set of calibration data points. To Include the

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point (0, 0) means that the (0, 0) point is added to the set of calibration data points if
it does not exist already. To Force the point (0, 0) means that curve-fitting
mathematical model represented by the CurveFit column is further constrained such
that the fitting equation/curve must pass through the point (0, 0). Note that the Force
and Include options are not meaningful for some Power and Logarithmic curve-fitting
models.
In addition, CurveFitOrigin includes the choice “Blank Offset”. In this case, the
following curve fit formula applies:
y = ax +BlankOffset
where blankOffset is the BlankResponseOffset column, which is the average target
response of “Blank” samples in the batch. The value is subtracted from each
calibration levels, and the Force Origin calibration curve is applied to calculate “a” in “
y = ax +BlankOffset ”

Enum Name UI XPath expression

Name
originIgnore Ignore *//CurveFitOrigin[.='originIgnore']

originInclude Include *//CurveFitOrigin[.='originInclude']

originForce Force *//CurveFitOrigin[.='originForce']

originBlankOffset Blank *//CurveFitOrigin[.='originBlankOffset']

Offset

CurveFitR2
CurveFitR2 is a measure of the quality of the calibration curve fit, known as R2 or the
coefficient of determination. It is a number between 0 and 1 such that a perfect fit (for
example, all calibration points falling on a straight line for linear fit) corresponds to
R2 = 1. CurveFitR2 is subject to the Curve Fit R2 outlier condition.

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CurveFitStatus
CurveFitStatus is a human-readable string that represents the success or error status
of the calibration curve fit and its subsequent use in converting the target response to
compound concentration. In English, its possible values include "Success",
"NotEnoughDataPoints", "NotConverged ", "ResponseOutOfRange", and
"UnknownError". This string is subject to localization in other supported languages.
The value “NotEnoughDataPoints” indicates that the number of calibration points is
insufficient for the curve fit of the specified type. The value “NotConverged” indicates
a poor match between the set of calibration data points and the selected curve fit type.
The value “ResponseOutOfRange” indicates that the response value cannot be
converted to a concentration value on the calibration curve. This can occur for a
quadratic curve fit, for example, if the target response is below the bottom or above
the top of the parabola. The value "UnknownError" corresponds to an internal
application error.

Enum Name UI Name XPath expression

Success Success *//CurveFitStatus[.='Success']

NotEnoughDataP NotEnoughDataP *//CurveFitStatus[.='NotEnoughDat

oints oints aPoints']

NotConverged NotConverged *//CurveFitStatus[.='NotConverged

']

ResponseOutOfR ResponseOutOfR *//CurveFitStatus[.='ResponseOutO

ange ange fRange']

UnknownError UnknownError *//CurveFitStatus[.='UnknownError

']

CurveFitWeight
CurveFitWeight is a human-readable string that represents the weighting function
applied to the various members of the set of (response, concentration) calibration data
points regressed using the curve-fitting mathematical model represented by the
CurveFit column. As the weighting function is applied to each data point in the

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regression set, it affects the contribution of each individual data point to the ultimate
determination of the regression equation. In English, its possible values include "None,
"1/x", "1/x^2", "1/y", and "1/y^2". This string (in particular for the case of "None") is
subject to localization in other supported languages. X or Y members of data points are
weighted as indicated by the CurveFitWeight string. In the case of "None", a weighting
factor of unity is applied to all X and Y components of all calibration data points.
In addition, the CurveFit choice includes “1/SD^2”. The weight assigned to each
calibration point is one over the variance (standard deviation squared) of the
responses of the replicate calibration points at the same level as that point. In this
case, if any of the levels have no replicates, the curve fit fails.
When the CurveFitOrigin is set to “originInclude” and CurveFitWeight is set to 1/x,
1/x^2, 1/y or 1/y^2, origin gets a weight of zero.

Enum Name UI XPath expression

Name
weightEqual None *//CurveFitWeight[.='weightEqual']

weightOneOverX 1/x *//CurveFitWeight[.='weightOneOverX']

weightOneOverXSqua 1/x^2 *//CurveFitWeight[.='weightOneOverXSqu

red ared']

weightOneOverY 1/y *//CurveFitWeight[.='weightOneOverY']

weightOneOverYSqare 1/y^2 *//CurveFitWeight[.='weightOneOverYSqa

d red']

weightLog Log *//CurveFitWeight[.='weightLog']

weightOneOverSDSqu 1/SD^ *//CurveFitWeight[.='weightOneOverSDSq

ared 2 uared']

DilutionHighestConcentration
DilutionHighestConcentration represents the highest concentration in the applied
DilutionPattern.

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DilutionPattern
DilutionPattern represents a scheme or series used to create the concentration
standards. A serial dilution pattern is typically accomplished by starting with the
DilutionHighestConcentration and repeatedly applying the dilution pattern.
Examples:
A pattern such as 1:10 means 1 part sample diluted with 9 parts liquid. For an
example of the 1:2 dilution pattern, see table below.

Standard Diluent (µl)

(pg/ml) (µl)
Number Volume

1 4000 50 µl 950 µl
2 2000 500 µl of #1 500 µl
3 1000 500 µl of #2 500 µl
4 500 500 µl of #3 500 µl
5 250 500 µl of #4 500 µl
DilutionPattern format is not limited to a single dilution factor.
Two more examples help illustrate the DilutionPattern and its effect on the serial
dilution sequence:
1) DilutionPattern of 1 : 2 : 2.5 with DilutionHighestConcentration = 500 yields the
following series: 500, 250, 100, 50, 20, 10, 4, 2, 0.8, 0.4, 0.16, 0.08…
2) DilutionPattern of 1 : 2 : 2.5 : 4 with DilutionHighestConcentration = 500 yields
the following series: 500, 250, 100, 25, 12.5, 5.0, 1.25, 0.625, 0.25, 0.0625…

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DynamicTargetCompoundID
DynamicTargetCompoundID represents a forward pointer from the user-defined
compound to the dynamic target. Null if there are no dynamic targets for this
compound. Equal to the CompoundID of the dynamic target compound actually used
for quantitation in the current sample at runtime.

DynamicTargetRank
DynamicTargetRank represents a unique integer for each user-defined compound ID.

ExpectedConcentration
ExpectedConcentration represents a concentration measurement expressed in units of
ConcentrationUnits. This value defines the nominal concentration for this compound
in the sample represented by SampleID.

FragmentorVoltage
FragmentorVoltage represents the acquisition parameter that controls the acceleration
of the ions from the source into the rest of the mass spectrometer (mass analyzer and
detection).

FragmentorVoltageDelta
FragmentorVoltageDelta defines the one-sided extent of the chromatograms/spectra
extraction range of the FragmentorVoltage. If this value is set, the actual extraction
range of chromatograms and spectra is given by the following formula:
FV range = [FragmentorVoltage – FragmentorVoltageDelta, FragmentorVoltage
+ FragmentorVoltageDelta]
In this formula, the bottom of the FV range is constrainded to be non-negative. The
quantifier and each of the qualifier ions can be assigned independent FV extraction
ranges.

FullWidthHalfMaximumLimitHigh
FullWidthHalfMaximumLimitHigh represents represents the higher limit for the full
width half maximum outlier. OutlierFullWidthHalfMaximum is set too Low if the

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calculated FullWidthHalfMaximum value of the primary peak is less than the

FullWidthHalfMaximumLimitLow.

FullWidthHalfMaximumLimitLow
FullWidthHalfMaximumLimitLow represents represents the lower limit for the full
width half maximum outlier. OutlierFullWidthHalfMaximum is set too Low if the
calculated FullWidthHalfMaximum value of the primary peak is less than the
FullWidthHalfMaximumLimitLow.

GraphicPeakChromatogram
GraphicPeakChromatogram represents a relative path and filename to a graphic (.emf)
file used in reporting.

Graphic 2: File reference to graphic.

GraphicPeakQualifiers
GraphicPeakQualifiers represents a relative path and filename to a graphic (.emf) file
used in reporting.

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Graphic 3: File reference to graphic.

GraphicPeakSpectrum
GraphicPeakSpectrum represents a relative path and filename to a graphic (.emf) file
used in reporting.

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Graphic 4: File reference to graphic.

GraphicTargetCompoundCalibration
GraphicTargetCompoundCalibration represents a relative path and filename to a
graphic (.emf) file used in reporting.

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Graphic 5: File reference to Calibration graphic.

ID
ID represents the user index for a compound.

InstrumentName
InstrumentName represents the name of a particular instrument. Typically,
InstrumentName is set by the sample information entered during acquisition.

InstrumentType
InstrumentType is defaulted to QQQ. As a rule, only one type of instrument comprises
a particular batch.

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Enum Name UI Name XPath expression

QQQ QQQ *//InstrumentType[.='QQQ']

QTOF QTOF *//InstrumentType[.='QTOF']

TOF TOF *//InstrumentType[.='TOF']

GCMS GCMS *//InstrumentType[.='GCMS']

LCMS LCMS *//InstrumentType[.='LCMS']

Unspecified

IntegrationParameters
IntegrationParameters represents a collection of parameters that modulate the
behavior of the General integration algorithm brought to bear on the signal indicated
by this TargetCompound row. The default value for IntegrationParameters is NULL.
Wherever this column is NULL, signal integration proceeds assuming the default
integration settings in the context of the integrator used.

IntegrationParametersModified
IntegrationParametersModified is true when the integration parameters for a
compound is modified at the sample level.

Integrator
Integrator represents the choice of Integrator algorithm from the following:
• Agile Integrator
• MS-MS Integrator
• General Integrator
• MS-MS (GC)

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• Universal
• Spectral Summer
The MS-MS Integrator is especially applicable to the signal characteristics of the triple
mass spectrometer.

Enum Name UI Name XPath expression

Agile Agile *//Integrator[.='Agile']

RTE General *//Integrator[.='RTE']

AutoMagic MS-MS *//Integrator[.='AutoMagic']

Genie Universal *//Integrator[.='Genie']

AutoMagic2 MS *//Integrator[.='AutoMagic2']

SpectralSummer Spectral *//Integrator[.='SpectralSummer'

Summer
General integrator was formerly called the RTE integrator.
Universal integrator was formerly called the GC-MS Genie integrator.

IonPolarity
IonPolarity represents an acquisition parameter that records the polarity of the ions
focused with voltages applied to a lens system located between the source and the
analyzer.

Enum Name UI Name XPath expression Summary

Positive Positive *//IonPolarity[.='Positive'] Positive
ion
polarity
Negative Negative *//IonPolarity[.='Negative'] Negative
ion
polarity

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Enum Name UI Name XPath expression Summary

Unassigned Unassigned *//IonPolarity[.='Unassigned’] Unknown
ion
polarity
Mixed Mixed *//IonPolarity[.='Mixed'] Contains
both
positive
and
negative
ion
polarity
data

IonSource
IonSource represents the acquisition parameter that record the type of source used in
the mass spectrometer including:
For example, with the triple (LC-QQQ):
• ESI: Electro Spray Ionization
• APCI: Atmospheric Pressure Chemical Ionization
• MultiMode (both)

ISTDCompoundID
ISTDCompoundID represents a link to another TargetCompound row. The
TargetCompound row so linked implies the internal standard compound with which is
associated the target compound represented by this TargetCompound row. If the
value of ISTDCompoundID is -1, then the target compound represented by this
TargetCompound row is not associated with an internal standard.

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ISTDConcentration
ISTDConcentration represents a concentration measurement expressed in units of
ConcentrationUnits. This value indicates the nominal concentration of internal
standard in any Sample under analysis versus this Quantitation DataSet class
instance. This value is only meaningful if this TargetCompound row has a value of true
for its ISTDFlag member.

ISTDFlag
ISTDFlag represents the value true if and only if this TargetCompound row represents
an internal standard compound.

ISTD 1: Relationship of Target to its associated ISTD (internal standard).

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ISTDResponseLimitHigh
ISTDResponseLimitHigh represents the upper limit criteria for the outlier
OutlierISTDResponse.

ISTDResponseLimitLow
ISTDResponseLimitLow represents the lower limit criteria for the outlier
OutlierISTDResponse.

ISTDResponseMaximumPercentDeviation
ISTDResponseMaximumPercentDeviation represents the upper limit criteria for the
outlier OutlierISTDResponsePercentDeviation.

ISTDResponseMinimumPercentDeviation
ISTDResponseMinimumPercentDeviation represents the lower limit criteria for the
outlier OutlierISTDResponsePercentDeviation.

KEGGID
KEGGID represents an identifier in KEGG (Kyoto Encyclopedia of Genes and
Genomes) database.

LeftRetentionTimeDelta
LeftRetentionTimeDelta represents a value expressed in units of minutes or percent of
nominal RetentionTime, as indicated by RetentionTimeDeltaUnits. It defines the offset
used to determine the lower bound for the retention-time window for signals which
are extracted in support of quantitating the chemical compound indicated by this
TargetCompound row.

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Example:
RetentionTime has a value of 5 minutes. LeftRetentionTimeDelta has a value of 0.1 and
RetentionTimeDeltaUnits has a value of 0 for Minutes. Then the lower bound on the
extraction window is 5 - 0.1 or 4.9 minutes. On the other hand if
RetentionTimeDeltaUnits is 1 for Percent and LeftRetentionTimeDelta is 20, then the
lower bound on the extraction window is 5 - 20% * 5 = 4 minutes. Default value is
1 minutes.

LibraryMatchScore
LibraryMatchScore records the measure of the correlation between the deconvoluted
peak’s spectrum and the standard spectrum from the library searched.
LibraryMatchScore is an indicator of the quality of the library match and low
LibraryMatchScores should be investigated and identify of the compound
identification confirmed.
The measure of 100 means a perfect match.

LibraryMatchScoreMinimum
LibraryMatchScoreMinimum represents the lower limit for the Library Match Score
outlier. OutlierLibraryMatchScore is set too Low if the LibraryMatchScore of this
compound is less than LibraryMatchScoreMinimum.

LibraryRetentionIndex
LibraryRetentionIndex records the retention index determined from the library
search.
LibraryRetentionIndex requires the compound is perceived using a retention time
calibration (RT CAL).
The RT CAL information holds the relationship between the retention time (RT) and
retention index (RI). Using the RI information in the library along with the RT CAL
mapping enables a user to search the library with RIs.

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LibraryRetentionTime
LibraryRetentionTime records the retention time from the library search.
LibraryRetentionTime is the expected RT stored in the library. Comparing the
LibraryRetentionTime with the actual RT is useful in evaluating the compound’s
identification.

LimitOfDetection
LimitOfDetection (LOD) represents the lowest quantity of a substance that can be
distinguished from the absence of that substance (a blank value). Typically, the blank
value plus three standard deviations is established as the LOD.

LimitOfQuantitation
LimitOfQuantitation (LOQ) represents the concentration at which quantitative results
can be reported with a high degree of confidence. Typically, the LOQ is determined by
an empirical approach, consisting of measuring progressively more dilute
concentrations of analyte.

LinearResponseRangeMax
LinearResponseRangeMax represents high end of the range of area responses over
which the quantifier response is linear vs. concentration.

LinearResponseRangeMin
LinearResponseRangeMin represents low end of the range of area responses over
which the quantifier response is linear vs. concentration.

MassAccuracyLimit
MassAccuracyLimit represents the limit for the Mass Accuracy outlier.
OutlierMassAccuracy is set too High if the MassAccuracy exceeds MassAccuracyLimit.
OutlierMassAccuracy is set too Low if the MassAccuracy is less than negative
MassAccuracyLimit.

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MassMatchScoreMinimum
MassMatchScoreMinimum represents the lower limit for the Mass Match Score outlier.
OutlierMassMatchScore is set too Low if the MassMatchScore of this compound is less
than MassMatchScoreMinimum.

MatrixAConcentrationLimitHigh
MatrixAConcentrationLimitHigh represents the upper limit for the Matrix Spike
outlier for type-A matrix compounds. OutlierMatrixSpikeOutOfLimits is set too High if
the FinalConcentration of a type-A matrix compound exceeds
MatrixAConcentrationLimitHigh.

MatrixAConcentrationLimitLow
MatrixAConcentrationLimitLow represents the lower limit for the Matrix Spike outlier
for type-A matrix compounds. OutlierMatrixSpikeOutOfLimits is set too Low if the
FinalConcentration of a type-A matrix compound is less than
MatrixAConcentrationLimitLow.

MatrixBConcentrationLimitHigh
MatrixBConcentrationLimitHigh represents the upper limit for the Matrix Spike
outlier for type-B matrix compounds. OutlierMatrixSpikeOutOfLimits is set too High if
the FinalConcentration of a type-B matrix compound exceeds
MatrixBConcentrationLimitHigh.

MatrixBConcentrationLimitLow
MatrixBConcentrationLimitLow represents the lower limit for the Matrix Spike outlier
for type-B matrix compounds. OutlierMatrixSpikeOutOfLimits is set too Low if the
FinalConcentration of a type-B matrix compound is less than
MatrixBConcentrationLimitLow.

MatrixSpikeConcentration
MatrixSpikeConcentration represents the expected concentration of a matrix spike
compound of either type A or type B. MatrixSpikeConcentration is used to calculate
the matrix spike percent recovery.

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MatrixSpikePercentRecoveryMaximum
MatrixSpikePercentRecoveryMaximum represents the upper limit for the Matrix Spike
Percent Recovery outlier. OutlierMatrixSpikePercentRecovery is set too High if the
percent recovery of this matrix compound exceeds
MatrixSpikePercentRecoveryMaximum.

MatrixSpikePercentRecoveryMinimum
MatrixSpikePercentRecoveryMinimum represents the lower limit for the Matrix Spike
Percent Recovery outlier. OutlierMatrixSpikePercentRecovery is set too Low if the
percent recovery of this matrix compound is less than
MatrixSpikePercentRecoveryMinimum.

MatrixSpikeMaximumPercentDeviation
MatrixSpikeMaximumPercentDeviation represents the limit for the Matrix Spike
Percent Difference outlier. OutlierMatrixSpikeOutsidePercentDeviation is set too High
if the percent difference between the concentrations for a given matrix compound in
the Matrix sample and in the MatrixDup sample exceeds
MatrixSpikeMaximumPercentDeviation.

MatrixSpikeBMaximumPercentDeviation
MatrixSpikeBMaximumPercentDeviation represents the limit for the Matrix Spike
Percent Difference outlier for type B matrix spike compound.
OutlierMatrixSpikeOutsidePercentDeviation is set too High if the percent difference
between the concentrations for a given matrix compound in the Matrix sample and in
the MatrixDup sample exceeds MatrixSpikeMaximumPercentDeviation.

MatrixTypeOverride
MatrixTypeOverride is an xml string that can record target compound columns on a
per sample per compound base based on the Matrix Type match. It’s used together
with MatrixType to define different outlier limits for different Matrix.

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MaximumAverageResponseFactorRSD
MaximumAverageResponseFactorRSD represents the limit for the Average Response
Factor RSD outlier. AverageOutlierResponseFactorRSD is set too High if
AverageResponseFactorRSD for this compound is greater than
MaximumAverageResponseFactorRSD.

MaximumBlankConcentration
MaximumBlankConcentration represents the limit for the Blank Concentration outlier.
OutlierBlankConcentrationOutsideLimit is set too High if the CalculatedConcentration
for this compound in a blank sample exceeds MaximumBlankConcentration.

MaximumBlankResponse
MaximumBlankResponse represents the limit for the Blank Response outlier.
OutlierBlankResponseOutsideLimit is set too High if the Response for this compound
in a blank or double-blank sample exceeds MaximumBlankResponse.
OutlierBlankResponseOutsideLimit is also set too High if the ISTD Response in a
double-blank sample exceeds MaximumBlankResponse.

MaximumCCResponseFactorDeviation
MaximumCCResponseFactorDeviation represents the maximum limit for the
CCAverageResponseFactor outlier calculation.

MaximumNumberOfHits
MaximumNumberOfHits is an integer which places an upper bound on the number of
peaks that will be stored as linked Peak rows and thus be candidates for quantitation.
The default value for MaximumNumberOfHits is nine.

MaximumPercentResidual
MaximumPercentResidual represents the largest percent residual of all enabled
calibration points for this compound. The percent residual of a calibration point is
defined as the percent difference between the actual response value and the result of
evaluating the curve fit formula at the calibration point’s concentration.

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Method Detection Limit

MethodDetectionLimit (MDL) represents the minimum concentration of a substance
that can be measured and reported with 99% confidence that the analyte concentration
is greater than zero, and is determined from analysis of a sample in a given matrix
containing the analyte.

MinimumAverageResponseFactor
MinimumAverageResponseFactor represents the limit for the Average Response
Factor outlier. OutlierAverageResponseFactor is set too Low if
AverageResponseFactor for this compound is less than
MinimumAverageResponseFactor.

MinimumCCRelativeResponseFactor
MinimumCCRelativeResponseFactor represents the minimum limit for the CC Relative
Response Factor outlier involved in the OutlierCCRelativeResponseFactor outlier.

MinimumPercentPurity
MinimumPercentPurity represents a lower limit for the Purity outlier. OutlierPurity is
set too Low if the calculated Purity for this compound is less than
MinimumPercentPurity.

MinimumSignalToNoiseRatio
MinimumSignalToNoiseRatio represents the limit for the Signal to Noise Ratio outlier.
OutlierSignalToNoiseRatioBelowLimit is set too Low if SignalToNoise for this
compound’s primary peak is less than MinimumSignalToNoiseRatio.

MolecularFormula
MolecularFormula store the compound’s composition of atoms.

Multiplier
Multiplier represents a conversion factor that is used to obtain the FinalConcentration
from the CalculatedConcentration:

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FinalConcentration = CalculatedConcentration × Multiplier

The value of the Multiplier is determined by the values of Dilution, SampleAmount,
and TotalSampleAmount:
Multiplier = DilutionMultiplier × SampleAmountMultiplier
Here:
DilutionMultiplier = Dilution, if defined ; otherwise 1
SampleAmountMultiplier = TotalSampleAmount ÷ SampleAmount , if both are defined ; otherwise 1

MZ
MZ represent the mass to charge ratio. In the case of a tandem mass spectrometry
experiment, MZ is a mass-to-charge measurement, in units of daltons per unit charge,
of the ions selected by the final-quadrupole stage in a tandem mass spectrometer used
to perform this experiment. In the case of a single-quadrupole mass spectrometry
experiment, MZ is a mass-to-charge measurement, in units of daltons per unit charge,
of the ions selected by the single quadrupole stage in this experiment.

MZAdditional
MZAdditional represent the additional MZs to be merged together with the quantifier
MZ as a single chromatogram trace. Multiple MZs are separated by “;”. Quantitation is
based on the merged EIC if this field is defined.

MZExtractionWindowFilterLeft
MZExtractionWindowFilterLeft represents the left side of the M/Z range for
chromatogram extraction. The compound chromatograms are extracted over the M/Z
range defined by
[MZ − MZExtractionWindowFilterLeft, MZ + MZExtractionWindowFilterRight]

MZExtractionWindowFilterRight
MZExtractionWindowFilterRight represents the right side of the M/Z range for
chromatogram extraction. The compound chromatograms are extracted over the M/Z
range defined by

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[MZ − MZExtractionWindowFilterLeft, MZ + MZExtractionWindowFilterRight]

MZExtractionWindowUnits
MZExtractionWindowUnits represents the units used for
MZExtractionWindowFilterLeft and MZExtractionWindowFilterRight.
The units are the following:
• Thomsons:
Thompson or m/z represents the physical quantity mass-to-charge ratio.
For example, the ion C7H72+ an ion will be observed at 45.5 m/z
• PPM:
Parts per million ("ppm") denotes one particle of a given substance for every
999,999 other particles. One part in 106 — a precision of 0.0001%
The user can alternatively establish the mass extraction window value using
ppm units.
ppm = 106 * ∆m accuracy / mmeasured
For example, at the theoretical mass of 1000 and a measured mass of 999.9
boundary is designated as 100 ppm.
• Percent:
Percent represents the mass extraction window as a percentage of the
theoretical mass.

Enum Name UI Name XPath expression

Thomsons m/z *//MZExtractionWindowUnits[.=' Thomsons
']
PPM ppm *//MZExtractionWindowUnits[.=’PPM’]

Percent Percent *//MZExtractionWindowUnits[.='Percent']

MZScanRangeLow
MZScanRangeLow represents the bottom of the M/Z scan range. It is applicable only to
those ScanType values that involve scanning the mass axis.

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The mass range limits are typically NULL by default.

If both limits are defined, then the values must be consistent (min <= max).
Internally, MZScanRangeLow or MZScanRangeLow does not influence the spectral
range actually extracted.

MZScanRangeHigh
MZScanRangeLow represents the top of the M/Z scan range. It is applicable only to
those ScanType values that involve scanning the mass axis.
The mass range limits are typically NULL by default.
If both limits are defined, then the values must be consistent (min <= max).
Internally, MZScanRangeLow or MZScanRangeLow does not influence the spectral
range actually extracted.

NeutralLossGain
NeutralLossGain represents the amount of neutral loss or gain, in M/Z units (daltons
per unit charge). This column is only applicable to Neutral Loss and Neutral Gain scan
types.

NoiseAlgorithmType
NoiseAlgorithmType represents the choice of algorithm to use for calculating the
SignalToNoiseRatio of a chromatogram peak. The following choices of
NoiseAlgorithmType are available:
• Peak-to-Peak
• Peak-to-Peak from Drift
• ASTM (default)
• RMS
• Auto RMS
The noise calculation divides the chromatographic range into N “noise regions” that
cover the entire range, excluding the peaks.

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Example:
If the chromatogram covers the retention time range of 0 to 3 minutes and there are
two peaks, one extending from 1.3 to 1.7 minutes, the other extending from 2.2
minutes to 2.5 minutes, then there will be N = 3 noise regions:
[0.0, 1.3], [1.7, 2.2], [2.5, 3.0]
Noise regions less than 3 points wide are eliminated. For the Peak-to-Peak and ASTM
algorithms, the low and high abundance values are computed from the chromatogram
over each noise region. Then, for the Peak-to-Peak algorithm, the noise is computed as
the maximum high-low difference over all noise regions:
Noise (Peak-to-Peak) = Max( Highn – Lown ) over n = 1..N.
For the ASTM algorithm, the noise is computed as the average of the (Highn – Lown)
differences for each noise region:
Noise (ASTM) = Average( Highn – Lown ) over n = 1..N.
For RMS (root-mean-square) noise algorithm, the system computes the root-mean-
square variation of abundance over each noise region and takes the maximum of the
RMS values over all regions. The Peak-to-Peak from Drift algorithm uses linear
regression to fit a drift line to each noise region and finds the difference of the
maximum positive and maximum negative displacements from the regression line. The
noise is then computed as the maximum displacement difference over all noise
regions.
For Auto RMS, this algorithm works by moving a Noise region window across
a defined noise region boundary and selecting the minimum noise value
calculated from the Noise region window.
In order to calculate the signal-to-noise ratio, the chromatogram must be
integrated first. A noise region boundary is defined with a Start time and
End time in minutes. A Noise region window is moved across this noise
region boundary one step at a time. At each step, at least three points must
be inside the window in order to calculate the root-mean-square noise value.
The smallest noise value computed is used. If the smallest noise value is 0,
then the noise value is set to 1/sqrt(bins). Bins is the number of points in the
first Noise region window.

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Enum Name UI Name XPath expression

PeaktoPeak PeaktoPeak *//NoiseAlgorithmType[.='PeaktoPea

k']
PeaktoPeakDrift PeaktoPeakDrif *//NoiseAlgorithmType[.='PeaktoPea
t kDrift']

ASTM ASTM *//NoiseAlgorithmType[.='ASTM']

RMS RMS *//NoiseAlgorithmType[.='RMS']

AutoRMS Auto RMS *//NoiseAlgorithmType[.=’AutoRMS’]

NoiseOfRawSignal
NoiseOfRawSignal represents the noise calculated for the extracted target signal.
NoiseOfRawSignal is calculated regardless of whether an integrated peak exists or not.
Different algorithms are supported as well as self-defined noise regions.

NoiseReference
NoiseReference defines from what sample noise is calculated.
If “Sample” is selected the noise is on the Sample. This is the original MH Quant behavior. If the
field is left blank (null) the behavior is identical to selecting “Sample”. If “Blank” is selected the
noise is calculated in the last blank run (sample type = Blank) which was acquired before the
injection.

NoiseRegions
NoiseRegions defines a retention time window which is used to evaluate the noise for
a particular chromatogram.
Assuming your chromatography is reproducible, you can pick a region in the
chromatogram and the SignalToNoiseRatio calculation uses that region to evaluate the
noise.

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NoiseStandardDeviationMultiplier
NoiseStandardDeviationMultiplier represents a multiplier that is applied to the noise
value during the calculation of the SignalToNoiseRatio of a peak. For a given
chromatogram, a NoiseStandardDeviationMultiplier value of 3 will result in a three-
fold increase in the reported noise and therefore, a three-fold reduction in
SignalToNoiseRatio. The default value of NoiseStandardDeviationMultiplier is 5.

OutlierAlternativePeak
OutlierAlternativePeak stores the flag resulting from the Alternative Peak outlier
condition evaluation. If enabled by default or by applying Outlier Setup, an associated
column is highlighted.

OutlierAverageResponseFactor
OutlierAverageResponseFactor stores the flag resulting from the Average Response
Factor outlier condition evaluation. If enabled by default or by applying Outlier Setup,
an associated column is highlighted.

OutlierAverageResponseFactorRSD
OutlierAverageResponseFactorRSD stores the flag resulting from the Average
Response Factor RSD outlier condition evaluation. If enabled by default or by
applying Outlier Setup, an associated column is highlighted.

OutlierBlankResponseOutsideLimit
OutlierBlankResponseOutsideLimit stores the flag resulting from the Blank Response
outlier condition evaluation. If enabled by default or by applying Outlier Setup, an
associated column is highlighted. See Outlier Details.

OutlierCCAverageResponseFactor
OutlierCCAverageResponseFactor stores the flag resulting from the Average CC
Response Factor outlier condition evaluation. If enabled by default or by applying
Outlier Setup, an associated column is highlighted.

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OutlierCCRelativeResponseFactor
OutlierCCRelativeResponseFactor stores the flag resulting from the Average CC
Relative Response Factor outlier condition evaluation. If enabled by default or by
applying Outlier Setup, an associated column is highlighted

OutlierCustomCalculation
OutlierCustomCalculation stores the flag resulting from the User Custom Calculation
condition evaluation. If enabled by default or by applying Outlier Setup, an associated
column is highlighted.

OutlierMethodDetectionLimit
OutlierMethodDetectionLimit stores the flag resulting from the Method Detection
Limit outlier condition evaluation. If enabled by default or by applying Outlier Setup,
an associated column is highlighted.

OutlierMinimumCurveFitR2
OutlierMinimumCurveFitR2 stores the flag resulting from the Curve Fit R2 outlier
condition evaluation. If enabled by default or by applying Outlier Setup, an associated
column is highlighted.

OutlierPeakNotFound
OutlierPeakNotFound stores the flag that indicates target peak is not found by
integrator. If enabled by default or by applying Outlier Setup, an associated column is
highlighted.

OutlierRelativeResponseFactor
OutlierRelativeResponseFactor stores the flag resulting from this Relative Response
Factor outlier condition evaluation. If enabled by default or by applying Outlier Setup,
an associated column is highlighted.

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OutlierRelativeStandardError
OutlierRelativeStandardError stores the flag resulting from this Relative Standard
Error condition evaluation. If enabled by default or by applying Outlier Setup, an
associated column is highlighted.

OutlierResponseCheckBelowLimit
OutlierResponseCheckBelowLimit stores the flag resulting from the
ResponseCheckMinimum condition evaluation. If enabled by default or by applying
Outlier Setup, an associated column is highlighted.

OutlierResponseFactor
OutlierResponseFactor stores the flag resulting from the Response Factor outlier
condition evaluation. If enabled by default or by applying Outlier Setup, an associated
column is highlighted.

OutlierSaturationRecovery
OutlierSaturationRecovery stores the flag resulting from the Saturation Recovery
outlier condition evaluation. If enabled by default or by applying Outlier Setup, an
associated column is highlighted.

PeakFilterThreshold
PeakFilterThreshold represents the type of threshold filter that is applied to the
chromatogram peaks that were detected by the integrator. The choice of
PeakFilterThreshold determines the interpretation of PeakFilterThresholdValue. The
following choices of PeakFilterThreshold are available:

PeakFilterThreshold Filter condition

PeakAreaAbsThreshold Peaks with area less than

PeakFilterThresholdValue are filtered out

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PeakAreaPctThreshold (default) Peaks whose area, divided by maximum peak

area, is less than
PeakFilterThresholdValue/100 are filtered
out
PeakHeightAbsThreshold Peaks with height less than
PeakFilterThresholdValue are filtered out
PeakHeightPctThreshold Peaks whose height, divided by maximum
peak height, is less than
PeakFilterThresholdValue/100 are filtered
out

Enum Name UI Name XPath expression

PeakAreaAbsThreshold PeakAreaAbsThres *//PeakFilterThreshold[.='
hold PeakAreaAbsThreshold']

PeakAreaPctThreshold PeakAreaPctThres *//PeakFilterThreshold[.='

hold PeakAreaPctThreshold']

PeakHeightAbsThreshold PeakHeightAbsThr *//PeakFilterThreshold[.='

eshold PeakHeightAbsThreshold']

PeakHeightPctThreshold PeakHeightPctThre *//PeakFilterThreshold[.='

shold PeakHeightPctThreshold']

PeakFilterThresholdValue
PeakFilterThresholdValue represents the threshold that is applied to the peak area or
height, depending on the choice of PeakFilterThreshold. Chromatogram peaks that are
below the PeakFilterThresholdValue are filtered out and are not considered as
candidate peaks for quantitation.

PeakSelectionCriterion
PeakSelectionCriterion represents the algorithm employed to select the peak which is
designated the “hit” i.e. the PrimaryHitPeakID. The criteria affect the mechanism of

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ranking the Peak rows associated with this TargetCompound row. The most suitable
Peak row is then chosen as the primary “hit”.
PeakSelectionCriterion has several possible values:

PeakSelectionCriterion Value
GreatestResponse GreatestResponse causes the ranking of the peaks
such that the Peak row that exhibits the greatest
integrator-determined response. For response, either
height or area will be used as indicated by the value of
the QuantitateByHeight column. This is the default
value.
Note there is only one primary “hit”. Other non-“hit”
peaks are considered alternative “hits”.

Close RT Close RT causes the ranking of the peaks such that the
Peak row that exhibits the closest integrator-
determined retention time, irrespective of quality and
fidelity of qualifier signal ratios is designated the
“hit”.
Note that other non-“hit” peaks are considered
alternative “hits”.

Close RT with Qualifiers Close RT with Qualifiers causes the ranking of the
peaks such that the Peak row that exhibits the best
retention time among the Peak rows for which all
qualifier ratio tolerances are satisfied is designated
the “hit”.
In the degenerate case in which there are no Peak row
which are so Qualified, this ranking algorithm will be
equivalent to Close RT.

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Greatest Q-Value Greatest Q-Value causes the ranking of the peaks such
that the Peak row that exhibits the nominal qualifier
ratios that are best satisfied by the actual ratios. A
correlation computation called QVALUE is performed
to measure the fidelity of the observed qualifier ratios
versus the nominal qualifier ratios.
The definition of the QVALUE function is a well-
defined statistic which yields a efficient measure of
the "goodness of fit" of the observed qualifier ratios to
the nominal qualifier ratios.

Examples:
Changing the peak selection criterion from Greatest Response to Close RT for the
target compound and for the ISTD helps avoid the larger spurious peaks.

Enum Name UI XPath expression

Name
GreatestRespon Greatest *//PeakSelectionCriterion[.='GreatestResp
se Respons onse']
e
CloseRT Close *//PeakSelectionCriterion[.='CloseRT']
RT
CloseRTQual Close *//PeakSelectionCriterion[.='CloseRTQual'
RT with ]
Qualifie
rs
GreatestQValue Greatest *//PeakSelectionCriterion[.='GreatestQVal
Q-Value ue']

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PlatesCalculationType
PlatesCalculationType represents the choices of formulas used by different
pharmacoepedia to calculate the theoretical plates number. The following types are
available:

Pharmacopeia Formula

Default 16 * (Tr / Wb) ^2

USP 16 * (Tr / Wb) ^2

EU 5.54 * (Tr / W50) ^2

JP 5.54 * (Tr / W50) ^2

Tr is the retention time

Wb is the peak width determine by the tangent method.

W50 is the peak width at 50% of the height of the peak.

PlatesLimit
PlatesLimit records the outlier limits for the Plates outlier.

PrimaryHitPeakID
PrimaryHitPeakID is a link to a single Peak table row with which this
TargetCompound row is associated. The Peak table row so identified is that Peak table
row which is selected by the Quantitation process for quantitating the compound
represented by this TargetCompound row.

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If the value of PrimaryHitPeakID is NULL, there are either no hits or the quantitation
has not yet been performed.
The assignment of the PrimaryHitPeakID is affected by the criteria set by the
PeakSelectionCriterion.

PubChemID
PubChemID stores the PubChem identification.

QCLCSMaximumRecoveryA
QCLCSMaximumRecoveryA represents the upper limit for the QC Laboratory Control
Spike outlier. OutlierQCLCSRecoveryOutOfLimits is flagged if the recovery of a
compound in a QC LCSA sample is higher than QCLCSMaximumRecoveryA.

QCLCSMaximumRecoveryB
QCLCSMaximumRecoveryB represents the upper limit for the QC Laboratory Control
Spike outlier. OutlierQCLCSRecoveryOutOfLimits is flagged if the recovery of a
compound in a QC LCSB sample is higher than QCLCSMaximumRecoveryB.

QCLCSMinimumRecoveryA
QCLCSMinimumRecoveryA represents the lower limit for the QC Laboratory Control
Spike outlier. OutlierQCLCSRecoveryOutOfLimits is flagged if the recovery of a
compound in a QC LCSA sample is lower than QCLCSMinimumRecoveryA.

QCLCSMinimumRecoveryB
QCLCSMinimumRecoveryB represents the lower limit for the QC Laboratory Control
Spike outlier. OutlierQCLCSRecoveryOutOfLimits is flagged if the recovery of a
compound in a QC LCSB sample is lower than QCLCSMinimumRecoveryB.

QCMaximumDeviation
QCMaximumDeviation represents the limit for the QC outlier. OutlierQCOutOfLimits is
flagged if the CalculatedConcentration of a target compound in a QC sample differs
from ExpectedConcentration by more than QCMaximumDeviation.

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QCMaximumPercentRSD
QCMaximumPercentRSD represents a setup parameter that affects the calculation of
the QC Maximum Percent Relative Standard Deviation outlier. For details, please see
the outlier description.

QualifierRatioMethod
QualifierRatioMethod represents the algorithm chosen to evaluate ratios of qualifier
signals to the target signal for this TargetCompound row. QualifierRatioMethod is an
integer value representing one of four possible means of determining these qualifier
ratios. A value of 0 for QualifierRatioMethod will determine the observed qualifier
ratios by simple divisions of integrator-determined responses. Sets of ratios will be
computed for each Peak row linked to this TargetCompound row. For each Peak row, a
set of observed qualifier ratios will be determined by dividing, in turn, the response of
each qualifier represented by a linked PeakQualifier row against the integrator-
determined response of the Peak row itself. The response value will be height or area
as indicated by the value of the QuantitateByHeight column. A value of 1, 2, or 3 for
QualifierRatioMethod will compute the sets of observed qualifier ratios using Mass
Spectrum peak ratios in lieu of the chromatographic-peak ratios used directly from the
qualifier signals which are used in case (0). From the integration results, the retention
times of the START, TOP, and END of the peak are retrieved. Spectra from the data
source used in this quantitation experiment are extracted at each of those retention
times. The intensities ("mass peaks") for the mass-to-charge domain value given by the
MZ column are considered. For qualifier Qi, let these intensities be start(Qi), top(Qi),
and end(Qi). For target, let these ratios be start(T), top(T), and end(T). A value of 1
computes each qualifier ratio as top(Qi) / top(T). A value of 2 computes each qualifier
ratio as (top(Qi) - LowFirstLast(Qi)) / (top(T) - LowFirstLast(T)) where
LowFirstLast(x) = min(start(x), end(x)) A value of 3 computes each qualifier ratio as
(top(Qi) - AvgFirstLast(Qi)) / (top(T) - AvgFirstLast(T)) where AvgFirstLast(x) =
(start(x) + end(x)) / 2
QualifierRatioMethod feature is not currently supported.

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QuantitateByHeight
QuantitateByHeight represents a flag indicating whether peak height or peak area is
used as the response for purposes of quantitation. For a value of false, area is used for
quantitation. For a value of true, height is used for quantitation. The choice of area or
height applies to all TargetQualifier rows associated with this TargetCompound row.

QuantitationMessage
QuantitationMessage represents a human-readable string that contains a list of the
error messages (if any) that resulted from this compound’s quantitation. If the
compound was quantitated successfully, QuantitationMessage is NULL. If there are
quantitation errors, QuantitationMessage contains a concatenation of all the error
messages, one message per line, prefixed with the compound name. This string is
subject to localization in other supported languages. Some examples of quantitation
errors that may appear in the QuantitationMessage in English are summarized in the
table below.

Quantitation Message Explanation

Integrator did not find any peaks The integrator could not find any peaks
in the chromatogram extracted at this
compound’s target M/Z value (defined by
the MZ column)
Qualifier M/Z=123: Integrator did not The integrator could not find any peaks
find any peaks in the chromatogram extracted at this
qualifier’s M/Z value
Qualifier M/Z=123: Qualifier peak not The qualifier peak does not satisfy the
found or does not match quantitation qualifier selection criteria for successful
criteria compound quantitation, such as qualifier
response ratio or retention time range.

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Response is outside the range of the The response of the compound’s primary
calibration curve fit peak cannot be converted to a
concentration value on the calibration
curve. This can occur for a quadratic
curve fit, for example, if the target
response is below the bottom or above
the top of the parabola.

QValueMinimum
QValueMinimum represents the lower limit for the Q Value outlier.

ReferenceMSPathName
ReferenceMSPathName represents a persistent store containing a serialized or
otherwise archived image of a Reference Mass Spectrum associated with the chemical
compound indicated by this TargetCompound row.
ReferenceMSPathName is not yet utilized in MS/MS product.

RelativeISTDMultiplier
RelativeISTDMultiplier affects only RelativeISTD analysis.
For Relative ISTD analysis, RelativeISTDMultiplier enters into the
CalculatedConcentration determination.
Response
* ISTDConcentration * ISTDRelativeMultiplier = CalculatedConcentration
ISTDResponse
Although the ISTD is often a heavy deuterated or carbon-13 analog, the ISTD can
deliver a different response for the same amount of light or heavy compound. Hence,
the RelativeISTDMultiplier offers a compound-based adjustment for Relative ISTD
analysis.

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RelativeResponseFactorMaximumPercentDeviation
RelativeResponseFactorMaximumPercentDeviation serves as the limit for the Relative
Response Factor outlier. RelativeResponseFactorMaximumPercentDeviation
represents the maximum allowed deviation of the relative response factor for any
calibration row of this compound from AverageRelativeResponseFactor.

RelativeRetentionTimeMaximumPercentDeviation
RelativeRetentionTimeMaximumPercentDeviation serves as the limit for the Relative
Retention Time outlier. RelativeRetentionTimeMaximumPercentDeviation represents
the maximum allowed relative percent deviation of the relative retention time of this
compound from AverageRelativeRetentionTime.

RelativeStandardError
RelativeStandardError represents a metric for the calibrarion curve fitting. The
calculation is as following:

𝑛𝑛 2
𝑥𝑥𝑖𝑖′ − 𝑥𝑥𝑖𝑖
%𝑅𝑅𝑆𝑆𝑆𝑆 = 100×�� � � /(𝑛𝑛 − 𝑝𝑝)
𝑥𝑥𝑖𝑖
𝑖𝑖=1

xi = True value of the calibration level i

x’i = Measured concentration of calibration level i
p = Number of terms in the fitting equation
(average = 1, linear = 2, quadratic = 3)
n = Number of calibration points

RelativeStandardErrorMaximum
RelativeStandardErrorMaximum represents an outlier upper limit for the RSE%
outlier.

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ResolutionCalculationType
ResolutionCaculationType represents the choices of formulas used by different
pharmacoepedia to calculate the peak resolution. The following types are available:
Default:

USP: 2 ∗ (𝑇𝑇𝑇𝑇, 2 − 𝑇𝑇𝑇𝑇, 1) /(𝑊𝑊𝑊𝑊, 1 + 𝑊𝑊𝑊𝑊, 2)

JP: 1.18 ∗ (𝑇𝑇𝑇𝑇, 2 − 𝑇𝑇𝑇𝑇, 1) /(𝑊𝑊50,1 + 𝑊𝑊50,2)
EU: 1.18 ∗ (𝑇𝑇𝑇𝑇, 2 − 𝑇𝑇𝑇𝑇, 1) /(𝑊𝑊50,1 + 𝑊𝑊50,2)
Valley Height/Peak Height: 𝑣𝑣/ℎ𝑒𝑒𝑒𝑒𝑒𝑒ℎ𝑡𝑡 𝑜𝑜𝑜𝑜 𝑡𝑡𝑡𝑡𝑡𝑡𝑡𝑡𝑡𝑡𝑡𝑡 𝑝𝑝𝑝𝑝𝑝𝑝𝑝𝑝
𝑣𝑣
Valley Height/Peak Height Average: 100 ∗ 2 ∗
ℎ1 +ℎ2

𝑣𝑣
Valley Height/Peak Height Sum: 100 ∗
ℎ1 +ℎ2

ResolutionLimit
ResolutionLimit serves as the limit for the Peak Resolution Below Limit outlier.

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ResponseCheckMinimum
ResponseCheckMinimum serves as the limit for the Response Check Below Limit
outlier.

ResponseFactorMaximumPercentDeviation
ResponseFactorMaximumPercentDeviation serves as the limit for the Response Factor
outlier. ResponseFactorMaximumPercentDeviation represents the maximum allowed
deviation of the response factor for any calibration row of this compound from
AverageResponseFactor.

ResponseFactorRSD
ResponseFactorRSD represents the relative standard deviation of Response Factor for
enabled calibration levels.

RetentionIndex
RetentionIndex records the back-calculated retention index as determined from the
library search.
LibraryRetentionIndex requires the compound is perceived using a retention time
calibration (RT CAL).

RetentionTime
RetentionTime represents, in units of minutes, the chromatographic retention time at
which the chromatographic peak for this TargetCompound row is associated. Note that
for a TargetCompound row for which ISTDCompoundID is not NULL, this nominal
retention time is subject to modulation by the ratio of the observed and nominal
retention times of the related Internal Standard compound. This ratio is readily
available by querying the retention-time information stored in the so-indicated
internal-standard TargetCompound row and its associated primary-hit Peak row.
Default value is 0.

RetentionTimeDeltaUnits
RetentionTimeDeltaUnits represents the choice of units for LeftRetentionTimeDelta
and RightRetentionTimeDelta. The choices are Minutes or Percent. If

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RetentionTimeDeltaUnits is set to Minutes, the values of LeftRetentionTimeDelta and

RightRetentionTimeDelta are interpreted as an offset in minutes from RetentionTime.
If RetentionTimeDeltaUnits is set to Percent, the values of LeftRetentionTimeDelta and
RightRetentionTimeDelta are interpreted as a percentage offset from RetentionTime.

Enum Name UI Name XPath expression

Minutes Minutes *//RetentionTimeDeltaUnits[.='Minutes']

Percent Percent *//RetentionTimeDeltaUnits[.='Percent']

RetentionTimeWindow
RetentionTimeWindow represents the full width of the range of allowed values of
RetentionTime. RetentionTimeWindow serves to define the limits for the Retention
Time outlier condition.

RetentionTimeWindowCC
RetentionTimeWindowCC represents the full width of the range of allowed values of
RetentionTime for CC SampleType. RetentionTimeWindowCC serves to define the
limits for the Retention Time CC outlier condition.

RetentionTimeWindowUnits
RetentionTimeWindowUnits represents the choice of units for RetentionTimeWindow.
The choices are Minutes or Percent. If RetentionTimeWindowUnits is set to Minutes,
the value of RetentionTimeWindow is interpreted as an offset in minutes from
RetentionTime. If RetentionTimeWindowUnits is set to Percent, the value of
RetentionTimeWindow is interpreted as a percentage offset from RetentionTime.

Enum Name UI Name XPath expression

Percent Percent *//RetentionTimeWindowUnits[.='Percent']

Minutes Minutes *//RetentionTimeWindowUnits[.='Minutes']

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RightRetentionTimeDelta
RightRetentionTimeDelta represents time expressed in units of minutes or percent of
nominal RetentionTime, as indicated by RetentionTimeDeltaUnits. It defines the offset
used to determine the upper bound for the retention-time window for signals which
are extracted in support of quantitating the chemical compound indicated by this
TargetCompound row.
Example:
RetentionTime has a value of 5 minutes. RightRetentionTimeDelta has a value of 0.1
and RetentionTimeDeltaUnits has a value of 0 for Minutes. Then the upper bound on
the extraction window is 5 + 0.1 or 5.1 minutes. On the other hand if
RetentionTimeDeltaUnits is 1 for Percent and RightRetentionTimeDelta is 20, then the
upper bound on the extraction window is 5 + 20% * 5 = 6 minutes. Default value is
1 minutes.

RxUnlabeledIsotopicDilution
RxUnlabeledIsotopicDilution is the Rx value used in calculations for Stable Labeled
Isotope quantitation technique. A full discussion of that technique is beyond the scope
of this document.

RyLabeledIsotopicDilution
RyLabeledIsotopicDilution is the RY value used in calculations for Stable Labeled
Isotope quantitation technique. A full discussion of that technique is beyond the scope
of this document.

SampleAmountLimitHigh
SampleAmountLimitHigh represents the upper limit for the Sample Amount outlier.
OutlierSampleAmountOutOfLimits is set too High if the FinalConcentration of this
compound exceeds SampleAmountLimitHigh.

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SampleAmountLimitLow
SampleAmountLimitLow represents the lower limit for the Sample Amount outlier.
OutlierSampleAmountOutOfLimits is set too Low if the FinalConcentration of this
compound is less than SampleAmountLimitLow.

SampleMaximumPercentRSD
SampleMaximumPercentRSD represents the upper limit for the SampleRSD outlier.
OutlierSampleOutsideRSD is set too High if the SampleRSD of this compound in the
batch is higher than SampleMaximumPercentRSD.

ScanType
ScanType represents a human-readable string describing the experimental technique
used to collect the data used to analyze the chemical compound represented by this
TargetQualifier row. Possible values include "MRM", "SRM", "Parent Ion Scan", or
“Neutral Loss Scan". This string is subject to localization in other supported languages.

Enum Name UI Name XPath expression

MRM MRM *//ScanType[.='MRM']

NeutralLoss Neutral Loss *//ScanType[.='NeutralLoss']

NeutralGain Neutral Gain *//ScanType[.='NeutralGain']

ProductIon Product Ion *//ScanType[.='ProductIon']

PrecursorIon Precursor Ion *//ScanType[.='PrecursorIon']

Ms1Scan Ms1 Scan *//ScanType[.='Ms1Scan']

Ms2Scan Ms2 Scan *//ScanType[.='Ms2Scan']

Ms1SIM Ms1 SIM *//ScanType[.='Ms1SIM']

Ms2SIM Ms2 SIM *//ScanType[.='Ms2SIM']

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SelectedMZ
SelectedMZ represents a mass-to-charge measurement, in units of daltons per unit
charge, of the ions selected by the first-quadrupole stage in a tandem mass
spectrometer used to perform this experiment.

SignalInstance
SignalInstance identifies which of several detectors of the same type to use.
SignalInstance is useful when there are two (or more) signals from the same kind of
detector. For example, two Flame Ionization Detectors (FID).
SignalInstance is NULL by default. If SignalInstance is NULL, the instance is set to 1 by
default.
{SignalType, SignalName, SignalInstance} together uniquely identify the signal.

SignalName
SignalName represents a particular part of the signal as defined by SignalType. For
example, for the variable wavelength detectors for liquid chromatography (LC), the
different wavelengths are labeled “A”, “B”, “C”… Hence, SignalName specifies the
actual wavelength within the entire Variable Wavelength Detector (VWD) SignalType.
SignalName is NULL by default. If SignalName is NULL, the first signal name for the
currently defined signal type is used. For MS SignalType, SignalName is ignored.

SignalRetentionTimeOffset
SignalRetentionTimeOffset is for future feature.

SignalToNoiseMultiplier
SignalToNoiseMultiplier is a multiplier for signal to noise ratio. If a value is set in the
“S/N Multiplier”, the final signal-to-noise value will be multiplied by the set value. For
example, to calculate the signal-to-noise as S/N = 2H/h with:
• H is the peak height.
• h is the noise value.
Set the “S/N Multiplier” value to “2.0”.

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SignalType
SignalType represents a type of signal acquired from a particular detector.. By
default, the signal is MS. Additional signal types include two dimensional (2D) signals
such as Flame Ionization Detector (FID). Further delineation of the SignalType is
identified using the SignalName.
Below is a list of acronyms for SignalTypes. Note that the list does not imply support.
ADC = Analogy to Digital Converter
DAD = Diode Array Detector
ECD = Electron Capture Detector
FID = Flame Ionization Detector
FLD = Fluorescence Detector
FPD = Flame Photometric Detector
MWD = Multiple Wavelength Detector
MS = Mass Spectrometer Detector (default)
NPD = Nitrogen Phosphorus Detector
RID = Refractive Index Detector
PID = Photo Ionization Detector
TCD = Thermal Conductivity Detector
VWD = Variable Wavelength Detector
UNK = Unknown

Smoothing
Smoothing represents the smoothing algorithm applied.
Choices include:
• None (default)
• Gaussian
• Quadratic/Cubic Savitzsky-Golay

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• Quartic/Qunitic Savitzsky-Golay
Qualifier chromatograms are smoothed using the same parameters as the target compound.

Smoothing is not recommended with the parameter-less integrator.

Smooth: Comparison of parameter-less integrator with and without previous smoothing on 5

injection of 670 fg of Homocysteine (transition 136 > 90 m/z) on column.

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Smoothing is not recommended since it will reduce the frequency domain of noise and spikes
and may results in additional integrated peaks. As can be seen, the RSDs for repetitive injections
are similar or even smaller when integrating unsmoothed chromatograms compared to
smoothed data.

Enum Name UI Name XPath expression

None 'None' *//@Smoothing[.='None']

Gaussian Gaussian *//@Smoothing[.=’Gaussian’

]

SavitzkyGolay23 Quadratic/Cubic Savitzsky- *//@Smoothing[.=’SavitzkyG

Golay olay23’]

SavitzkyGolay45 • Quartic/Qunitic *//@Smoothing[.=’SavitzkyG

Savitzsky-Golay olay45’]

SmoothingFunctionWidth
SmoothingFunctionWidth represents the width of the moving weighted averaged
window.
The function width defines how many points are averaged at each smoothing step. So if the
function width is 5, then:

a.) The first five points (0, 1, …, 4) are averaged (with appropriate weights). The result is
the value in the output object for the middle point of that group (the point with index =
2).

b.) The next group of five points (1, 2, …, 5) are averaged to get the new value for point 3

c.) The next group of five points (2, 3, …, 6) are averaged …

SmoothingFunctionWidth must be at least 4 for SavitzskyGolay23 and at least 6 for

SavitzskyGolay45 (enforced by method validation)

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SmoothingGaussianWidth
SmoothingGaussianWidth represents the width of the Gaussian function.
SmoothingGaussianWidth weights are calculated to give a smoothing function that is
Gaussian in shape, with a specified width. The width is specified as the “Gaussian
width”, and is in units of “points”. I.e., a value of 3.5 specifies a Gaussian whose width is
3.5 times the spacing of the points.

SmoothingGaussianWidth must be positive and not greater than

SmoothingFunctionWidth.

SpectrumBaselineThreshold
SpectrumBaselineThreshold represents the counts to be subtracted in a point-to-point
manner before spectrum extraction. In Quantitation software, this parameter defaults
to null.

SpectrumExtractionOverride
SpectrumExtractionOverride represents what spectrum is used to calculate the reference
library match score and in conjunction with the “Override spectrum” checkbox in the Compound
Information Properties dialog box, it determines which spectrum is displayed in the Compound
Information Window.
If the field is left empty or set to “Default” the Spectrum Extraction Override has no effect and the
spectrum extracted to calculate the Library Match Score is based on the Scan Type defined in the
method.
If the field is set to “Scan”, the “Scan” spectrum is extracted (if present in the data file) to calculate
the Library Match Score, overriding the Scan Type defined in the method. For example, processing
SIM/Scan data.
If the field is set to “Product Ion”, the “Product Ion” spectrum is extracted (if present in the data
file) to calculate the Library Match Score, overriding the Scan Type defined in the method. For
example, processing Targeted MS/MS data.
If the field is set to “Deconvoluted Scan”, deconvolution will be run and a component spectrum (if
found) will be used to calculate the Library Match Score. Note that this field has no effect if a valid
Reference Library is not set in the Globals Setup.

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SpectrumScanInclusion
SpectrumScanInclusion represents how spectrum is extracted.
SpectrumScanInclusion defaults to “Average”, where spectrum is average of all spectra
within defined RT range. If SpectrumScanInclusion is set to “Apex”, it extracts a single
spectrum from the top of the peak.

SpectrumPeakHeightPercentThreshold
SpectrumPeakHeightPercentThreshold represents the percentage of the peak height to
use to extract and average spectra. When this parameter is set, the average spectrum
will include spectra within the RT range where all points on the EIC is above the
specified percentage of peak height. In TOF/QTOF flavors, it defaults to 10%.

SpectrumPercentSaturationThreshold
SpectrumPercentSaturationThreshold represents the maximum percentage of
saturation to include in the average. If a peak in the spectrum is above the given
percentage of being saturated, that spectrum will be excluded from the average.
If a Reference Pattern Library is specified in the method, only masses (+/-
MZExtractionWindow) in the pattern library are monitored for saturation. For other
masses even though their abundances could be above saturation limit, the scan lines
are not excluded from average since they are not contributing to the accurate mass
match scores.
If mass accuracy outlier or reference library is specified, only target ion and qualifier
ions (+/- MZExtractionWindow) are monitored for saturation when calculating average
spectrum.
In TOF/QTOF flavors, it defaults to 10%.

SubList
SubList is a Boolean flag that can categorize compounds as part of a particular set of
the compounds in the quantitation method.
The column does not have any effect on any calculation, but potentially can be used
for report customization.
For example, mark a set of compounds to designate they are on/off a list.
Note that the Sublist column displays as “OnOff” in UI.

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SurrogateConcentration
SurrogateConcentration represents the expected concentration of this surrogate
compound, expressed in units of ConcentrationUnits. SurrogateConcentration is used
to evaluate the Surrogate outlier and Surrogate Percent Recovery outlier conditions.
SurrogateConcentration is only meaningful for compounds of type Surrogate.

SurrogateConcentrationLimitHigh
SurrogateConcentrationLimitHigh represents the upper limit for the Surrogate outlier.
OutlierSurrogateOutOfLimits is set too High if the FinalConcentration of this
compound exceeds SurrogateConcentrationLimitHigh.

SurrogateConcentrationLimitLow
SurrogateConcentrationLimitLow represents the lower limit for the Surrogate outlier.
OutlierSurrogateOutOfLimits is set too Low if the FinalConcentration of this
compound is less than SurrogateConcentrationLimitLow.

SurrogatePercentRecoveryMaximum
SurrogatePercentRecoveryMaximum represents the upper limit for the Surrogate
Percent Recovery outlier. OutlierSurrogatePercentRecovery is set too High if the
FinalConcentration of this compound exceeds SurrogatePercentRecoveryMaximum.

SurrogatePercentRecoveryMinimum
SurrogatePercentRecoveryMinimum represents the lower limit for the Surrogate
Percent Recovery outlier. OutlierSurrogatePercentRecovery is set too Low if the
FinalConcentration of this compound is less than SurrogatePercentRecoveryMinimum.

SymmetryCalculationType
SymmetryCaculationType represents the choices of formulas used by different
pharmacoepedia to calculate the peak symmetry (tailing factor). The following types
are available:

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Default:

USP/JP/EU:

• W-5 is the peak width at 5% height of the peak.

• Wf-5% is the front peak width at 5% height of the peak.

SymmetryLimitHigh
SymmetryLimitHigh represents the higher limit which indicates tailing for the
Symmetry outlier. OutlierSymmetry is set too High if the calculated Symmetry value
of the primary peak is greater than the SymmetryLimitHigh.

SymmetryLimitLow
SymmetryLimitLow represents the lower limit which indicates fronting for the
Symmetry outlier. OutlierSymmetry is set too Low if the calculated Symmetry value
of the primary peak is less than the SymmetryLimitLow.

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TargetCompoundIDStatus
TargetCompoundIDStatus is an internal string.

ThresholdNumberOfPeaks
ThresholdNumberOfPeaks represents a Peak Filter parameter that defines the
maximum number of chromatogram peaks retained by the integrator.
Example:
If ThresholdNumberOfPeaks is set to 10, then of all the peaks that are found by the
integrator, up to a maximum of 10 largest peaks shall be passed to the Quantitation
Engine.

TimeReferenceFlag
TimeReferenceFlag has the value true if and only if this TargetCompound row
represents a time reference compound. Only internal standard compounds can be
designated as time reference compounds.
If compound B is a time reference for compound A, then the Quantitation Engine will
multiply the retention time of A’s peaks by the ratio of the actual-to-expected retention
time of B’s primary hit peak.
TimeReference allows a time correction for a particular target compound. The
approach is useful in the case where the target compound’s retention time drifts and
the related ISTD used as the time reference also experiences the same relative shift.
As a result, the Quantitation Engine will look for this target compound in a shifted
retention time.
Note that the extract retention time window does not shift, just the retention time
where the target is expected. With the Peak Selection criteria set to Cloest Retention
Time, this shift in the expected retention time can improved the peak selection,
especially when another peak exists in the same extracted chromatogram.

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TimeReference: Application of Closest RT with ISTD TimeReference.

TimeSegment
TimeSegment represents the index of the acquisition time segment that was used to
acquire the signal for this compound.

Transition
Transition represents a human-readable string that expresses the M/Z values
measured for this compound. The format of the Transition string depends on
ScanType. When ScanType = MRM, the transition string has the format “SelectedMZ ->
MZ”, where SelectedMZ is the precursor ion and MZ is the product ion.

TriggeredTransitions
TriggeredTransitions is a comma-separated string that represents Triggered MRM
transitions. This column is populated automatically from the acquisition method when
creating a new quantitation method from accquired MRM data. Values can also be
entered manually.
When extracting a spectrum, if the TriggeredTransitions string is not null, it will be parsed and
an EIC will be extracted for each triggered transition in the list. The latest start-of-data point in
RT defines the trigger point, RT_trigger, and the compound spectrum will be extracted over the
RT range = [RT_trigger, RT_end], where RT_end is the end of the primary target peak. For the

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(non-triggered) MRM case, the TriggeredTransitions column will be null and the spectrum
extraction will occur as it normally does.

UncertaintyRelativeOrAbsolute
UncertaintyRelativeOrAbsolute clarifies the specification of tolerance for actual vs.
nominal qualifier signal ratios. Its value is Relative (default) or Absolute. This value
applies to all TargetQualifier rows associated with this TargetCompound row.
Example:
Consider a nominal qualifier signal ratio of 80 percent between Qualifier Q1 and this
target compound, with a 20 per cent uncertainty. If UncertaintyRelativeOrAbsolute is
Relative, then the tolerance bounds for the qualifier ratio are 64 to 96, because 20 per
cent of 80 is 16. If UncertaintyRelativeOrAbsolute is Absolute, then the tolerance
bounds for the qualifier ratio are 60 to 100, because 20 per cent uncertainty is treated
as an absolute offset from 80 per cent.

Enum Name UI Name XPath expression

Absolute Absolute *//@UncertaintyRelativeOrAbsolute[.=’Abso

lute’]

Relative Relative *//@UncertaintyRelativeOrAbsolute[.=’Rela

tive’]

UserAnnotation
UserAnnotation stores an arbitrary user-defined string.
UserAnnotation is editable in Batch-at-a-Glance. It’s a per compound per sample
information.
If a method that contains User Annotation values is saved, the User Annotation values are
removed when the method is opened and applied to a new batch.

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UserCustomCalculation
UserCustomCalculation stores a result from a custom calculation.
UserCustomCalculation work with a scripting mechanism requiring .NET Framework
programming skills.

UserCustomCalculationLimitHigh
UserCustomCalculationLimitHigh represents the upper limit for the triggered user
custom calculation. Calculation producing results higher than the limit set the outlier
to “High”.

UserCustomCalculationLimitLow
UserCustomCalculationLimitLow represents the upper limit for the triggered user
custom calculation. Calculation producing results higher than the limit set the outlier
to “Low”.

UserDefined
UserDefined stores an arbitrary user-defined string.
UserDefined is editable in Batch-at-a-Glance, on a per compound basis. If a method that
contains User Defined values is saved, the User Defined values are retained when the method is
opened and applied to a batch.

UserDefined1
UserDefined1 stores an arbitrary user-defined string.
UserDefined is editable in Batch-at-a-Glance, on a per compound basis. If a method that
contains User Defined values is saved, the User Defined values are retained when the method is
opened and applied to a batch.

UserDefined2
UserDefined2 stores an arbitrary user-defined string.
UserDefined is editable in Batch-at-a-Glance, on a per compound basis. If a method that
contains User Defined values is saved, the User Defined values are retained when the method is
opened and applied to a batch.

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UserDefined3
UserDefined3 stores an arbitrary user-defined string.
UserDefined is editable in Batch-at-a-Glance, on a per compound basis. If a method that
contains User Defined values is saved, the User Defined values are retained when the method is
opened and applied to a batch.

UserDefined4
UserDefined4 stores an arbitrary user-defined string.
UserDefined is editable in Batch-at-a-Glance, on a per compound basis. If a method that
contains User Defined values is saved, the User Defined values are retained when the method is
opened and applied to a batch.

UserDefined5
UserDefined5 stores an arbitrary user-defined string.
UserDefined is editable in Batch-at-a-Glance, on a per compound basis. If a method that
contains User Defined values is saved, the User Defined values are retained when the method is
opened and applied to a batch.

UserDefined6
UserDefined6 stores an arbitrary user-defined string.
UserDefined is editable in Batch-at-a-Glance, on a per compound basis. If a method that
contains User Defined values is saved, the User Defined values are retained when the method is
opened and applied to a batch.

UserDefined7
UserDefined7 stores an arbitrary user-defined string.
UserDefined is editable in Batch-at-a-Glance, on a per compound basis. If a method that
contains User Defined values is saved, the User Defined values are retained when the method is
opened and applied to a batch.

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UserDefined8
UserDefined8 stores an arbitrary user-defined string.
UserDefined is editable in Batch-at-a-Glance, on a per compound basis. If a method that
contains User Defined values is saved, the User Defined values are retained when the method is
opened and applied to a batch.

UserDefined9
UserDefined9 stores an arbitrary user-defined string.
UserDefined is editable in Batch-at-a-Glance, on a per compound basis. If a method that
contains User Defined values is saved, the User Defined values are retained when the method is
opened and applied to a batch.

UserDefinedTargetCompoundID
UserDefinedTargetCompoundID stores a back pointer from dynamic target to the user-defined
parent compound. Null for user-defined target compounds. For dynamic target compounds,
points to the CompoundID of the “parent” (user-defined) target compound. Set at Method
Setup time.

WavelengthExtractionRangeHigh
WavelengthExtractionRangeHigh represents the wavelength that defines the high limit
of the range used to extract the UV-vis spectral signal.

WavelengthExtractionRangeLow
WavelengthExtractionRangeLow represents the wavelength that defines the low limit
of the range used to extract the UV-vis spectral signal.

WavelengthReferenceRangeHigh
WavelengthReferenceRangeHigh represents the wavelength that defines the high limit
of the range used for the UV-vis spectral reference signal.

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WavelengthReferenceRangeLow
WavelengthReferenceRangeLow represents the wavelength that defines the low limit
of the range used for the UV-vis spectral reference signal.

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TargetQualifier Table

Primary Key
{BatchID, SampleID, CompoundID, QualifierID} serves as the primary key. The
composite of the BatchID and SampleID and CompoundID unique identify each row in
this table. The keys in the Quantitation DataSet are not show in the user interface.
A primary key value must be unique with in the table. A composite key is a primary
key that incorporates more than one column.

BatchID
BatchID uniquely identifies the batch. BatchID is part of the composite primary key.
The BatchID is typically set to -1 because Batch-at-a-Glance analyzes one batch.

SampleID
SampleID uniquely identifies the sample in the batch. SampleID is part of the
composite primary key. Thus, each sample in the batch is assigned a unique SampleID.

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CompoundID
CompoundID uniquely identifies the sample in the batch. CompoundID is part of the
composite primary key.
Thus, each compound in the batch is assigned a unique CompoundID.

QualifierID
QualifierID uniquely identifies the qualifier(s) for this compound. QualifierID is part
of the composite primary key. Thus, each qualifier for this compound is assigned a
unique QualifierID.

AreaSum
AreaSum controls summing of the qualifier response to the target response. AreaSum
is false by default.
If this flag has a value of true, then for purposes of quantitation the qualifier response
is cumulated with the response of the associated target signal (and possibly with
responses of other qualifier signals also associated with the same target).
Note that the target peak displays as the target response, not the target plus qualifier
summed responses. In addition, the qualifier ratio is also calculated in the same
manner in either ase i.e. non-area summed or area summed.

CellAcceleratorVoltage
CellAcceleratorVoltage represents a meta data from LCQQQ acquisition.

CollisionEnergy
CollisionEnergy represents the amount of collision-induced dissociation (CID)
occurring in the triple (QQQ) collision cell. CID is a mechanism to fragment molecular
ions in the gas phase. The molecular ions are accelerated by this electrical potential
too high kinetic energy in the vacuum of a mass spectrometer and to collide in the
higher pressure collision cell with neutral gas molecules (nitrogen). In the collision
some of the kinetic energy is converted into internal energy which results in bond
breakage and the fragmentation of the molecular ion into smaller fragments.

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CollisionEnergyDelta
CollisionEnergyDelta defines the one-sided extend of the chromatograms/spectra
extraction range of the CollisionEnergy. If this value is set, the actual extraction range
of chromatograms and spectra is given by the following formula:
CE range = [CollisionEnergy – CollisionEnergyDelta, CollisionEnergy +
CollisionEnergyDelta]
The quantifier and each of the qualifier ions can be assigned independent CE
extraction ranges.

FragmentorVoltage
FragmentorVoltage represents the acquisition parameter that controls the acceleration
of the ions from the source into the rest of the mass spectrometer (mass analyzer and
detection).

FragmentorVoltageDelta
FragmentorVoltageDelta defines the one-sided extent of the chromatograms/spectra
extraction range of the FragmentorVoltage. If this value is set, the actual extraction
range of chromatograms and spectra is given by the following formula:
FV range = [FragmentorVoltage – FragmentorVoltageDelta, FragmentorVoltage +
FragmentorVoltageDelta]
In this formula, the bottom of the FV range is constrainded to be non-negative. The
quantifier and each of the qualifier ions can be assigned independent FV extraction
ranges.

GraphicPeakQualifierChromatogram
GraphicPeakQualifierChromatogram represents a relative path and filename to a
graphic (.emf) file used in reporting.

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Graphic 6: File reference to graphic.

IntegrationParameters
IntegrationParameters names a persistent store containing a collection of parameters
to modulate the behavior of the integration algorithm brought to bear on the signal
indicated by this TargetQualifier row. The default value for IntegrationParameters is
NULL. Wherever this column is null, signal integration proceeds assuming the same
integration settings as target quantifier ion are used.

IntegrationParametersModified
IntegrationParametersModified is true when the integration parameters for a
compound is modified at the sample level.

IonPolarity
IonPolarity represents an acquisition parameter that records the polarity of the ions
focused with voltages applied to a lens system located between the source and the
analyzer.

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Enum UI Name XPath expression Summary

Name
Positive Positive *//IonPolarity[.='Positive'] Positive ion
polarity
Negative Negative *//IonPolarity[.='Negative'] Negative ion
polarity
Unassigned Unassigned *//IonPolarity[.='Unassigned’] Unknown ion
polarity
Mixed Mixed *//IonPolarity[.='Mixed'] Contains both
positive and
negative ion
polarity data

MZ
MZ represents a mass-to-charge measurement in units of Daltons per unit charge, of
the ions selected in the stage before the ions hit the detector.
In MRM, the combination of SelectMZ (precursor ion) and MZ (product ion) determine
the transition.
For single quadrupole modes, MZ sets the mass filter for the ions.
MZ is analogous to and serves exactly the same role for the qualifier signal represented
by this TargetQualifier row as does TargetCompound.MZ for the target signal
represented by the associated TargetCompound row given by CompoundID.

MZExtractionWindowFilterLeft
MZExtractionWindowFilterLeft is the m/z value that controls the range on the left of
the extracted m/z ion. The default value is 0.3.

MZExtractionWindowFilterRight
MZExtractionWindowFilterRight the m/z value that controls the range on the right of
the extracted m/z ion. The default value is 0.7.

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MZExtractionWindowUnits
MZExtractionWindowUnitsLeft represents the units used for
MZExtractionWindowFilterLeft and MZExtractionWindowFilterRight.
The units are the following:
• Thomsons:
Thompson or m/z represents the physical quantity mass-to-charge ratio.
For example, the ion C7H72+ an ion will be observed at 45.5 m/z
• PPM:
Parts per million (“ppm”) denotes one particle of a given substance for every
999,999 other particles. One part in 106 — a precision of 0.0001%
The user can alternatively establish the mass extraction window value using
ppm units.
Ppm = 106 * ∆m accuracy / mmeasured
For example, at the theoretical mass of 1000 and a measured mass of 999.9
boundary is designated as 100 ppm.
• Percent:
Percent represents the mass extraction window as a percentage of the
theoretical mass.

Enum Name UI Name Xpath expression

Thomsons m/z *//MZExtractionWindowUnits[.=’ Thomsons
‘]
PPM ppm *//MZExtractionWindowUnits[.=’PPM’]

Percent Percent *//MZExtractionWindowUnits[.=’Percent’]

OutlierPeakNotFound
OutlierPeakNotFound stores the flag that indicates qualifier peak is not found by
integrator. If enabled by default or by applying Outlier Setup, an associated column is
highlighted.

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PeakFilterThreshold
PeakFilterThreshold represents the type of threshold filter that is applied to the
chromatogram peaks that were detected by the integrator. The choice of
PeakFilterThreshold determines the interpretation of PeakFilterThresholdValue. The
following choices of PeakFilterThreshold are available:

PeakFilterThreshold Filter condition

PeakAreaAbsThreshold Peaks with area less than
PeakFilterThresholdValue are filtered out
PeakAreaPctThreshold (default) Peaks whose area, divided by maximum
peak area, is less than
PeakFilterThresholdValue/100 are
filtered out
PeakHeightAbsThreshold Peaks with height less than
PeakFilterThresholdValue are filtered out
PeakHeightPctThreshold Peaks whose height, divided by maximum
peak height, is less than
PeakFilterThresholdValue/100 are
filtered out

PeakFilterThresholdValue
PeakFilterThresholdValue represents the threshold that is applied to the peak area or
height, depending on the choice of PeakFilterThreshold. Chromatogram peaks that are
below the PeakFilterThresholdValue are filtered out and are not considered as
candidate peaks for quantitation.

OutlierPeakNotFound
OutlierPeakNotFound stores the flag that indicates target qualifier peak is not found
by integrator. If enabled by default or by applying Outlier Setup, an associated column
is highlighted.

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QualifierName
QualifierName stores qualifier’s metadata in terms of the CompoundName.

QualifierRangeMaximum
QualifierRangeMaximum is the value stored after the qualifier ratio calculation. The
qualifier range sets the upper limit for the qualifier ratio value. Thus, comparing the
calculated qualifier ratio directly against this QualifierRangeMaximum determines if
the qualifier falls within range.

QualifierRangeMinimum
QualifierRangeMinimum is the value stored after the qualifier ratio calculation. The
qualifier range sets the lower limit for the qualifier ratio value. Thus, comparing the
calculated qualifier ratio directly against this QualifierRangeMinimum to determines if
the qualifier falls within range.

QuantitationMessage
QuantitationMessage records issues for a particular sample.
Example:
If the qualifier signal is not present for a compound that requires a qualifier present,
the QuantitationMessage records this issue.

RelativeResponse
RelativeResponse expresses a nominal relative ratio of the integrator-determined
responses of the signal for this TargetQualifier row versus the signal for the associated
TargetCompound row. Default value is unity indicating that the response of the
qualifier signal is equal to the response of its associated target signal.

ScanType
ScanType represents a human-readable string describing the experimental technique
used to collect the data used to analyze the chemical compound represented by this
TargetCompound row. Possible values include "MRM", "SRM", "Parent Ion Scan", or
“Neutral Loss Scan". This string is subject to localization in other supported languages.

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Enum Name UI Name XPath expression

MRM MRM *//ScanType[.='MRM']

NeutralLoss Neutral Loss *//ScanType[.='NeutralLoss']

NeutralGain Neutral Gain *//ScanType[.='NeutralGain']

ProductIon Product Ion *//ScanType[.='ProductIon']

PrecursorIon Precursor Ion *//ScanType[.='PrecursorIon']

Ms1Scan Ms1 Scan *//ScanType[.='Ms1Scan']

Ms2Scan Ms2 Scan *//ScanType[.='Ms2Scan']

Ms1SIM Ms1 SIM *//ScanType[.='Ms1SIM']

Ms2SIM Ms2 SIM *//ScanType[.='Ms2SIM']

SelectedMZ
SelectedMZ represents a mass-to-charge measurement, in units of daltons per unit
charge, of the ions selected by the first-quadrupole stage in a tandem mass
spectrometer used to perform this experiment.
The SelectedMZ sets the precursor ion in MS/MS scan type such as Multiple Reaction
Monitoring (MRM) or Product Ion scan.
In MRM, the qualifier transition’s precursor ion (SelectedMZ) is assigned as a different
precursor ion than the Target transition’s precursor ion.
For example,
• 335 -> 200 (Compound1 Target transition)
• 337 -> 200 (Compound1 Qualifier transition)
Often used to establish another qualifier transition utilizing the isotope ratio with
compounds containing 35Cl / 37 Cl or 79Br / 81Br.

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ThresholdNumberOfPeaks
ThresholdNumberOfPeaks is a maximum number of peaks found by the integrator.

Transition
Transition represents a human-readable string that expresses the M/Z values
measured for this compound. The format of the Transition string depends on
ScanType. When ScanType = MRM, the transition string has the format “SelectedMZ ->
MZ”, where SelectedMZ is the precursor ion and MZ is the product ion.

Uncertainty
Uncertainty is a value, which, along with the RelativeResponse column, defines
tolerance bounds for the nominal qualifier ratio for this TargetQualifier row.
UncertaintyRelativeOrAbsolute column determines whether the uncertainty is a
percent of the RelativeResponse or an absolute margin.
Example:
Consider a nominal qualifier signal ratio of 80 percent between Qualifier Q1 and this
target compound, with a 20 per cent uncertainty. If UncertaintyRelativeOrAbsolute is
0, then the tolerance bounds for the qualifier ratio are 64 to 96, because 20 per cent of
80 is 16. If UncertaintyRelativeOrAbsolute is 1, then the tolerance bounds for the
qualifier ratio are 60 to 100, because 20 per cent uncertainty is treated as an absolute
offset from 80 per cent.

UserDefined
UserDefined stores an arbitrary user-defined string.
UserDefined is editable in Batch-at-a-Glance.

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PeakQualifier Table

Primary Key
{BatchID, SampleID, CompoundID, PeakID, QualifierID } serves as the primary key.
The composite of the BatchID and SampleID and CompoundID and PeakID and
QualifierID and unique identify each row in this table. The keys in the Quantitation
DataSet are not show in the user interface.
A primary key value must be unique with in the table. A composite key is a primary
key that incorporates more than one column.

BatchID
BatchID uniquely identifies the batch. BatchID is part of the composite primary key.
The BatchID is typically set to -1 because Batch-at-a-Glance analyzes one batch.

SampleID
SampleID uniquely identifies the sample in the batch. SampleID is part of the
composite primary key. Thus, each sample in the batch is assigned a unique SampleID.

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CompoundID
CompoundID uniquely identifies the sample in the batch. CompoundID is part of the
composite primary key. Thus, each compound in the batch is assigned a unique
CompoundID.

PeakID
PeakID uniquely identifies the qualifier(s) for this compound. PeakID is part of the
composite primary key.
Thus, each qualifier peak for this compound is assigned a unique PeakID.

QualifierID
QualifierID uniquely identifies the qualifier(s) for this compound. QualifierID is part
of the composite primary key. Thus, each qualifier for this compound is assigned a
unique QualifierID.

Area
Area contains the integrator-determined area of the peak represented by this
PeakQualifier row.

BaselineEnd
BaselineEnd is expressed in counts. Baseline represents the height of the trailing
baseline endpoint.

BaselineEndOriginal
BaselineEndOriginal records the BaselineEnd before performing manual integration.

BaselineStandardDeviation
BaselineStandardDeviation stores an integration metric that measures the variation of
the baseline.

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BaselineStart
BaseLineStart is expressed in counts. Baseline represents the height of the leading
baseline endpoint.
Baseline regions are equivalent to noise regions only if the following two conditions
hold:
1. the integrator provides the baseline region information
2. no user-defined regions are specified.
The parameterless integrators such as the Agile integrator provide baseline region
information.

BaselineStartOriginal
BaselineStartOriginal records the Baseline Start before performing manual
integration.

CoelutionScore
CoelutionScore is a measurement of how well this qualifier ion coelutes with the
quantifier ion. The Coelution score uses the retention time of the quantifier ion and
the quantifier ion as well as the peak width and the peak symmetry of the quantifier
ion and the qualifier ion.

FullWidthHalfMaximum
FullWidthHalfMaximum is the peak width at half height.

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Height
Height contains the integrator-determined height of the peak represented by this peak.
Typically, Area is used as the measure of the size of the peak.

IntegrationEndTime
IntegrationEndTime contains the integrator-determined peak-end chromatographic
retention time value associated with the peak represented by this PeakQualifier row.

IntegrationEndTimeOriginal
IntegrationEndTimeOriginal records the IntegrationEndTime before performing
manual integration.

IntegrationMetricQualityFlags
IntegrationMetricQualityFlags stores the reasons record by the MS-MS integrator.
• Based on several peak characteristics:
• Peak height
• Peak area
• Peak width
• Peak symmetry

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• Merged peaks to the right or left

• Level of spikes on a peak

Enum Name UI Name Xpath expression

NoProblem No *//IntegrationMetricQualityFlags[.=’NoProb
Problem lem’]

InterferencePr Interfere *//IntegrationMetricQualityFlags[.=’Interf

oblem nce erenceProblem’]
Problem
• PeakAr Peak *//IntegrationMetricQualityFlags[.=’PeakAr
ea area ea’]

WidthProblem Width *//IntegrationMetricQualityFlags[.=’WidthP

Problem roblem’]

Spiky Spiky *//IntegrationMetricQualityFlags[.=’Spiky’

]

MergedProble Merged *//IntegrationMetricQualityFlags[.=’Merged

m Problem Problem’]

SeriousProble Serious *//IntegrationMetricQualityFlags[.=’Seriou

m Problem sProblem’]

Note: the string of integrator problems can include multiple problem separated by
commas.
For example: “WidthProblem, SeriousProblem”

IntegrationQualityMetric
IntegrationQualityMetric stores the type of integration metric found by the MS-MS
integrator. IntegrationQualityMetric relates to the OutlierIntegrationQualityMetric.
IntegrationQualityMetric is classifies the peak into categories:

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Accepted:

Inspect:

Reject:

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Enum Name UI Name Xpath expression

Accepted Accepted *//IntegrationQualityMetric[.=’Accepted’]

• Inspect Inspect *//IntegrationQualityMetric[.=’Inspect’]

Rejected Rejected *//IntegrationQualityMetric[.=’Rejected’]

IntegrationStartTime
IntegrationStartTime contains the integrator-determined peak-start chromatographic
retention time value associated with the peak represented by this PeakQualifier row.

IntegrationStartTimeOriginal
IntegrationStartTimeOriginal records the IntegrationStartTime before performing
manual integration.

ManuallyIntegrated
ManuallyIntegrated flag is true if and only if the integration results stored for this
peak has been manually updated.

MassAccuracy
MassAccuracy is the difference between the actual centroided spectral mass and
expected MZ. It’s measured in the unit as determined by the
MZExtractionWindowUnits setting (Thomsons, PPM, Percent).

MZ

MZ records the actual MZ used for mass accuracy calculation. In feature detection
case, it is the feature assigned mass.

NoiseRegions
NoiseRegions records the actual regions that are used for the noise calculation.

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OutlierQualifierCoelutionScore
OutlierQualifierCoelutionScore stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted. See Outlier Details.

OutlierQualifierFullWidthHalfMaximum
OutlierQualifierFullWidthHalfMaximum stores the flag resulting from this outlier
condition evaluation. If enabled by default or by applying Outlier Setup, an associated
column is highlighted. See Outlier Details.

OutlierQualifierIntegrationQualityMetric
OutlierQualifierIntegrationQualityMetric stores the flag resulting from this outlier
condition evaluation. If enabled by default or by applying Outlier Setup, an associated
column is highlighted.

OutlierQualifierMassAccuracy
OutlierQualifierMassAccuracy stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted. See Outlier Details.

OutlierQualifierOutOfLimits
OutlierQualifierOutOfLimits stores the outlier flag for the OutlierQualifierOutOfLimits.

OutlierQualifierResolutionFront
OutlierQualifierResolutionFront stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted. See Outlier Details.

OutlierQualifierResolutionRear
OutlierQualifierResolutionRear stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted. See Outlier Details.

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OutlierQualifierSignalToNoiseRatio
OutlierQualifierSignalToNoiseRatio stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted. See Outlier Details.

OutlierQualifierSymmetry
OutlierQualifierSymmetry stores the outlier flag for the OutlierQualifierOutOfLimits.

OutlierSaturationRecovery
OutlierSaturationRecovery stores the flag resulting from the Saturation Recovery
outlier condition evaluation. If enabled by default or by applying Outlier Setup, an
associated column is highlighted.

QualifierResponseRatio
QualifierResponseRatio sets the expected ratio between the target ion and its qualifier
ion. For example, this ratio is typically measured to confirm the presence of a
compound follows a certain fragmentation pattern.

QualifierResponseRatioOriginal

QualifierResponseRatioOriginal records the QualifierResponseRatio before performing

the manual integration.

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ResolutionFront
ResolutionFront is the chromatographic resolution of primary peak with the peak in
front of it. It calculates the height of the valley between the peaks as a percent of the
average height of the peaks.

ResolutionRear
ResolutionRear is the chromatographic resolution of primary peak with the rear peak
next to it. It calculates the height of the valley between the peaks as a percent of the
average height of the peaks.

RetentionTime
RetentionTime contains the integrator-determined peak-apex chromatographic
retention time value associated with the peak represented by this PeakQualifier row.

RetentionTimeOriginal
RetentionTimeOriginal records the Retention Time before performing manual
integration.

SaturationRecoveryRatio
SaturationRecoveryRatio represents the ratio of the restored feature peak height to
the original feature peak height. The feature peak and recovery of feature peak are
determined by the feature detection algorithm for accurate mass data.

Saturation Recovery Ratio Recovery Status

Null Feature is not saturated

0 Feature is saturated and not recovered

>0 Feature is saturated but recovered

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SignalToNoiseRatio
SignalToNoiseRatio represents the ratio of the signal to noise based on the
NoiseAlgorithmType for each peak that identifies a compound amount. The S/N ratio
is typically measures a significance of the signal strength above the noise.

Symmetry
Symmetry represents the balance between the back and front of the peak. Symmetry
of 1.0 means the peak is balanced. Smaller numbers less than one indicate asymmetry
and peak fronting whereas larger numbers indicate peak tailing.
Symmetry = Distance (tail) / Distance (front)

UserCustomCalculation
UserCustomCalculation stores a result from a custom calculation.
UserCustomCalculation work with an undocumented scripting mechanism.

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Peak Table

Primary Key
{BatchID, SampleID, CompoundID, PeakID } serves as the primary key. The
composite of the BatchID and SampleID and CompoundID and PeakID and unique
identify each row in this table. The keys in the Quantitation DataSet are not show in
the user interface.
A primary key value must be unique with in the table. A composite key is a primary
key that incorporates more than one column.

BatchID
BatchID uniquely identifies the batch. BatchID is part of the composite primary key.
The BatchID is typically set to -1 because Batch-at-a-Glance analyzes one batch.

SampleID
SampleID uniquely identifies the sample in the batch. SampleID is part of the
composite primary key. Thus, each sample in the batch is assigned a unique
SampleID.

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CompoundID
CompoundID uniquely identifies the sample in the batch. CompoundID is part of the
composite primary key. Thus, each compound in the batch is assigned a unique
CompoundID.

PeakID
PeakID uniquely identifies the peak(s) for this compound. PeakID is part of the
composite primary key.
Thus, each peak for this compound is assigned a unique PeakID.

Accuracy
Accuracy gives the relative error of the computed concentration versus the expected
concentration.

AlternativePeakRTDiff
AlternativePeakRTDiff is the RT difference between the primary peak and the better
alternative peak identified by the AlternativePeakCriteria.

Alternative Deconvoluted Peak LMS is better than Target Peak deconvoluted LMS, matching
against Target reference.

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AlternativeTargetHit
AlternativeTargetHit is only reported when a Target peak is Found AND Target Deconvoluted
(TD) peak is Found. Alternative Hit demonstrates NIST search result. The search result is shown
as string which can be further parsed by report, the format of the string is { TargetRank; NIST
LMS for target compound; Top NIST hit CompoundName; Top NIST hit CAS#; Top NIST hit LMS;
library Comopund ID; library Spectrum ID }. Library Compound ID and Library Spectrum ID are
used by reporting system to retrieve compound library spectrum.

Area
Area represents the integrator-determined area of the peak represented by this Peak
row.

AreaCorrectionResponse
AreaCorrectionResponse is the product of the integrated area of the area correction
signal and the area correction factor, as specified in the associated TargetCompound
row. If the area correction signal is NULL in the associated TargetCompound row, then
AreaCorrectionResponse is zero.

BaselineDraw
BaselineDraw contains graphics information used to draw the baseline calculation
points for a peak.
This value consists of 5 numbers: Baseline1Start, Baseline1End, Baseline2Start,
Baseline2End, BaselineOffset. They are illustrated in the figure below. BaselineOffset
is Y coordinate of the middle of the boxes. BaselineStandardDeviation is height of the
boxes.

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BaselineEnd
BaselineEnd is expressed in counts. It represents the height of the trailing baseline
endpoint.

BaselineEndOriginal
BaselineEndOriginal records the BaselineEnd before performing manual integration.

BaselineStandardDeviation
BaselineStandardDeviation is a metric calculated for all parameterless integrators:
MS-MS, MS-MS (GC), and Agile.

BaselineStart
BaselineStart is expressed in counts. It represents the height of the leading baseline
endpoint.

BaselineStartOriginal
BaselineStartOriginal records the Baseline Start before performing manual
integration.

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CalculatedConcentration
CalculatedConcentration is expressed in the units given by the ConcentrationUnits
value in the associated TargetCompound row. It indicates the concentration value
calculated by the quantitation algorithm for the peak represented by this Peak row.

CapacityFactor
CapacityFactor is a measure of the retention of a peak that is independent of column
geometry or mobile phase flow rate. It is the ratio of the amount of time a solute
spends in the stationary and mobile phases. For example, a solute with a k’ = 6 is twice
as retained by the stationary phase (but not the column) as a solute with a k’ = 3. The
capacity factor does not provide absolute retention information; it provides relative
retention information. An unretained compound has a capacity factor of 0. Tr is the
retention time. To is the retention time of an unretained compound. The equation is

(Tr - To) / To

CCISTDResponseRatio
CCISTDResponseRatio stores ISTD response deviation in any sample type from the
most recent Continuing Calibration sample.

CCResponseRatio
CCResponseRatio stores the compound’s CC response ratio to the initial calibration at
the same calibration level.

EstimatedConcentration
EstimatedConcentration stores a range that estimates the concentration of a
tentatively identified compound after Unknowns Analysis.
Typically, the range is derived from the averaged response factor of all the target
compounds. The estimate is typically within an order of magnitude.

FinalConcentration
FinalConcentration is the typically the amount reported for this sample’s compound.

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FullWidthHalfMaximum
FullWidthHalfMaximum is the peak width at half height.

GroupNumber
GroupNumber is an integer that uniquely identifies the signal-correlation-algorithm
peak-group within the space of all peaks collected to analyze the associated
TargetCompound. The peak group for this Peak row is comprised of its peak and its
associated PeakQualifier rows’ peaks.

Height
Height contains the integrator-determined height of the peak represented by this Peak
row.

IntegrationEndTime
IntegrationEndTime contains the integrator-determined peak-end chromatographic
retention time value associated with the peak represented by this Peak row.

IntegrationEndTimeOriginal
IntegrationEndTimeOriginal records the IntegrationEndTime before performing
manual integration.

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IntegrationMetricQualityFlags
IntegrationMetricQualityFlags stores the reasons record by the MS-MS integrator.
Based on several peak characteristics:
• Peak height
• Peak area
• Peak width
• Peak symmetry
• Merged peaks to the right or left
• Level of spikes on a peak

IntegrationStartTime
IntegrationStartTime contains the integrator-determined peak-start chromatographic
retention time value associated with the peak represented by this Peak row.

IntegrationStartTimeOriginal
IntegrationStartTimeOriginal records the IntegrationStartTime before performing
manual integration.

ISTDConcentrationRatio
ISTDConcentrationRatio is used whenever the peak represented by this Peak row is
related to an internal-standard peak, and in that case is the ratio of the computed
concentrations for this peak and that of the internal standard peak. Wherever this
peak is not related to an internal-standard peak, this value is undefined.

ISTDResponsePercentDeviation
ISTDResponsePercentDeviation is the deviation of a compound’s internal standard
response (area or height) from the average ISTD response calculated from the existing
calibration.

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ISTDResponseRatio
ISTDResponseRatio is used whenever the peak represented by this Peak row is related
to an internal-standard peak, and in that case is the ratio of the determined responses
for this peak and that of the internal standard peak. Wherever this peak is not related
to an internal-standard peak, this value is undefined.
The ISTDResponseRatio is adjusted to take into account isotope ratios.

ManuallyIntegrated
ManuallyIntegrated flag is true if and only if the integration results stored for this
peak have been manually updated.

MassAbundanceScore
MassAbundanceScore is the calculated comparison of the mass abundance in the
actual spectrum compared to the normalized mass abundance ratios of synthesized
spectral pattern.

MassAccuracy
MassAccuracy is the difference between the actual centroided spectral mass and
expected MZ. It’s measured in the unit as determined by the
MZExtractionWindowUnits setting (Dalton, PPM, Percent).

MassAccuracyScore
MassAccuracyScore is the calculated comparison of the mass accuracy in the actual
spectrum compared to the mass accuracy of synthesized spectral pattern.

MassMatchScore
MassMatchScore is the weighted aggregate of the individual metrics calculated when
comparing an actual spectrum with a spectrum pattern synthesized from a formula.

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MassSpacingScore
MassSpacingScore is the calculated comparison of the mass isotopic spacing in the
actual spectrum compared to the mass isotopic spacing of synthesized spectral
pattern.

MatrixSpikePercentRecovery
MatrixSpikePercentRecovery is a value calculated in the
OutlierMatrixSpikePercentRecovery.

MatrixSpikePercentDeviation
MatrixSpikePercentDeviation is a value calculated in the
OutlierMatrixSpikePercentDeviation.

MZ
MZ records the actual MZ used for mass accuracy calculation. In feature detection
case, it is the feature assigned mass.

Noise
Noise is calculated based on the selected NoiseAlgorithmType for each peak that
identifies a compound amount.

NoiseRegions
NoiseRegions records the actual regions that are used for the noise calculation.

OutlierAccuracy
OutlierAccuracy stores the flag resulting from this outlier condition evaluation. If
enabled by default or by applying Outlier Setup, an associated column is highlighted.

OutlierBelowLimitOfDetection
OutlierBelowLimitOfDetection stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted. See Outlier Details.

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OutlierBelowLimitOfQuantitation
OutlierBelowLimitOfQuantitation stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted.

OutlierBlankConcentrationOutsideLimit
OutlierBlankConcentrationOutsideLimit stores the flag resulting from this outlier
condition evaluation. If enabled by default or by applying Outlier Setup, an associated
column is highlighted. See Outlier Details.

OutlierCapacityFactor
OutlierCapacityFactor stores the flag resulting from this outlier condition evaluation.
If enabled by default or by applying Outlier Setup, an associated column is highlighted.
See Outlier Details.

OutlierCCISTDResponseRatio
OutlierCCISTDResponseRatio stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted. See Outlier Details.

OutlierCCResponseRatio
OutlierCCResponseRatio stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted. See Outlier Details.

OutlierCCRetentionTime
OutlierCCRetentionTime stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted. See Outlier Details.

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OutlierFullWidthHalfMaximum
OutlierFullWidthHalfMaximum stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted. See Outlier Details.

OutlierLibraryMatchScore
OutlierLibraryMatchScore stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted. See Outlier Details.

OutlierMassAccuracy
OutlierMassAccuracy stores the flag resulting from this outlier condition evaluation. If
enabled by default or by applying Outlier Setup, an associated column is highlighted.
See Outlier Details.

OutlierMassMatchScore
OutlierMassMatchScore stores the flag resulting from this outlier condition evaluation.
If enabled by default or by applying Outlier Setup, an associated column is highlighted.
See Outlier Details.

OutlierMatrixSpikeGroupRecovery
OutlierMatrixSpikeGroupRecovery stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted. See Outlier Details.

OutlierOutOfCalibrationRange
OutlierOutOfCalibrationRange stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted. See Outlier Details.

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OutlierPlates
OutlierPlates stores the flag resulting from this outlier condition evaluation. If
enabled by default or by applying Outlier Setup, an associated column is highlighted.
See Outlier Details.

OutlierQValue
OutlierQValue stores the flag resulting from this outlier condition evaluation. If
enabled by default or by applying Outlier Setup, an associated column is highlighted.
See Outlier Details.

OutlierIntegrationQualityMetric
OutlierIntegrationQualityMetric stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted. See Outlier Details.

OutlierISTDResponse
OutlierISTDResponse stores the flag resulting from this outlier condition evaluation.
If enabled by default or by applying Outlier Setup, an associated column is highlighted.
See Outlier Details.

OutlierISTDResponsePercentDeviation
OutlierISTDResponsePercentDeviation stores the flag resulting from this outlier
condition evaluation. If enabled by default or by applying Outlier Setup, an associated
column is highlighted. See Outlier Details.

OutlierMatrixSpikeOutOfLimits
OutlierMatrixSpikeOutOfLimits stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted. See Outlier Details.

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OutlierMatrixSpikeOutsidePercentDeviation
OutlierMatrixSpikeOutsidePercentDeviation stores the flag resulting from this outlier
condition evaluation. If enabled by default or by applying Outlier Setup, an associated
column is highlighted.

OutlierMatrixSpikePercentRecovery
OutlierMatrixSpikePercentRecovery stores the flag resulting from this outlier
condition evaluation. If enabled by default or by applying Outlier Setup, an associated
column is highlighted. See Outlier Details.

OutlierPurity
OutlierPurity stores the flag resulting from this outlier condition evaluation. If
enabled by default or by applying Outlier Setup, an associated column is highlighted.
See Outlier Details.

OutlierQCLCSRecoveryOutOfLimits
OutlierQCLCSRecoveryOutOfLimits stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted. See Outlier Details.

OutlierQCOutOfLimits
OutlierQCOutOfLimits stores the flag resulting from this outlier condition evaluation.
If enabled by default or by applying Outlier Setup, an associated column is highlighted.
See Outlier Details.

OutlierQCOutsideRSD
OutlierQCOutsideRSD stores the flag resulting from this outlier condition evaluation.
If enabled by default or by applying Outlier Setup, an associated column is highlighted.
See Outlier Details.

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OutlierRelativeRetentionTime
OutlierRelativeRetentionTime stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted. See Outlier Details.

OutlierResolutionFront
OutlierResolutionFront stores the flag resulting from this outlier condition evaluation.
If enabled by default or by applying Outlier Setup, an associated column is highlighted.
See Outlier Details.

OutlierResolutionRear
OutlierResolutionRear stores the flag resulting from this outlier condition evaluation.
If enabled by default or by applying Outlier Setup, an associated column is highlighted.
See Outlier Details.

OutlierRetentionTime
OutlierRetentionTime stores the flag resulting from this outlier condition evaluation.
If enabled by default or by applying Outlier Setup, an associated column is highlighted.
See Outlier Details.

OutlierSampleAmountOutOfLimits
OutlierSampleAmountOutOfLimits stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted. See Outlier Details.

OutlierSampleOutsideRSD
OutlierSampleOutsideRSD stores the flag resulting from this outlier condition evaluation. If
enabled by default or by applying Outlier Setup, an associated column is highlighted. See
Outlier Details.

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OutlierSignalToNoiseRatioBelowLimit
OutlierSignalToNoiseRatioBelowLimit stores the flag resulting from this outlier
condition evaluation. If enabled by default or by applying Outlier Setup, an associated
column is highlighted. See Outlier Details.

OutlierSurrogateOutOfLimits
OutlierSurrogateOutOfLimits stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted. See Outlier Details.

OutlierSurrogatePercentRecovery
OutlierSurrogatePercentRecovery stores the flag resulting from this outlier condition
evaluation. If enabled by default or by applying Outlier Setup, an associated column is
highlighted. See Outlier Details.

OutlierSymmetry
OutlierSymmetry stores the flag resulting from this outlier condition evaluation. If
enabled by default or by applying Outlier Setup, an associated column is highlighted.
See Outlier Details.

Plates
The number of theoretical plates of the column efficiency. Theoretical plates
is a concept and a column does not contain anything resembling physical
distillation plates or any other similar feature. Theoretical plates numbers are
an indirect measure of peak width for a peak at a specific retention time.
Columns with high plate numbers are considered to be more efficient (higher
column efficiency) than columns with lower plate numbers. A column with a
high number of plates will have a narrower peak at a given retention time
than a column with a lower number of plates.
Different pharmacopeia uses different formulas to determine the value for
Plates.

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Pharmacopeia Formula

Default 16 * (Tr / Wb) ^2

USP 16 * (Tr / Wb) ^2

EU 5.54 * (Tr / W50) ^2

JP 5.54 * (Tr / W50) ^2

Tr is the retention time

Wb is the peak width determine by the tangent method.

W50 is the peak width at 50% of the height of the peak.

Theoretical plate numbers are only valid for a specific set of conditions.
Isothermal temperature conditions are required and temperature programs
result in highly inflated plate numbers. When comparing theoretical plate
numbers between columns, the same temperature conditions and peak
retention (k’) are required for the comparison to be valid.

Purity
Purity aka Peak Purity estimates the percentage of the component ions from the
spectra that group together and constitute the target relative to other components
present.

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Peak Purity 1: Spectral deconvolution estimates the “purity” of the compound by evaluating
other co-eluting spectral signals.

Diagram shows a visualization of the components resulting from applying a

deconvolution algorithm to the mass spectrometric scan data.
The purity calculation entails running a deconvolution on the entire chromatographic range of
the sample. However, the new algorithm differs from the previously released versions (prior to
B.05.02) in several important aspects:

1) The identification of the component that matches the target compound (the “target
component”) uses a different set of criteria that makes it more robust:
a. For each component found by deconvolution, the system finds all component
spectrum peaks that fall within the m/z delta range of the target quantifier m/z.
b. For every such component spectrum peak, the system checks if the
corresponding ion peak (EIC peak) has an apex within the RT range of the target
quantifier peak.
c. The component with the largest such peak is identified as the target
component.
2) If the system fails to find a target component for any given target compound, it re-tries
by running the full-sample deconvolution in “high-resolution” mode, using a window
size factor that is reduced by a factor of 2. The high-resolution results are cached and
are searched for any target compound that cannot be found in the normal-resolution
component list. The automatic generation of the high-resolution results allows many
target components to be identified that were previously missed.

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3) The system attempts to detect “double components” that share the same RT and base
peak m/z. The presence of such component doublets can strongly bias the purity
estimate to the downside. Component doublets can occur if the RT window size factor is
too small. Therefore, the system attempts to recover automatically by re-running the
full-sample deconvolution in “low-resolution” mode, using a window size factor that is
increased by a factor of 2. The low-resolution results are cached and are searched for
any target that is matched to a component doublet.
4) The new purity calculation uses a different formula that gives more meaningful results
in cases of severe interference. (The old purity definition can yield zero purity for such
cases.) The new definition of purity uses the following formula:

Purity(Target compound) = Area(Target component shape) / SUM(

Area(Contributing component shape))

The SUM is over all contributing components. A contributing component is any

component that has spectral peaks within m/z delta range of the target quantifier m/z
and overlaps the target peak in retention time.

QvalueComputed
QvalueComputed contains a correlation statistic called QVALUE which measures the
fidelity of the observed qualifier ratios versus the nominal qualifier ratios. The
QVALUE function is a well-defined statistic that yields an efficient measure of the
“goodness of fit” of the observed qualifier ratios to the nominal qualifier ratios.
For all hits a QVALUE is computed as described here. For Target Compound Entries with no
qualifier signals, the QVALUE is defined as 100. For Target Compound Entries with k qualifier
signals qi , 1 <= I <= k, define ri as the expected ratio of qualifier peak for qi to the target
peak. Then define ri ‘ as the observed qualifier ratio as determined by the above Qualifier Ratio
Computation. Now define the total ratio deviation D:

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Then the QVALUE is the closest integer to max { 100 – D, 1 }.

QvalueSort
QvalueSort is equal to QvalueComputed unless the PeakSelectionCriterion for the
associated TargetCompound is Greatest Response or Closest Retention Time, in which
case it is zero.

ReferenceLibraryMatchScore
ReferenceLibraryMatchScore records the measure of the correlation between the
spectrum and the reference library spectrum, or in the case of “Target Deconvolution”,
between deconvoluted spectrum and the reference library spectrum. The reference
library can be generated from a high level calibration sample or from an existing
library.
ReferenceLibraryMatchScore is an indicator of the quality of the match between the
sample spectrum and the reference library spectrum. A score of 100 means a perfect
match.

RelativeRetentionTime
RelativeRetentionTime represents the ratio of the target compound’s retention time to
the related ISTD’s retention time. RelativeRetentionTime is a value used in calculation
of OutlierRelativeRetentionTime.

ResolutionFront
ResolutionFront is the chromatographic resolution of primary peak with the peak in
front of it (left peak). Different pharmacopeia uses different formulas to determine the
value for Resolution.

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Pharmacopeia Formula

Default

USP 2 ∗ (𝑇𝑇𝑇𝑇, 2 − 𝑇𝑇𝑇𝑇, 1) /(𝑊𝑊𝑊𝑊, 1 + 𝑊𝑊𝑊𝑊, 2)

EU 1.18 ∗ (𝑇𝑇𝑇𝑇, 2 − 𝑇𝑇𝑇𝑇, 1) /(𝑊𝑊50,1 + 𝑊𝑊50,2)

JP 1.18 ∗ (𝑇𝑇𝑇𝑇, 2 − 𝑇𝑇𝑇𝑇, 1) /(𝑊𝑊50,1 + 𝑊𝑊50,2)

Valley Height/Peak Height 𝑣𝑣/ℎ2

Valley Height/Peak Height 2𝑣𝑣

100 ∗
Average ℎ1 + ℎ2

Valley Height/Peak Height 𝑣𝑣

100 ∗
Sum ℎ1 + ℎ2

• Tr,2 is the retention time of the right peak in the peak pair.

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• Tr,1 is the retention time of the left peak in the peak pair.
• Sigma is half the peak width at inflection points.
• Wb is the peak width determine by the tangent method.
• W50 is the peak width at 50% of the height of the peak.

ResolutionRear
ResolutionRear is the chromatographic resolution of primary peak with the rear peak
next to it (right peak). Different pharmacopeia uses different formulas to determine
the value for Resolution.

Pharmacopeia Formula

Default

USP 2 ∗ (𝑇𝑇𝑇𝑇, 2 − 𝑇𝑇𝑇𝑇, 1) /(𝑊𝑊𝑊𝑊, 1 + 𝑊𝑊𝑊𝑊, 2)

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1.18 ∗ (𝑇𝑇𝑇𝑇, 2 − 𝑇𝑇𝑇𝑇, 1) /(𝑊𝑊50,1

EU
+ 𝑊𝑊50,2)

1.18 ∗ (𝑇𝑇𝑇𝑇, 2 − 𝑇𝑇𝑇𝑇, 1) /(𝑊𝑊50,1

JP
+ 𝑊𝑊50,2)

Valley Height/Peak Height 𝑣𝑣/ℎ1

Valley Height/Peak Height 2𝑣𝑣

100 ∗
Average ℎ1 + ℎ2

Valley Height/Peak Height 𝑣𝑣

100 ∗
Sum ℎ1 + ℎ2

• Tr,2 is the retention time of the right peak in the peak pair.
• Tr,1 is the retention time of the left peak in the peak pair.
• Sigma is half the peak width at inflection points.
• Wb is the peak width determine by the tangent method.
• W50 is the peak width at 50% of the height of the peak.

ResponseOriginal
ResponseOriginal records the target response before performing manual integration.

ResponseRatio
ResponseRatio is used whenever the peak represented by this Peak row is related to
an internal-standard peak, and in that case is the ratio of the determined responses for
this peak and that of the internal standard peak. Wherever this peak is not related to
an internal-standard peak, this value is undefined.

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RetentionIndex
RetentionIndex is calculated from the RT calibration file specified in the library
method. The RTCalibration stores an array of RT/RI points which are used with
Retention Indices.

RetentionTime
RetentionTime contains the integrator-determined peak-apex chromatographic retention
time value associated with the peak represented by this Peak row.

RetentionTimeDifference
RetentionTimeDifference is expressed in minutes. RetentionTimeDifference gives the
difference between the expected retention time of the target (possibly corrected for
internal-standard retention time) and the SelectedGroupRetentionTime of this Peak
row.

RetentionTimeDifferenceKey
RetentionTimeDifferenceKey is expressed in millisecond. Its value depends on the
PeakSelectionCriterion value in the associated TargetCompound. Whenever the
PeakSelectionCriterion is not Greatest Peak Response, RetentionTimeDifferenceKey is
the absolute value of RetentionTimeDifference. Otherwise it is zero.

RetentionTimeOriginal
RetentionTimeOriginal records the Retention Time before performing manual
integration.

SampleRSD
SampleRSD is the relative standard deviation (RSD) of the final concentration for all
samples of the same SampleGroup and of sample type Sample in the batch. If
SampleGroup is not assigned, RSD for all samples of the sample type Sample in the
batch is calculated.

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SaturationRecoveryRatio
SaturationRecoveryRatio represents the ratio of the restored feature peak height to
the original feature peak height. The feature peak and recovery of feature peak are
determined by the feature detection algorithm for accurate mass data.
Saturation Recovery Ratio = null => Feature is Not Saturated

Saturation Recovery Ratio != null => Feature is Saturated

Saturation Recovery Ratio == 0 => Feature is Saturated and not recovered

Saturation Recovery Ratio > 0 => Feature is Saturated but recovered

SelectedGroupRetentionTime
SelectedGroupRetentionTime contains the aggregate (average) retention time assigned
to the peak group containing this peak during the application of the signal-correlation
algorithm to the set of peaks (containing this peak and its associated PeakQualifier
peaks). The details of the signal-correlation algorithm are beyond the scope of this
document.

SelectedTargetRetentionTime
SelectedTargetRetentionTime contains the retention time assigned to this peak by the
integration algorithm.

SignalToNoiseRatio
SignalToNoiseRatio represents the strength of the signal. SignalToNoiseRatio is
calculated by several different algorithms set by NoiseAlgorithmType. Refer to
Qualitative Analysis documentation for further details.

SurrogatePercentRecovery
SurrogatePercentRecovery is a value used in the calculation of the
OutlierSurrogatePercentRecovery.

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Symmetry
Symmetry represents the balance between the back and front of the peak. Symmetry
of 1.0 means the peak is balanced. Smaller numbers than one indicate asymmetry and
peak fronting. Larger numbers than one indicate asymmetry and peak fronting.
Symmetry = Distance (tail) / Distance (front)

TargetResponse
TargetResponse contains the (possibly area-summed or area-corrected) Area value
when the associated TargetCompound row has its QuantByHeight column set to false.
If this column is true, TargetResponse contains the same value as the Height column.

UserCustomCalculation
UserCustomCalculation stores a result from a custom calculation.
UserCustomCalculation work with an undocumented scripting mechanism.

UserCustomCalculation1
UserCustomCalculation1 stores a result from a custom calculation.
UserCustomCalculation work with an undocumented scripting mechanism.

UserCustomCalculation2
UserCustomCalculation2 stores a result from a custom calculation.
UserCustomCalculation work with an undocumented scripting mechanism.

UserCustomCalculation3
UserCustomCalculation3 stores a result from a custom calculation.
UserCustomCalculation work with an undocumented scripting mechanism.

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Quantitation DataSet schema

UserCustomCalculation4
UserCustomCalculation4 stores a result from a custom calculation.
UserCustomCalculation work with an undocumented scripting mechanism.

Width
Width contains the integrator-determined peak width, in units of minutes, of the peak
represented by this Peak row.

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 Quantitation DataSet schema

Calibration Table

Primary Key
{BatchID, SampleID, CompoundID, LevelID} serves as the primary key. The
composite of the BatchID and SampleID and CompoundID and LevelID and unique
identify each row in this table. The keys in the Quantitation DataSet are not show in
the user interface.
A primary key value must be unique with in the table. A composite key is a primary
key that incorporates more than one column.

BatchID
BatchID uniquely identifies the batch. BatchID is part of the composite primary key.
The BatchID is typically set to -1 because Batch-at-a-Glance analyzes one batch.

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Quantitation DataSet schema

SampleID
SampleID uniquely identifies the sample in the batch. SampleID is part of the
composite primary key.
Thus, each sample in the batch is assigned a unique SampleID.

CompoundID
CompoundID uniquely identifies the sample in the batch. CompoundID is part of the
composite primary key. Thus, each compound in the batch is assigned a unique
CompoundID.

LevelID
LevelID uniquely identifies the peak(s) for this compound. LevelID is part of the
composite primary key.
Thus, each level in this calibration for this compound is assigned a unique LevelID.

CalibrationSTDAcquisitionDateTime
CalibrationSTDAcquisitionDateTime records the date and time of the data file that is
used to establish the calibration row.

CalibrationSTDPathName
CalibrationSTDPathName names a persistent store of the data used to establish this
calibration level. It’s a full path name.

CalibrationType
CalibrationType sub classifies or partitions the set of Calibration rows associated
with a TargetCompound. CalibrationType designates the type of sample involved in
the calibration curve. Is optional and not normally used.
One possible application is to partition six Levels into a five-point Daily Calibration
and a one-point Continuing Calibration. The names DailyCalibration and
ContinuingCalibration would be applied accordingly to these six levels.

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Enum Name UI Name Xpath expression

Calibration Calibration *//CalibrationType[.=’Calibration’]

QC QC *//CalibrationType[.=’QC’]

Method Method *//CalibrationType[.=’Method’]

CC CC *//CalibrationType[.=’CC’]

ZeroStandard Zero *//CalibrationType[.=’ZeroStandard’]

Standard

LevelAverageCounter
LevelAverageCounter tallies the number of times the LevelResponse value for this
Calibration row has been arithmetically averaged since the last time the
LevelResponse value was completely replaced, or the inception of this Calibration row,
whichever occurred later.

LevelConcentration
LevelConcentration is the nominal concentration value for this calibration units.
LevelConcentration is expressed in units as given by the ConcentrationUnits value in
the associated TargetCompound row.

LevelEnable
LevelEnable is true if and only if the (LevelConcentration, LevelResponse) point for
this Calibration row is in play in terms of the calibration equation for the associated
TargetCompound.

Quantitative Analysis Quantitation DataSet 173

Quantitation DataSet schema

For example, the sample acquired in CMAMCal_L2.d has the compound Cocaine
calibration point disabled.

LevelLastUpdateTime
LevelLastUpdateTime records the date and time for last change to the calibration row.
This column is set whenever the calibration row is updated or analyzed.

LevelName
LevelName is a descriptive string for this Calibration row.
LevelName connects a calibration or QC sample with a concentration and allows the
association of replicate samples together.

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 Quantitation DataSet schema

For example, two samples one Calibration and one QC are run at level L2. All samples
run at level L2 share the same concentration.
When multiple calibration samples are run at the same level, these calibration samples
are considered replicates.
Note that a separate LevelName can denote a QC concentration, independent of the
Calibration concentrations.

LevelResponse
LevelResponse is the response value associated with this calibration level.
LevelResponse can be height or area based on the QuantByHeight flag of the
associated TargetCompound row.

LevelResponseFactor
LevelResponseFactor is the Response / ISTDConcentration for ISTD corrected
analysis. LevelResponseFactor is just the Response / Concentration.

LevelRSD
LevelRSD is the relative standard deviation of the enabled calibration points
(replicates) at a particular level.

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Quantitation DataSet schema

This calibration level metric is computed as follows. For each calibration level n =
1…N, the average, standard deviation of the current compound’s LevelResponse are
calculated over all enabled replicates (m=1…Mn) at calibration level n:
Mn
1
Avg n =
Mn
∑ LevelResponse
m =1
m,n

∑ (LevelResponse − Avg n )
Mn
1
SDn =
2

−1
m,n
Mn m =1

For each calibration level n with Mn > 1, LevelRSD is set as follows:

SDn
LevelRSDn = × 100
Avg n
where LevelRSD is %RSD or the relative standard deviation (RSD) of all enabled
replicates in level n, expressed in percent. If only one replicate exists at a particular
level M, LevelRSD is set to NULL.

176 Quantitative Analysis Quantitation DataSet

 Outliers Overview

Outliers Overview
Outliers is a mechanism built into Batch-at-a-Glance that enables the identification of
measurements that are outside set boundaries. The boundaries are set in the method
and the measurements that are calculated as outliers (exceptions) are identified by
assigning a flag {High, Low} to a specified Outlier column. In addition, the outlier is
identified in the Batch-at-a-Glance user interface by marking the associated column.

Outliers Enabled by Default

Several outliers are considered applicable enough to be enabled by default:
Outlier Associated Column/Table Comment

Integration Quality IntegrationMetricQualityFlags Defaulted: Using Agile

Metric Integrator
(Peak table)
Qualifier Integration IntegrationMetricQualityFlags Defaulted: Using Agile
Quality Metric Integrator
(PeakQualifier table)
Peak Not Found OutlierPeakNotFound
(Peak table)
Qualifier Peak Not OutlierPeakNotFound
Found
(PeakQualifier table)
Accuracy Accuracy Defaulted: +/-20%

Qualifier Ratio QualifierResponseRatio Defaulted: +/- 20%

(PeakQualifier)

Quantitative Analysis Quantitation DataSet 177

Outliers Overview

RetentionTime RetentionTime Defaulted: +/- 5%

relative
Relative Retention Time RetentionTime Defaulted: +/- 10%
relative
Outlier Details

Summary of Outlier Specifications

Zero
Peak
Outlier Outlier Highlighted Sample Compound
Type Flags Column Types Types Peaks Behavior

Calibrati Do not
Low, Peak.Accur on, QC, All except flag
Accuracy High acy CC ISTD Primary*

Peak.Altern Do not
Alternativ Low, ativePrakRT flag
e Peak High Diff All All Primary

TargetComp
Average ound.Avera
Respons geRespons All except
e Factor Low eFactor All ISTD N/A

Average TargetComp
Respons ound.Avera
e Factor geRespons All except
RSD High eFactorRSD All ISTD N/A

Blank Peak.Calcul Do not

Concentr atedConcen flag
ation High tration Blank Target Primary

Blank Blank, Do not

Target for
Respons Peak.Target DoubleB flag
Blank, All
e High Response lank Primary
for

178 Quantitative Analysis Quantitation DataSet

 Outliers Overview

Zero
Peak
Outlier Outlier Highlighted Sample Compound
Type Flags Column Types Types Peaks Behavior
DoubleBlan
k

CC Do not
Respons Low, Peak.Target flag
e Ratio High Response CC Target Primary*

CC ISTD Do not
Respons Low, Peak.Target flag
e Ratio High Response CC ISTD Primary*

CC TargetComp Do not
Average ound.Avera flag
Respons Low, geRespons
e Factor High eFactor CC All N/A

CC Do not
Relative flag
Respons Peak.Target
e Factor Low Response CC Target N/A

CC Do not
Retention Low, Peak.Retent flag
Time High ionTime CC All Primary*

Sample.Acq
CC Time High DateTime All N/A N/A

All Do not
except flag
blanks,
Peak.Calcul Calibrati
Calibratio Low, atedConcen on, and All except
n Range High tration QC ISTD Primary

Quantitative Analysis Quantitation DataSet 179

Outliers Overview

Zero
Peak
Outlier Outlier Highlighted Sample Compound
Type Flags Column Types Types Peaks Behavior

TargetComp
Curve Fit ound.Curve All except
R2 Low FitR2 All ISTD N/A

TargetComp
Custom ound.UserC
Calculati Low, ustomCalcul
on High ation All Target N/A

Full Do not
Width flag
Half Peak.FullWi
Maximu Low, dthHalfMaxi
m High mum All All Primary*

Integratio Peak.Integr Do not

n Quality Low, ationQuality flag
Metric High Metric All All Primary

All Do not
ISTD except flag
Respons Low, Peak.Target DblBlan
e High Response k ISTD Primary*

ISTD Peak.ISTDR All Do not

Respons esponsePer except flag
e Percent Low, centDeviatio DblBlan
Deviation High n k ISTD Primary*

Library Peak.Refere Do not

Match nceLibraryM All except flag
Score Low atchScore All ISTD Primary

180 Quantitative Analysis Quantitation DataSet

 Outliers Overview

Zero
Peak
Outlier Outlier Highlighted Sample Compound
Type Flags Column Types Types Peaks Behavior

Peak.Calcul All Do not

Limit of atedConcen except flag
Detection Low tration blanks All Primary*

Limit of Peak.Calcul All Do not

Quantitati atedConcen except flag
on Low tration blanks All Primary*

Mass Low, Peak.Mass Do not

Accuracy High Accuracy All All Primary* flag

Mass Do not
Match Peak.Mass All except flag
Score Low MatchScore All ISTD Primary*

Matrix, Do not
Matrix Low, Peak.FinalC MatrixD flag
Spike High oncentration up MatrixSpike Primary*

Matrix Do not
Spike Peak.Matrix Matrix, flag
Group Low, SpikePerce MatrixD
Recovery High ntRecovery up All Primary*

Matrix Do not
Spike Peak.Matrix Matrix, flag
Percent Low, SpikePerce MatrixD
Recovery High ntRecovery up MatrixSpike Primary*

Matrix Do not
Spike Peak.Matrix Matrix, flag
Percent SpikePerce MatrixD
Deviation High ntDeviation up MatrixSpike Primary

Quantitative Analysis Quantitation DataSet 181

Outliers Overview

Zero
Peak
Outlier Outlier Highlighted Sample Compound
Type Flags Column Types Types Peaks Behavior

Method Peak.Calcul All Do not

Detection atedConcen except flag
Limit Low tration blanks All Primary*

TargetComp All All and

Peak Not ound.Target except ISTD in
Found Low Response blanks blanks N/A

Peak Do not
Symmetr Low, Peak.Symm flag
y High etry All All Primary*

Qualifier PeakQualifi Do not

Coelution er.Coelution flag
Score Low Score All All N/A

Qualifier PeakQualifi Do not

Integratio er.Integratio flag
n Quality Low, nQualityMet
Metric High ric All All N/A

TargetQualif Do not
Qualifier ier.Qualifier All All and flag
Peak Not ResponseR except ISTD in
Found Low atio blanks Blank N/A

PeakQualifi Do not
er.Qualifier All flag
Qualifier Low, ResponseR except
Ratio High atio blanks All N/A

Peak.Calcul Do not
Low, atedConcen flag
QC High tration QC Target Primary*

182 Quantitative Analysis Quantitation DataSet

 Outliers Overview

Zero
Peak
Outlier Outlier Highlighted Sample Compound
Type Flags Column Types Types Peaks Behavior

Peak.Target Do not
QC RSD High Response QC Target Primary flag

QC Do not
(Info. flag
column
Contain
Peak.Matrix s LCSA
Low, SpikePerce or All except
QC LCS High ntRecovery LCSB) ISTD Primary*

Prak.QValu Do not
QValue Low eComputed All All Primary flag

Relative
Respons Low, Peak.Target All except
e Factor High Response All ISTD N/A

Relative Peak.Relati Do not

Retention Low, veRetention All except flag
Time High Time All ISTD Primary

Resolutio Peak.Resol Do not

n Front Low utionFront All All Primary* flag

Resolutio Peak.Resol Do not

n Rear Low utionRear All All Primary* flag

Respons Peak.Target Respon Do not

e Check Low Response seCheck Target Primary* flag

Respons Low, Peak.Target All except

e Factor High Response All ISTD N/A

Quantitative Analysis Quantitation DataSet 183

Outliers Overview

Zero
Peak
Outlier Outlier Highlighted Sample Compound
Type Flags Column Types Types Peaks Behavior

Retention Low, Peak.Retent Do not

Time High ionTime All All Primary flag

Sample Low, Peak.FinalC Do not

Amount High oncentration Sample Target Primary* flag

Sample Peak.Sampl Do not

RSD High eRSD Sample All Primary flag

Saturatio Peak.Satura Do not

n tionRcovery flag
Recovery High Ratio All All Primary*

Signal To Peak.Signal Do not

Noise ToNoiseRati flag
Ratio Low o All All Primary

All Do not
Spectral except All except flag
Purity Low Peak.Purity blanks ISTD Primary*

All Do not
Surrogat Low, Peak.FinalC except flag
e High oncentration blanks Surrogate Primary*

All Do not
Surrogat Peak.Surrog except flag
e Percent Low, atePercentR double
Recovery High ecovery blank Surrogate Primary*

184 Quantitative Analysis Quantitation DataSet

 Outliers Overview

Notes:
A * indicates that if the primary peak is not found, the compound and its containing
sample will be flagged with a quantitation message, not with an outlier flag.
Throughout this table, “blanks” refers to all samples of type Blank and Double Blank.
Integration Quality Metric outlier is enabled only if a parameterless integrator (Agile
integrator or MS-MS integrator) is used.
Qualifier Integration Quality Metric outlier is enabled only if a parameterless
integrator (Agile integrator or MS-MS integrator) is used.
For the QC RSD outlier, all QC samples in a level will be flagged.
Relative Response Factor and Relative Retention Time outliers apply only to
compounds that have an ISTD.
Response Factor outlier applies only to compounds that do NOT have an ISTD.

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Outliers

Outliers
Below are detailed definitions and explanations of the outliers. Outliers are detected,
calculated and reported during analysis. Outliers are useful in detecting results that
exceed defined limits. These exceptions focus the analyst on the sample and
compounds results that need review.

Peak Result
This set of outliers are grouped together to handle exceptions related to Peak Results.

Peak Not Found

This outlier metric is a measure of whether the compound’s target ion has an
associated peak. This outlier applies to all compound types and all sample types
except Double blank and Blank, it also applies to ISTD compounds in Blank sample.
This outlier metric is determined by looking for the associated Peak row for
that compound and determining if that peak row exists.-
The outlier is set too Low if the Peak row does not exist.

Retention Time
This outlier metric is a measure of whether the current peak is within the Retention
Time (RT) window. This outlier applies to the primary peak of all compound types and
all sample types.
This outlier metric is determined by comparing the peak’s retention time
(RetentionTime in the Peak table) against the method’s retention time (RetentionTime
in the Target Compound table) and testing if the deviation is within the retention time
window (RetentionTimeWindow), which can be expressed either in minutes or
percent, as defined by RetentionTimeWindowUnits. If RetentionTimeWindowUnits are
Minutes, the outlier is set as follows:

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 Outliers

1
High if RT > RTmethod + RTWindow
2
1
Low if RT < RTmethod − RTWindow
2
If RetentionTimeWindowUnits are Percent, the outlier is set as follows:
 1 RTWindow 
High if RT > RTmethod 1 + 
 2 100 
 1 RTWindow 
Low if RT < RTmethod 1 − 
 2 100 
When the outlier is set, the RetentionTime column of the Peak table is highlighted.
For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:
RetentionTimeWindow
RetentionTimeWindowUnits

Relative Retention Time

This outlier metric is a measure of whether the current peak is within the Relative
Retention Time (RRT) window. This outlier applies to the primary peak of all
compound types except ISTD and all sample types.
This outlier metric is determined as follows:
For each enabled calibration point n = 1..N of a target compound’s calibration table,
compute RRTn as the ratio of the calibration peak’s retention time to the related ISTD
retention time:
( RTn ) Compound
RRTn =
( RTn ) IS

Compute AverageRelativeRetentionTime ( RRT ) over N enabled Calibration and QC

points:

Quantitative Analysis Quantitation DataSet 187

Outliers

N
1
RRT =
N
∑ RRT
n =1
n

Compute the percent deviation of a peak’s relative retention time (RRT):

RRT − RRT
RRTPercentDeviation = × 100
RRT
The outlier is set if the absolute value of the RRTPercentDeviation of a compound’s
peak is greater than RelativeRetentionTimeMaximumPercentDeviation:
High if RRTPercentDeviation > RRTMaxPercentDeviation
Low if RRTPercentDeviation < − RRTMaxPercentDeviation
When the outlier is set, the RelativeRetentionTime column of the Peak table is
highlighted.
For the outlier to activate, the following must be set in the Quantitation Method
Editor:
Target must have a related ISTD
RelativeRetentionTimeMaximumPercentDeviation
Example:
RelativeRetentionTimeMaximumPercentDeviation = 5%.
Target’s RetentionTime = 2.22 min.
ISTD’s RetentionTime = 2.00 min.
RelativeRetentionTime = 2.22 / 2.00 = 1.11
AverageRelativeRetentionTime = Sum (RRT) / N for all the compound’s enabled
Calibration and QC points = 1.00
RRTPercentDeviation = (1.11–1.00 / 1.00 )*100= 11.1%
RelativeRetentionTimeMaximumPercentDeviation = 10%
Since the peak’s RelativeRetentionTimePercentDeviation exceeds the
RelativeRetentionTimeMaximumPercentDeviation, this outlier is set too High.

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Integration Quality Metric

This outlier metric is a measure of the quality of the current peak’s integration. This
outlier applies to the primary peak of all compound types and all sample types.
This outlier metric is determined by examining the parameterless (MS-MS or Agile)
integrator metric stored in the IntegrationQualityMetric. If the peak’s
IntegrationQualityMetric is “Rejected” or “Inspect”, the outlier is set too High and Low,
respectively.

The integrated peak’s IntegrationQualityMetric column is highlighted, and the outlier

message describes the reason why the peak has been rejected or “inspect”, as reported
by the integrator in the IntegrationMetricQualityFlags column.
For the outlier to activate, the Integrator must be set to a parameterless (MS-MS or
Agile) integrator.

Resolution
This outlier metric is a measure of how well two neighboring peaks are seperated. This
outlier applies to the primary peaks of all compound types and all sample types.
This outlier metric is determined by comparing the calculated resolution value of the
primary peak against a user-defined limit ResolutionLimit.
The outlier is set too Low or High based on different calculations
Peak resolution is calculated differently if different pharmacopeia is selected.

Quantitative Analysis Quantitation DataSet 189

Outliers

Pharmacopeia Formula Outlier Fully Seperated

Default 2𝑣𝑣 Low 100

100×(1 − )
ℎ1 + ℎ2

USP 2 × (𝑇𝑇𝑟𝑟,2 − 𝑇𝑇𝑟𝑟,1 ) /(𝑊𝑊𝑏𝑏,1 Low NAN

+ 𝑊𝑊𝑏𝑏,2 )

EU 1.18 × (𝑇𝑇𝑟𝑟,2 − 𝑇𝑇𝑟𝑟,1 ) Low NAN

/(𝑊𝑊50,1
+ 𝑊𝑊50,2 )

JP 1.18 × (𝑇𝑇𝑟𝑟,2 − 𝑇𝑇𝑟𝑟,1 ) Low NAN

/(𝑊𝑊50,1
+ 𝑊𝑊50,2 )

ValleyHeight/Peak Height 𝑣𝑣/ℎ1 High 0

190 Quantitative Analysis Quantitation DataSet

 Outliers

Valley Height/Peak 2𝑣𝑣 High 0

100 ×
Height Average ℎ1 + ℎ2

Valley Height/Peak 𝑣𝑣 High 0

100 ×
Height Sum ℎ1 + ℎ2

• 𝑇𝑇𝑟𝑟,2 is the retention time of the right peak in the peak pair.
• 𝑇𝑇𝑟𝑟,1 is the retention time of the left peak in the peak pair.
• 𝑊𝑊𝑏𝑏 is the peak width determined by the tangent method.
• 𝑊𝑊50 is the peak width at 50% of the height of the peak.

When the outlier is set, the ResolutionFront and/or ResolutionRear columns are
highlighted.
For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:
• ResolutionLimit

Symmetry
This outlier metric is a measure of whether the peak symmetry is below or above the
preset limits. This outlier applies to the primary peaks of all compound types and all
sample types.
This outlier metric is determined by comparing the calculated Symmetry value of the
primary peak against a user-defined limits SymmetryLimitLow and
SymmetryLimitHigh
The outlier is set too High if

Symmetry > SymmetryLimitHigh

The outlier is set too Low if

Symmetry < SymmetryLimitLow

Quantitative Analysis Quantitation DataSet 191

Outliers

Peak symmetry is calculated as the ratio (at the 10% of the peak height) of the distance between
the peak apex and the back side of the chromatographic curve to the distance between the peak
apex and the front side of the chromatographic curve for default setting; and is calculated as the
ratio (at the 5% of the peak height) of the peak width to the distance between the peak apex
and the front side of the chromatographic curve for all other pharacoepeia settings.

Pharmacopeia Formula

Default

Symmetry = CB/AC

USP/EU/JP/CP

When the outlier is set, the Symmetry column is highlighted.

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 Outliers

For the outlier to activate, the following columns must be set in the Quantitation Method Editor:

• SymmetryLimitHigh

• SymmetryLimitLow

Full Width Half Maximum

This outlier metric is a measure of whether the full width half maximum (FWHM) is
outside the preset limit. This outlier applies to the primary peaks of all compound
types and all sample types.
This outlier metric is determined by comparing the calculated FullWidthHalfMaximum
value of the primary peak against a user-defined limits
FullWidthHalfMaximumLimitLow and FullWidthHalfMaximumLimitHigh.
The outlier is set too High if
𝐹𝐹𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢ℎ𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻 > 𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹ℎ𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻ℎ
The outlier is set too Low if
𝐹𝐹𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢ℎ𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻 < 𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝑖𝑖𝑖𝑖𝑖𝑖ℎ𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻
Full width half maximum is calculated as the peak width at the half height.
When the outlier is set, the FullWidthHalfMaximum column is highlighted.
For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:
• FullWidthHalfMaximumLimitHigh

• FullWidthHalfMaximumLimitLow

Purity
This outlier metric is a measure of whether the spectral purity of a peak is below the preset
limit. This outlier applies to the primary peaks of all compound types except ISTD and all sample
types except Blank and Double Blank.

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Outliers

This outlier metric is determined by comparing the calculated spectral purity of the
primary peak, in percent, contained in the Purity column, against a user-defined
minimum limit MinimumPercentPurity. The outlier is set too Low if
Purity < MinimumPercentPurity

The purity calculation entails running a deconvolution on the entire chromatographic range of
the sample. However, the new algorithm differs from the previously released versions (prior to
B.05.02) in several important aspects:

1) The identification of the component that matches the target compound (the “target
component”) uses a different set of criteria that makes it more robust:
a. For each component found by deconvolution, the system finds all component
spectrum peaks that fall within the m/z delta range of the target quantifier m/z.
b. For every such component spectrum peak, the system checks if the
corresponding ion peak (EIC peak) has an apex within the RT range of the target
quantifier peak.
c. The component with the largest such peak is identified as the target
component.
2) If the system fails to find a target component for any given target compound, it re-tries
by running the full-sample deconvolution in “high-resolution” mode, using a window
size factor that is reduced by a factor of 2. The high-resolution results are cached and
are searched for any target compound that cannot be found in the normal-resolution
component list. The automatic generation of the high-resolution results allows many
target components to be identified that were previously missed.
3) The system attempts to detect “double components” that share the same RT and base
peak m/z. The presence of such component doublets can strongly bias the purity
estimate to the downside. Component doublets can occur if the RT window size factor is
too small. Therefore, the system attempts to recover automatically by re-running the
full-sample deconvolution in “low-resolution” mode, using a window size factor that is
increased by a factor of 2. The low-resolution results are cached and are searched for
any target that is matched to a component doublet.
4) The new purity calculation uses a different formula that gives more meaningful results
in cases of severe interference. (The old purity definition can yield zero purity for such
cases.) The new definition of purity uses the following formula:

194 Quantitative Analysis Quantitation DataSet

 Outliers

Purity(Target compound) = Area(Target component shape) / SUM(

Area(Contributing component shape))

The SUM is over all contributing components. A contributing component is any

component that has spectral peaks within m/z delta range of the target quantifier m/z
and overlaps the target peak in retention time.

When the outlier is set, the Purity column is highlighted.

For the outlier to activate, the following columns must be set in the Quantitation Method Editor:

• MinimumPercentPurity
• SpectrumExtractionOverride set to “Deconvoluted Scan”

Plates
This outlier metric is a measure of the column efficiency. A capillary column/any
chromatography column does not contain anything resembling physical distillation
plates or other similar features. Theoretical plate numbers are indirect measure of
peak width for a peak at a specific retention time. Columns with plate numbers are
considered to be more efficient than columns with lower plate numbers. A column
with a high number of plates will have a narrower peak at a given retention time than
a column with a lower number of plates.
Different pharmacopeia uses different formulas to determine the value for Plates.

Pharmacopeia Formula

Default 16 * (Tr / Wb) ^2

USP / CP 16 * (Tr / Wb) ^2

EU / JP / CP 5.54 * (Tr / W50) ^2

Chinese Pharmacopoeia allows either choice of calculation.

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• Tr is the retention time

• Wb is the peak width determine by the tangent method.
• W50 is the peak width at 50% of the height of the peak.
This outlier metric is determined by comparing the calculated plate numbers of the
primary peak (Plates in the Peak table) against a user-defined minimum limit
(PlatesLimit). The outlier is set to Low if

Plates <PlatesLimit
When the outlier is set, the Plates column is highlighted.
For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:
PlatesLimit

Capacity Factor
This outlier metric is a measure of the retention of an analyte on the chromatographic
column. It is the ratio of the amount of time a solute spends in the stationary and
mobile phases. For example, a solute with a k’ = 6 is twice as retained by the
stationary phase (but not the column) as a solute with a k’ = 3. The retention factor
does not provide absolute retention information; it provides relative retention
information. An unretained compound has a retention factor of 0.
𝑘𝑘’ = (𝑇𝑇𝑟𝑟 − 𝑇𝑇0 ) /𝑇𝑇0
where 𝑇𝑇𝑟𝑟 is the retention time of the analyte. 𝑇𝑇0 is the retention time of an unretained
compound, i.e., column void time (ColumnVoidTime). The outlier is set to Low if
𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶 < 𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶
When the outlier is set, the CapacityFactor column is highlighted.
For the outlier to activate, the following column must be set in the Quantitation
Method Editor:
CapacityFactorLimit

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Signal To Noise Ratio

This outlier metric is a measure of whether the peak signal-to-noise ratio is below the
preset limit. This outlier applies to the primary peaks and qualifiers of all compound
types and all sample types.
This outlier metric is determined by comparing the calculated signal-to-noise ratio of
the primary peak (SignalToNoiseRatio in the Peak table) against a user-defined
minimum limit (MinimumSignalToNoiseRatio). The outlier is set too Low if
SignalToNoiseRatio < MinimumSignalToNoiseRatio
When the outlier is set, the SignalToNoiseRatio column is highlighted.
For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:
MinimumSignalToNoiseRatio

Limit Of Detection
This outlier metric is a measure of whether the current quantitated amount is below
the limit of detection (LOD) threshold. This outlier applies to the primary peaks of all
compound types and all sample types except:
• Blank
• Double Blank
If no primary peak is found, the sample is flagged with a quantitation error message,
not with an outlier flag.
This outlier metric is determined by comparing the quantitated amount
(CalculatedConcentration) against a user-defined limit of detection
(LimitOfDetection). The outlier is set too Low if
CalculatedConcentration < LimitOfDetection
When the outlier is set, the CalculatedConcentration column is highlighted.
For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:

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LimitOfDetection

Limit Of Quantitation
This outlier metric is a measure of whether the current quantitated amount is below
the limit of quantitation (LOQ) threshold. This outlier applies to the primary peaks of
all compound types and all sample types except Blank and Double Blank. If no
primary peak is found, the sample is flagged with a quantitation error message, not
with an outlier flag.
This outlier metric is determined by comparing the quantitated amount
(CalculatedConcentration) against a user-defined limit of quantitation
(LimitOfQuantitation). The outlier is set too Low if
CalculatedConcentration < LimitOfQuantitation
When the outlier is set, the CalculatedConcentration column is highlighted.
For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:
LimitOfQuantitation

Method Detection Limit

This outlier metric is a measure of whether the current quantitated amount is below
the method detection limit (MDL) threshold. This outlier applies to the primary peaks
of all compound types and all sample types except Blank and Double Blank. If no
primary peak is found, the sample is flagged with a quantitation error message, not
with an outlier flag.
This outlier metric is determined by comparing the quantitated amount
(CalculatedConcentration) against a user-defined method detection limit
(MethodDetectionLimit). The outlier is set too Low if
CalculatedConcentration < MethodDetectionLimit
When the outlier is set, the CalculatedConcentration column is highlighted.
For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:

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MethodDetectionLimit

Qualifier
This set of outliers are grouped together to handle exceptions related to Qualifiers.

Qualifier Peak Not Found

This outlier metric is a measure of whether the compound’s qualifier ions have
associated peaks. This outlier applies to all compound types and all sample types
except Double blank and Blank, it also applies to ISTD compounds in Blank sample.
This outlier metric is determined by looking for the associated PeakQualifier
row for that compound and determining if that peak row exists.
The outlier is set too Low if the PeakQualifier row does not exist when target
ion is found.

Qualifier QValue
This outlier metric is a measure of the fidelity of the observed qualifier ratios versus
the nominal qualifier ratios. The QVALUE function is a well-defined statistic that
yields an efficient measure of the “goodness of fit” of the observed qualifier ratios to
the nominal qualifier ratios.
For all hits a QVALUE is computed as described here. For Target Compound Entries
with no qualifier signals, the QVALUE is defined as 100. For Target Compound
Entries with k qualifier signals qi , 1 <= I <= k, define ri as the expected ratio of
qualifier peak for qi to the target peak. Then define ri ‘ as the observed qualifier ratio
as determined by the above Qualifier Ratio Computation. Now define the total ratio
deviation D:

Then the QVALUE is the closest integer to max { 100 – D, 1 }.

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Outliers

This outlier metric is determined by comparing the QValueComputed of the qualifier

ion against a user defined limit QValueMinimum.
The outlier is set to Low if
𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄 < 𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄
When the outlier is set, the QValueComputed column is highlighted.
For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:
• QValueMinimum

Qualifier Ratio
This outlier metric is a measure of whether the current qualifier’s peak ratio is above
or below the qualifier peak ratio limits. In preparing a quantitation method, you can
assign a ratio to the quantifier and qualifier ions with an associated uncertainty. This
criterion is useful is confirming the identity of the compound analyzed because that
compound follows a certain fragmentation pattern which results in the predicted
ratios. This outlier applies to all compounds and all sample types except Double Blank.
This outlier metric is determined by comparing the response (area or height) of the
qualifier signal to the response of the quantifier signal. The response ratio, stored as
QualifierResponseRatio, is tested against QualifierRangeMaximum and
QualifierRangeMinimum. These limits are computed as follows:
If UncertaintyRelativeOrAbsolute = Absolute,
QualifierRangeMinimum = RelativeResponse – Uncertainty
QualifierRangeMaximum = RelativeResponse + Uncertainty
If UncertaintyRelativeOrAbsolute = Relative,
QualifierRangeMinimum = RelativeResponse × (100 – Uncertainty)/100
QualifierRangeMaximum = RelativeResponse × (100 + Uncertainty)/100
The outlier is set too High if
QualifierResponseRatio > QualifierRangeMaximum

200 Quantitative Analysis Quantitation DataSet

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The outlier is set too Low if

QualifierResponseRatio < QualifierRangeMinimum
When the outlier is set, the QualifierResponseRatio column is highlighted.
For the outlier to activate, the following must be set in the Quantitation Method
Editor:
Uncertainty (percent)
UncertaintyRelativeOrAbsolute
Example:
For a qualifier ion that has a QualifierResponseRatio of 40% and a % uncertainty of 20:
If UncertaintyRelativeOrAbsolute is set to “Relative”, the acceptable range is from
QualifierRangeMinimum =32% to
QualifierRangeMaximum =48%.
If UncertaintyRelativeOrAbsolute is set to “Absolute”, the acceptable range is from
QualifierRangeMinimum =20% to
QualifierRangeMaximum =60%.

Qualifier Coelution Score

This outlier metric is a measure of how well this qualifier ion coelutes with the
quantifier ion. The Coelution score uses the retention time of the quantifier ion and
the quantifier ion as well as the peak width and the peak symmetry of the quantifier
ion and the qualifier ion.
This outlier metric is determined by comparing the calculated CoelutionScore value of the
qualifier ion against a user-defined limits CoelutionScoreLimit.

The outlier is set too Low if

𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶 < 𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶

When the outlier is set, the CoelutionScore column is highlighted.

For the outlier to activate, the following columns must be set in the Quantitation Method Editor:

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• CoelutionScoreLimit

Qualifier Integration Quality Metric

This outlier metric is a measure of the quality of a qualifier peak’s integration. This
outlier applies to all the qualifier peaks of all compounds and sample types.
This outlier metric is determined by examining the parameterless (MS-MS or Agile)
integrator metric stored in the IntegrationQualityMetric of the PeakQualifier table. If
the peak’s IntegrationQualityMetric is “Rejected” or “Inspect”, the outlier is set too
High and Low, respectively. The integrated peak’s IntegrationQualityMetric column is
highlighted, and the outlier message describes the reason why the peak has been
rejected or “inspect”, as reported by the MS-MS integrator in the
IntegrationMetricQualityFlags column.
When the outlier is set, the IntegrationQualityMetric column of the PeakQualifier table
is highlighted.
For the outlier to activate, the Integrator must be set to MS-MS or Agile integrator.

Qualifier Peak Symmetry

This outlier metric is a measure of whether the qualifier peak symmetry is below or
above the preset limits. This outlier applies to the qualifier peaks of all compound
types and all sample types.
This outlier metric is determined by comparing the calculated Symmetry value of the
primary peak against a user-defined limits SymmetryLimitLow and
SymmetryLimitHigh
The outlier is set too High if

𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆 > 𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆ℎ

The outlier is set too Low if

𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆 < 𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆

Peak symmetry is calculated as the ratio (at the 5% of the peak height) of the distance between
the peak apex and the back side of the chromatographic curve to the distance between the peak
apex and the front side of the chromatographic curve.

202 Quantitative Analysis Quantitation DataSet

 Outliers

Symmetry = CB/AC

When the outlier is set, the Symmetry column is highlighted.

For the outlier to activate, the following columns must be set in the Quantitation Method Editor:

• SymmetryLimitHigh

• SymmetryLimitLow

Qualifier Peak Full Width Half Maximum

This outlier metric is a measure of whether the full width half maximum (FWHM) of a
qualifier peak is outside the preset limit. This outlier applies to all qualifier peaks of
all compound types and all sample types.
This outlier metric is determined by comparing the calculated FullWidthHalfMaximum
value of the qualifier peak against a user-defined limits
FullWidthHalfMaximumLimitLow and FullWidthHalfMaximumLimitHigh.
The outlier is set too High if
𝐹𝐹𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢ℎ𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻 > 𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹ℎ𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻ℎ
The outlier is set too Low if
𝐹𝐹𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑢𝑑𝑑𝑡𝑡ℎ𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻 < 𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹𝐹ℎ𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻𝐻
Full width half maximum is calculated as the peak width at the half height.

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When the outlier is set, the FullWidthHalfMaximum column is highlighted.

For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:
• FullWidthHalfMaximumLimitHigh
• FullWidthHalfMaximumLimitLow

ISTD
This set of outliers are grouped together to handle exceptions related to internal
standard correction (ISTD).

ISTD Response
This outlier metric is a measure of whether the internal standard response (area or
height) is above or below preset limits. This outlier applies to the primary peak of
every ISTD compound in all sample types except Double Blank. If no primary peak is
found, the sample is flagged with a quantitation error message, not with an outlier
flag.
This outlier metric is determined by comparing the TargetResponse column of the
primary peak of an ISTD compound against the limits ISTDResponseLimitLow,
ISTDResponseLimitHigh.
The outlier is set too High if

TargetResponse > ISTDResponseLimitHigh

The outlier is set too Low if

TargetResponse < ISTDResponseLimitLow

When the outlier is set, the TargetResponse column is highlighted.

For the outlier to activate, the following columns must be set in the Quantitation Method Editor:

• ISTDResponseLimitLow

• ISTDResponseLimitHigh

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ISTD Response Percent Deviation

This outlier metric is a measure of whether the internal standard response (area or
height) deviates more than the user defined percent limits from the average ISTD
response calculated from the existing calibration.
A poor injection as well as matrix enhancement or suppression could cause the ISTD
response to exceed the limits.
This outlier applies to the primary peak of every ISTD compound in all sample types
except Double Blank. If no primary peak is found, the sample is flagged with a
quantitation error message, not with an outlier flag.
The outlier is set too High if
𝐼𝐼𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆 > 𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝑀𝑀𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎
Where
𝐼𝐼𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆
𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝑖𝑖 − 𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴(𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼)𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐
= ×100
𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴(𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼)𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑛𝑛
The outlier is set too Low if
𝐼𝐼𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆 < 𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼)
To support backward compatibility, if only a maximum limit is set, the lower limit will
be set to – 𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼.
When the outlier is set, the ISTDResponsePercentDeviation column is highlighted.
For the outlier to activate, the following column must be set in the Quantitation
Method Editor:
• ISTDResponseMaximumPercentDeviation (can set maximum limit only)
• ISTDResponseMinimumPercentDeviation

Sample
This set of outliers are grouped together to handle exceptions related to Samples.

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Sample Amount
This outlier metric is a measure of whether the current quantitated amount is above or
below preset sample limits. This outlier applies to the primary peak of every Target
compound in all samples of type Sample. If no primary peak is found, the sample is
flagged with a quantitation error message, not with an outlier flag.
This outlier metric is determined by comparing the quantitated amount adjusted by
the Multiplier (FinalConcentration) against the limits SampleAmountLimitLow,
SampleAmountLimitHigh.
The outlier is set too High if
FinalConcentration > SampleAmountLimitHigh
The outlier is set too Low if
FinalConcentration < SampleAmountLimitLow
When the outlier is set, the FinalConcentration column is highlighted.
For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:
SampleAmountLimitLow
SampleAmountLimitHigh.

Sample Relative Standard Deviation

This outlier metric is a measure of whether the standard deviation of the final
concentration for samples within the same SampleGroup is greater than a pre-
determined limit. For samples that are not assigned any SampleGroup, they are
considered to be in the same SampleGroup. This outlier applies to the primary peak of
every Target compound in all samples of type Sample. If no primary peak is found, the
sample is flagged with a quantitation error message, not with an outlier flag.
This outlier is calculated as follows:
For each SampleGroup x, calculate the average and standard deviation of current
compound’s FinalConcentration over all Sample samples (m=1…Mx)

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Mx
1
Avg x =
Mx
∑ FinalConcentration
m =1
m, x

∑ (FinalConcentration − Avg x )
Mx
1
SD x =
2

−1
m, x
Mx m =1

SD x
% RSD x = × 100
Avg x

For each sample group, the outlier is set too High if

%𝑅𝑅𝑅𝑅𝑅𝑅𝑥𝑥 > 𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆
When the outlier is set, the SampleRSD column is highlighted.
For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:
SampleMaximumPercentRSD

Blank
This set of outliers are grouped together to handle exceptions related to Blanks.

Blank Concentration
This outlier metric is a measure of whether the calculated concentration for a
compound in a blank sample is greater than the preset maximum limit. This outlier
applies to the primary peaks of all Target compounds in all samples of type Blank.
This outlier metric is determined by comparing the quantitated amount
(CalculatedConcentration) for each compound in a blank sample against that
compound’s user-defined maximum limit (MaximumBlankConcentration). The outlier
is set too High if

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CalculatedConcentration > MaximimBlankConcentration

When the outlier is set, the CalculatedConcentration column is highlighted.
For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:
MaximumBlankConcentration

Blank Response
This outlier metric is a measure of whether the target response for a compound in a
blank sample is greater than the preset maximum limit. This outlier applies to the
primary peaks of all Target compounds in all samples of type Blank and DoubleBlank.
This outlier also applies to all compounds in samples of type DoubleBlank.
This outlier metric is determined by comparing the target response for each compound
in a blank sample against that compound’s user-defined maximum limit
(MaximumBlankResponse). The outlier is set too High if
𝑇𝑇𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎 > 𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀
When the outlier is set, the TargetResponse column is highlighted.
For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:
MaximumBlankResponse

Calibration
This set of outliers are grouped together to handle exceptions related to Calibration.

Accuracy
This outlier metric is a measure of whether the quantitated amount for a calibration
sample or QC or CC is above or below a pre-determined relative deviation from an
expected value. This outlier applies to the primary peak of every compound type
except ISTD in the Calibration, QC and CC samples. If no primary peak is found, the
sample is flagged with a quantitation error message, not with an outlier flag.

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This outlier metric is determined by examining the ratio of the peak’s quantitated
amount (CalculatedConcentration) to the expected amount (ExpectedConcentration).
The Accuracy of quantitation of a given compound is defined as follows:
CalculatedConcentration
Accuracy = × 100
ExpectedConcentration
The Accuracy outlier is set too Low if
Accuracy <100 − MaxAccuracyDeviation
The Accuracy outlier is set too High if
Accuracy >100 + MaxAccuracyDeviation
For all but the lowest calibration level (the LOQ level), MaxAccuracyDeviation =
AccuracyMaximumPercentDeviation. For the lowest calibration level,
MaxAccuracyDeviation is computed as follows:
MaxAccuracyDeviation (lowest calibration level ) =
AccuracyMaximumPercentDeviation
× AccuracyLimitMultiplierLOQ
By default, AccuracyLimitMultiplierLOQ is set to 1. When the outlier is set, the
Accuracy column is highlighted.
For the outlier to activate, the following columns must be set:
AccuracyMaximumPercentDeviation
ExpectedConcentration
AccuracyLimitMultiplierLOQ

Average Response Factor

This outlier metric is a measure of whether the current compound has a calibration
curve that satisfies the average response factor criteria. An average response factor
flagged below the limit can indicate a poor response for the compound. This outlier
applies to all compound types except ISTD and to all sample types.
This outlier metric is determined as follows:

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For each enabled calibration point n=1…N in the compound’s calibration table with a
non-zero concentration, the system computes the LevelResponseFactor which is either
the response factor (RF) or the relative response factor (RRF) of the calibration level,
depending on whether the compound has an ISTD:
 RFn , if no ISTD 
LevelResponseFactorn =  
 RRFn , if ISTD 
( LevelResponse) n
RFn =
( LevelConcentration) n

LevelResponsen × ISTDConc n
RRFn ==
LevelConc n × ISTDResponsen

Compute AverageResponseFactor over all enabled calibration points:

N
1
AverageResponseFactor =
N
∑ LevelResponseFactor
n =1
n

The outlier is set too Low if

AverageResponseFactor < MinimumAverageResponseFactor

When the outlier is set, the AverageResponseFactor column is highlighted.

For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:
MinimumAverageResponseFactor
Note that the value of MinimumAverageResponseFactor must be set knowing whether
the compound has an ISTD or not.

Average Response Factor RSD

This outlier metric is a measure of whether the standard deviation of response factor
across the entire calibration curve is greater than a pre-determined limit. A response
factor RSD flagged above the limit can indicate a poor calibration for the compound.
This outlier applies to all compound types except ISTD and to all sample types.

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This outlier metric is determined as follows:

Compute AverageResponseFactor over all enabled calibration points:
1 N
AverageResponseFactor = ∑ LevelResponseFactorn
N n =1

∑𝑁𝑁
𝑛𝑛=1(𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝑛𝑛 − 𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴)
2
𝜎𝜎 = �
𝑁𝑁 − 1
𝜎𝜎
%𝑅𝑅𝑅𝑅𝑅𝑅 = 100×
𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴
The outlier is set too High if

%𝑅𝑅𝑅𝑅𝑅𝑅 > 𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀

When the outlier is set, the AverageResponseFactorRSD column is highlighted.

For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:
MaximumAverageResponseFactorRSD
Note that the value of MaximumAverageResponseFactorRSD must be set knowing
whether the compound has an ISTD or not.

Calibration Range
This outlier metric is a measure of whether the current quantitated amount for non-
calibration or non-QC samples is within the range of points comprising the calibration
curve.
Note that Quality Controls (QCs) are not considered part of the calibration curve. This
outlier applies to the primary peak of target compound only and to all sample types
except:
• Blank
• Double Blank
• Matrix Blank

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• QC
• CC
• Calibration.
The Calibration samples are excluded in order to prevent the lowest and highest
calibration points from being pushed out of range by the curve fit residuals.
The outlier is set too High if
CalculatedConcentration > HighestLevelConcentration
where HighestLevelConcentration is the level concentration of the highest enabled
(LevelEnable) calibration point.
The outlier is set too Low if
CalculatedConcentration < LowestLevelConcentration
where LowestLevelConcentration is the level concentration of the lowest enabled
(LevelEnable) calibration point.
When the outlier is set, the CalculatedConcentration column is highlighted.
This outlier is always activated unless the batch uses the standard addition
quantitation.

Curve Fit R2
This outlier metric is a measure of whether the calibration curve of the current
compound has a coefficient of determination (R2) that is below the minimum
threshold. This outlier applies to all compound types except ISTD and to all sample
types.
This outlier metric is determined by examining the compound’s curve fit R2 value
(CurveFitR2) and testing if it lies above CurveFitMinimumR2.
Curve fit R2 values below the minimum are flagged as Low.
When the outlier is set, the CurveFitR2 column is highlighted.
For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:

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CurveFitMinimumR2

Relative Response Factor

This outlier metric is a measure of whether the relative response factor (RRF) of the
current calibration level is close enough to the average RRF for this compound. This
outlier applies to all compound types except ISTD and to all sample types.
This outlier metric is determined by examining the ratio of each calibration level
response factor (LevelResponseFactor) to the AverageResponseFactor and
determining if the ratio is within the limit defined by the
RelativeResponseFactorMaximumPercentDeviation. The outlier is set to as follows:
 RRFMaximumPercentDeviation 
High if RRFn > RRF × 1 + 
 100 
 RRFMaximumPercentDeviation 
Low if RRFn < RRF × 1 − 
 100 
where RRFn is the relative response factor for calibration level n:
LevelResponsen × ISTDConc n
RRFn =
LevelConc n × ISTDResponsen

and RRF is the average relative response factor over all enabled calibration levels
with a non-zero concentration:
N
1
RRF =
N
∑ RRF
n =1
n

For technical reasons, it is not possible to highlight Calibration table columns like
LevelResponseFactor. Therefore, when this outlier is set, the TargetResponse column
in the Peak table is highlighted which is the limit column for this outlier.
For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:
RelativeResponseFactorMaximumPercentDeviation
Note: This outlier applies only to compounds that have an ISTD.

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Relative Standard Error

This outlier metric is a measure of whether the relative standard error (RSE) across
the entire calibration curve is greater than a pre-determined limit. A RSE flagged
above the limit can indicate a poor calibration for the compound. This outlier applies
to all compound types except ISTD and to all sample types.
This outlier metric is determined as follows:
Compute RSE over all enabled calibration points:

𝑛𝑛 2
𝑥𝑥 ′ − 𝑥𝑥𝑖𝑖
%𝑅𝑅𝑅𝑅𝑅𝑅 = 100×�� � 𝑖𝑖 � /(𝑛𝑛 − 𝑝𝑝)
𝑥𝑥𝑖𝑖
𝑖𝑖=1

Where,
xi = True value of the calibration level i
x’i = Measured concentration of calibration level i
p = Number of terms in the fitting equation
(average = 1, linear = 2, quadratic = 3)
n = Number of calibration points

The outlier is set to High if

%𝑅𝑅𝑅𝑅𝑅𝑅 > 𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅
When the outlier is set, the RSE column is highlighted.
For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:
RelativeStandardErrorMaximum.

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Response Factor
This outlier metric is a measure of whether the response factor (RF) of the current
calibration level is close enough to the average response factor for this compound.
This outlier applies to all compound types except ISTD and to all sample types.
This outlier metric is determined by comparing each calibration level response factor
(LevelResponseFactor) to the AverageResponseFactor and testing if the relative
deviation is within the limit defined by the
ResponseFactorMaximumPercentDeviation. The outlier is set as follows:
 RFMaximumPercentDeviation 
High if RFn > RF × 1 + 
 100 
 RFMaximumPercentDeviation 
Low if RFn < RF × 1 − 
 100 
where RFn is the response factor for calibration level n:
( LevelResponse) n
RFn =
( LevelConcentration) n

and RF is the average response factor over all enabled calibration levels with a non-zero
concentration:
N
1
RF =
N
∑ RF
n =1
n

For technical reasons, it is not possible to highlight Calibration table columns like
LevelResponseFactor. Therefore, when this outlier is set, the TargetResponse column
in the Peak table is highlighted which is the limit column for this outlier.
For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:
ResponseFactorMaximumPercentDeviation
Note: This outlier applies only to compounds that do NOT have an ISTD.

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QC
This set of outliers are grouped together to handle exceptions related to Quality
Controls (QC).

QC
This outlier metric is a measure of whether the current quantitated amount for a
compound in a QC sample is within pre-determined limits from the expected amount.
This outlier applies to the primary peak of each Target compound in the QC samples.
If no primary peak is found, the sample is flagged with a quantitation error message,
not with an outlier flag.
This outlier metric is determined by examining the peak’s quantitated amount
(CalculatedConcentration) and testing if that amount falls with a pre-defined interval
QCMaximumDeviation from ExpectedConcentration.
The outlier is set too High if
CalculatedConc > ExpectedConc + QCMaximumDeviation
The outlier is set too Low if
CalculatedConc < ExpectedConc − QCMaximumDeviation
When the outlier is set, the CalculatedConcentration column is highlighted.
For the outlier to activate, the following columns must be set:
QCMaximumDeviation
ExpectedConcentration

QC LCS Recovery
This outlier metric is a measure of whether the recovery of laboratory control
standards are within pre-determined limits. This outlier applies to the primary peak of
all compounds in all QC samples whose SampleInformation column contains either
“LCSA” or “LCSB”.

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This QC LCS Recovery is calculated as follows and the recovery is deposited to the
MatrixSpikePercentRecovery column
𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶
𝑄𝑄𝐶𝐶 𝐿𝐿𝐿𝐿𝐿𝐿 𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅 = ×100
𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿 𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐
The outlier metric is determined by testing if the QC LCS Recovery falls within the limits.

The outlier is set too High if

𝑄𝑄𝑄𝑄 𝐿𝐿𝐿𝐿𝐿𝐿 𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅 > 𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑎𝑎𝑥𝑥𝑥𝑥𝑥𝑥𝑥𝑥𝑥𝑥𝑥𝑥𝑥𝑥𝑥𝑥𝑥𝑥𝑥𝑥𝑥𝑥𝑥𝑥𝑥𝑥

The outlier is set too Low if

𝑄𝑄𝑄𝑄 𝐿𝐿𝐿𝐿𝐿𝐿 𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅 < 𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄

The SampleInformation value controls the choice of either the LCSA or LCSB limits. In other
words, SampleInformation assigned “LCSA” sets LCSA recovery limits, whereas
SampleInformation assigned “LCSB” sets LCSB limits.

When the outlier is set, the MatrixSpikePercentRecovery column is highlighted for all
QC samples in a given level.
For the outlier to activate, the following columns must be set:
• SampleInformation column must contain “LCSA” or “LCSB”
• QCLCSMaximumRecoveryA
• QCLCSMinimumRecoveryA
• QCLCSMaximumRecoveryB
• QCLCSMinimumRecoveryB

QC Relative Standard Deviation

This outlier metric is a measure of whether the standard deviation of the target
response for a set of QC samples at a given level is less than a pre-determined limit.
This outlier applies to the primary peak of each Target compound in all QC samples
within a given concentration level.

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This outlier is computed as follows. For each QC level n = 1…N, the average, standard
deviation of the current compound’s TargetResponse are calculated over all QC
samples (m=1…Mn) at QC level n:
Mn
1
Avg n =
Mn
∑ TargetResponse
m =1
m,n

∑ (TargetResponse − Avg n )
Mn
1
SDn =
2

−1
m,n
Mn m =1

For each QC level n with Mn > 1, the outlier is set as follows:

High if % RSDn > QCMaximumPercentRSD
where %RSDn is the relative standard deviation (RSD) of all QC points in level n,
expressed in percent:
SDn
% RSDn = × 100
Avg n
When the outlier is set, the TargetResponse column is highlighted for all QC samples in
a given level.
For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:
QCMaximumPercentRSD.

CC
This set of outliers are grouped together to handle exceptions related to Continuing
Calibration (CC).

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CC Average Response Factor

This outlier metric is a measure of whether the response factor of a compound in a CC sample
deviates too much from the average response factor of the initial calibration. This outlier applies
to all compounds in CC sample(s).

This outlier metric is determined by computing the relative deviation of the

LevelResponseFactor of a compound in the CC sample from the
AverageResponseFactor for the same compound and comparing the result with the
maximum allowed limit MaximumCCResponseFactorDeviation.
The outlier is calculated as follows. The compound’s CC response factor deviation between CC
and initial calibration is

 LevelResponseFactor _ CC 
CCResponseFactorDeviation = 1 − × 100
 AverageResponseFactor _ Init 

Here, LevelResponseFactor_CC is the response factor for the compound in the CC sample,
AverageResponseFactor_Init is the average response factor for the same compound, and the
average is over all enabled Calibration and QC levels.

The outlier is set too High either if

CCResponseFactorDeviation > MaximumCCResponseFactorDeviation

The outlier is set too Low if

CCResponseFactorDeviation < -MaximumCCResponseFactorDeviation

When the outlier is set, the AverageResponseFactor column is highlighted.

For the outlier to activate, the following columns must be set in the Quantitation Method Editor:

MaximumCCResponseFactorDeviation

CC ISTD Response Ratio

This outlier metric is a measure of whether the response of an ISTD compound in any sample
deviates too much from the previous most recent CC sample or last calibration sample. This
outlier applies to the primary peaks of all ISTD compounds in all sample(s).

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Outliers

The outlier is determined by computing the ratio of the TargetResponse of the primary
peak of each ISTD compound in a sample and in the previous CC sample or the last
calibration sample, and comparing the result with the limits
CCISTDResponseRatioLimitHigh and CCISTDResponseRatioLimitLow.
The outlier is calculated as follows. The ISTD compound’s response ratio to the CC ISTD response
is

ISTDResponse
CCISTDResponseRatio = × 100
ISTDResponse _ CC

where ISTDResponse_CC is the ISTD compound response in the previous most recent CC sample
and ISTDResponse is the compound response in any sample.

The outlier is set too High either if

CCISTDResponseRatio > CCISTDResponseRatioLimitHigh

The outlier is set too Low either if

CCISTDResponseRatio < CCISTDResponseRatioLimitLow

when the outlier is set, the CCISTDResponseRatio column is highlighted.

For the outlier to activate, the following columns must be set in the Quantitation Method Editor:

• CCISTDResponseRatioLimitHigh

• CCISTDResponseRatioLimitLow

CC Relative Response Factor

This outlier metric is a measure of whether the relative response factor (RRF) of the compound
in a CC is too small. This outlier applies to all Target compounds in CC sample(s).

This outlier metric is determined by computing the relative response factor for each
compound in the CC sample and comparing it to the minimum limit defined by
MinimumCCRelativeResponseFactor.
The outlier is set too Low if:

RRFCC < MinimumCCRelativeResponseFactor

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where RRFCC is the relative response factor for the CC sample:

LevelResponseCC × ISTDConcCC
RRFCC =
LevelConcCC × ISTDResponseCC

For technical reasons, it is not possible to highlight Calibration table columns like
LevelResponseFactor. Therefore, when this outlier is set, the TargetResponse column
in the Peak table is highlighted.
For the outlier to activate, the following columns must be set in the Quantitation Method Editor:

• MinimumCCRelativeResponseFactor
Note: This outlier applies only to compounds that have an ISTD.

CC Response Ratio
This outlier metric is a measure of whether the response of a target compound in a CC
sample deviates too much from the initial calibration. This outlier applies to the
primary peaks of all Target compounds in compounds in CC sample(s).
• This outlier metric is determined by computing the ratio of the TargetResponse
of the primary peak of each compound in the CC sample and in the calibration
sample at the same concentration level, and comparing the result with the
limits CCResponseRatioLimitHigh, CCResponseRatioLimitLow.
The outlier is calculated as follows. The compound’s CC response ratio to the initial calibration is

TargetResponse _ CC
CCResponseRatio = × 100
TargetResponse _ Init
where TargetResponse_CC is the compound response in the CC sample and TargetResponse_Init
is the compound response in the calibration sample at the same concentration level as the CC
sample.

The outlier is set too High either if

CCResponseRatio > CCResponseRatioLimitHigh

The outlier is set too Low either if

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CCResponseRatio < CCResponseRatioLimitLow

When the outlier is set, the TargetResponse column is highlighted.

For the outlier to activate, the following columns must be set in the Quantitation Method Editor:

• CCResponseRatioLimitLow

• CCResponseRatioLimitHigh

CC Retention Time
This outlier metric is a measure of whether the actual retention time of a compound in a CC
sample is within the Retention Time (RT) window centered on the expected RT, as defined in the
method. This outlier applies to the primary peak of all compound types in CC sample(s).

• This outlier metric is determined by comparing the peak’s retention time

(RetentionTime in the Peak table) against the method’s retention time (RetentionTime
in the Target Compound table) and testing if the deviation is within the retention time
window (RetentionTimeWindowCC), expressed in minutes.

The outlier is set as follows:

1
High if RT > RTmethod + RTWindowCC
2
1
Low if RT < RTmethod − RTWindowCC
2

When the outlier is set, the RetentionTime column of the Peak table is highlighted.
For the outlier to activate, the following columns must be set in the Quantitation Method Editor:

• RetentionTimeWindowCC

CC Time
This outlier metric is a measure of the time elapsed between the acquisition time stamps of any
sample and last continuing calibration sample or last calibration sample. This outlier applies to
all sample types.

222 Quantitative Analysis Quantitation DataSet

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This outlier metric is determined by computing ElapsedTime, which is the difference

between the acquisition timestamp of any sample and the acquisition timestamp of
last CC Sample or last calibration sample, and comparing ElapsedTime to the
maximum allowed limit CCMaximumElapsedTimeInHours.
ElapsedTime is computed as follows:

𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸 = 𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇(𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆) − 𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇(𝐶𝐶𝐶𝐶)

Here TimeStamp is the AcqDateTime column of each sample.

The outlier is set too High if

ElapsedTime > CCMaximumElapsedTimeInHours

When the outlier is set, the AcqDateTime column of the Sample table is highlighted.
For the outlier to activate, the following batch global parameter must be set to a number
greater than 0.

• CCMaximumElapsedTimeInHours

Matrix
This set of outliers are grouped together to handle exceptions related to Matrix Spikes.

Matrix Spike
This outlier metric is a measure of whether the current quantitated amount for a
Matrix Spike sample type is above or below pre-determined limits. This outlier applies
to the primary peak of each MatrixSpike compound in the samples of type Matrix and
MatrixDup. If no primary peak is found, the sample is flagged with a quantitation error
message, not with an outlier flag.
This outlier metric is determined by examining the peak’s quantitated amount
adjusted by the Multiplier (FinalConcentration3F5) and testing if that amount falls
with the MatrixSpikeConcentrationLimitLow and MatrixSpikeConcentrationLimitHigh
limits.

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The outlier is calculated as follows. The amount of the current compound in a matrix
sample m = 1, 2 is computed as
MatrixAmount m = FinalConcentration m

Here FinalConcentration1 is the FinalConcentration of the current compound in the

Matrix Spike sample and FinalConcentration2 is the FinalConcentration of the
current compound in the Matrix Duplicate sample. Note that the FinalConcentration
in the Matrix Blank sample is not used in computing MatrixAmountm.
Note
Using the Final Concentration takes into account a dilution factor. Hence, diluting the
MatrixSpike at any stage of sample preparation is taken into account in measuring
against the expected concentration.
The outlier is set too High if
MatrixAmountm > MatrixSpikeConcentrationLimitHigh
The outlier is set too Low if
MatrixAmountm < MatrixSpikeConcentrationLimitLow
When the outlier is set, the FinalConcentration column is highlighted.
For the outlier to activate, the following must be set:
Compound type is set as MatrixSpike
Sample type is set as Matrix Spike or Matrix Duplicate
MatrixSpikeConcentrationLimitLow
MatrixSpikeConcentrationLimitHigh

Matrix Spike Percent Deviation

This outlier metric is a measure of whether the difference in the quantitated amounts
between the Matrix Spike sample and the Matrix Duplicate sample is above or below
the pre-determined percent limit. This outlier applies to the primary peak of each
MatrixSpike compound in the samples of type Matrix and MatrixDup.

224 Quantitative Analysis Quantitation DataSet

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This outlier metric is determined by examining the peak’s quantitated amount

adjusted by the Multiplier (FinalConcentration) compared to the expected amount
(MatrixSpikeConcentration ) and testing if MatrixSpikePercentDeviation, the
difference in MatrixSpikePercentRecovery between Matrix Spike and Matrix Duplicate,
is outside the MatrixSpikeMaximumPercentDeviation.
The outlier is set too High if
MatrixSpikePercentDeviation > MaxPercentDeviation
where

FinalConcentration1 − FinalConcentration 2
MatrixSpikePercentDeviation = × 100
MatrixSpikeConcentration
Here FinalConcentration1 is the FinalConcentration of the current compound in the
Matrix Spike sample and FinalConcentration2 is the FinalConcentration of the
current compound in the Matrix Duplicate sample.
The SampleInformation value controls the choice of either the Matrix(A) or MatrixB expected
concentration and limits. In other words, SampleInformation assigned “MatrixB” sets MatrixB
limits and Matrix(B) expected concentration, whereas SampleInformation assigned “MatrixA”
sets MatrixA limits and MatrixA expected concentration. Any unmatched value of
SampleInformation defaults to Matrix(A).

When the outlier is set, the MatrixSpikePercentDeviation column is highlighted.

For the outlier to activate, the following must be set:
Compound type is set as MatrixSpike
Sample type is set as Matrix Spike or Matrix Duplicate
Matrix Duplicate sample in same batch
MatrixSpikeConcentration
MatrixSpikeMaximumPercentDeviation

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Outliers

Matrix Group Percent Recovery

This outlier metric is similar to Matrix Spike Percent Recovery but differs from the latter in two
ways:

1) Matrix Group Percent Recovery applies to all compound types;

2) Matrix Group Percent Recovery applies only within a given matrix spike group. A matrix
spike group is group of samples that share the same value of the MatrixSpikeGroup
column. Note that a batch may contain multiple matrix spike groups.
3) Samples of type Sample can play the role of the Matrix Blank within a matrix spike
group.

This outlier metric is calculated separately for each matrix spike group. It is
determined by examining the peak’s quantitated amount adjusted by the Multiplier
(FinalConcentration) compared to the expected MatrixSpikeConcentration or
MatrixSpikeBConcentration and testing if that percent recovery
(MatrixSpikePercentRecovery) falls with the MatrixSpikePercentRecoveryMinimum
and MatrixSpikePercentRecoveryMaximum limits or the
MatrixSpikeBPercentRecoveryMinimum and MatrixSpikeBPercentRecoveryMaximum
limits.
The outlier is calculated as follows. For the Matrix and MatrixDup samples, the
current compound’s percent recovery (MatrixSpikePercentRecovery) is
FinalConcentration m − MatrixBlankConcentration
MatrixRecovery = × 100
MatrixSpikeConcentration
Here FinalConcentrationm is the FinalConcentration of the current compound in the Matrix
sample or in the MatrixDup sample; MatrixBlankConcentration is the FinalConcentration of the
current compound in the MatrixBlank sample or in the target Sample that belongs to the same
matrix spike group.

The SampleInformation value controls the choice of either the Matrix(A) or MatrixB expected
concentration and limits. In other words, SampleInformation assigned “MatrixB” sets MatrixB
limits and Matrix(B) expected concentration, whereas SampleInformation assigned “MatrixA”
sets MatrixA limits and MatrixA expected concentration. Any unmatched value of
SampleInformation defaults to Matrix(A).

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 Outliers

Membership in a matrix spike group is subject to the following assumptions/requirements:

1. A matrix spike group can contain one or more sample of type Sample or MatrixBlank.
This is the “unspiked” sample. If no “unspike” sample present in the matrix spike group,
MatrixBlankConcentration is considered as zero.

2. A matrix spike group must contain at least one sample of type Matrix or MatrixDup.
These are the “spiked” samples.

3. If a matrix spike group contains multiple “unspiked” samples, only the first “unspiked”
sample is used; the others are ignored.

4. Any group that does not satisfy the assumptions 1) and 2) is ignored.

5. The Matrix Spike Group Recovery outlier is calculated for each “spiked” sample in the
group.

The outlier is set too High if

MatrixRecovery > MatrixSpikePercentRecoveryMaximum

The outlier is set too Low if

MatrixRecovery < MatrixSpikePercentRecoveryMinimum

When the outlier is set, the MatrixSpikePercentRecoverycolumn is highlighted.

For the outlier to activate, the following must be set:

• Sample type is set as Matrix or MatrixDup

• Matrix, MatrixDup, and MatrixBlank samples in the same batch

• MatrixSpikeConcentration

• MatrixSpikePercentRecoveryMinimum

• MatrixSpikePercentRecoveryMaximum

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Outliers

Matrix Spike Percent Recovery

This outlier metric is a measure of whether the ratio of the current quantitated
amount to expected amount for a Matrix Spike sample is above or below pre-
determined pre-defined limits. This criterion is often used to measure the fixed
boundaries from the expected recovery for a Matrix Spike compound. This outlier
applies to the primary peak of each MatrixSpike compound in the samples of type
Matrix and MatrixDup. If no primary peak is found, the sample is flagged with a
quantitation error message, not with an outlier flag.
This outlier metric is determined by examining the peak’s quantitated amount
adjusted by the Multiplier (FinalConcentration) compared to the expected
MatrixSpikeConcentration and testing if that percent recovery
(MatrixSpikePercentRecovery) falls with the MatrixSpikePercentRecoveryMinimum
and MatrixSpikePercentRecoveryMaximum limits.
The outlier is calculated as follows. For the Matrix Spike and the Matrix Duplicate
samples, the current compound’s percent recovery (MatrixSpikePercentRecovery) is
FinalConcentration m − MatrixBlankConcentration
MatrixRecovery = × 100
MatrixSpikeConcentration
Here FinalConcentrationm is the FinalConcentration of the current compound in the
Matrix Spike sample or in the Matrix Duplicate sample; MatrixBlankConcentration is
the FinalConcentration of the current compound in the Matrix Blank sample.
The outlier is set too High if
MatrixRecovery > MatrixSpikePercentRecoveryMaximum
The outlier is set too Low if
MatrixRecovery < MatrixSpikePercentRecoveryMinimum
When the outlier is set, the MatrixSpikePercentRecovery column is highlighted.
For the outlier to activate, the following must be set:

• Compound type is set as MatrixSpike

• Sample type is set as Matrix or MatrixDup

• A single triplet of Matrix, MatrixDup, and MatrixBlank samples in the same batch

228 Quantitative Analysis Quantitation DataSet

 Outliers

• MatrixSpikeConcentration
• MatrixSpikePercentRecoveryMinimum
• MatrixSpikePercentRecoveryMaximum
• MatrixGroup is not assigned

Surrogate
This set of outliers are grouped together to handle exceptions related to Surrogates.

Surrogate
This outlier metric is a measure of whether the current quantitated amount for a
surrogate compound type is above or below pre-determined limits. This outlier applies
to the primary peak of each Surrogate compound in all sample types except Blank and
DoubleBlank. If no primary peak is found, the sample is flagged with a quantitation
error message, not with an outlier flag.
This outlier metric is determined by examining the peak’s quantitated amount
(FinalConcentration) adjusted by the Multiplier and testing if that amount falls within
the SurrogateConcentrationLimitLow and SurrogateConcentrationLimitHigh limits.
The outlier is set too High if
SurrogateAmount > SurrogateConcentrationLimitHigh
The outlier is set too Low if
SurrogateAmount < SurrogateConcentrationLimitLow
Here SurrogateAmount is the FinalConcentration of the current surrogate compound.
When the outlier is set, the FinalConcentration column is highlighted.
For the outlier to activate, the following must be set in the Quantitation Method
Editor:
• Compound type is Surrogate
• SurrogateConcentrationLimitLow

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Outliers

• SurrogateConcentrationLimitHigh

Surrogate Percent Recovery

This outlier metric is a measure of whether the current quantitated amount for a
surrogate compound type is above or below pre-determined limits. This criterion is
often used to measure the fixed boundaries from the expected recovery for a surrogate
compound. This outlier applies to the primary peak of each Surrogate compound in all
sample types except DoubleBlank. If no primary peak is found, the sample is flagged
with a quantitation error message, not with an outlier flag.
This outlier metric is determined by examining the peak’s quantitated amount
adjusted by the Multiplier (FinalConcentration) compared to the expected
SurrogateConcentration and testing if the ratio falls with the
SurrogatePercentRecoveryMinimum and SurrogatePercentRecoveryMaximum limits.
The outlier is calculated as follows. The current surrogate compound’s percent
recovery (SurrogatePercentRecovery) is
FinalConcentration
SurrogateRecovery = × 100
SurrogateConcentration
The outlier is set too High if
SurrogateRecovery > SurrogatePercentRecoveryMaximum
The outlier is set too Low if
SurrogateRecovery < SurrogatePercentRecoveryMinimum
When the outlier is set, the SurrogatePercentRecovery column is highlighted.
For the outlier to activate, the following must be set in the Quantitation Method
Editor:
Compound type is Surrogate
SurrogateConcentration
SurrogatePercentRecoveryMinimum
SurrogatePercentRecoveryMaximum

230 Quantitative Analysis Quantitation DataSet

 Outliers

Response Check
This set of outliers are grouped together to handle exceptions related to Response
Check.

Response Check
This outlier metric is a measure of whether the Response Check sample compounds
pass the minimum response criterion. This outlier applies to the primary peak of every
Target compound in samples of type ResponseCheck. If no primary peak is found, the
sample is flagged with a quantitation error message, not with an outlier flag.
This outlier metric is determined by comparing the TargetResponse column of the
primary peak of each compound in the Response Check sample against
ResponseCheckMinimum.
The outlier is set too Low if
TargetResponse < ResponseCheckMinimum
When the outlier is set, the TargetResponse column is highlighted.
For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:
• ResponseCheckMinimum

Mass
This set of outliers are grouped together to handle exceptions related to Mass.

Library Match Score

This outlier metric is a measure of the correlation between the extracted spectrum and
the reference library spectrum. The reference library can be generated from a high
level calibration sample or from an existing library.

Quantitative Analysis Quantitation DataSet 231

Outliers

ReferenceLibraryMatchScore is an indicator of the quality of the match between the

sample spectrum and the reference library spectrum. A score of 100 means a perfect
match.
The outlier is set too Low if

𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅𝑅ℎ𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆 < 𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿𝐿ℎ𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆

When the outlier is set, the ReferenceLibraryMatchScore column of the Peak table is
highlighted.
For the outlier to activate, the following columns must be set in the Quantitation Method Editor:

• LibraryMatchScoreMininum

Mass Accuracy
This outlier metric is a measure of mass difference beween expected MZ and the actual
centroided spectral mass against a user-defined limit. This outlier applies to the primary peak of
all compound types and all sample types.

The Mass Accuracy is the mass assignment of the averaged scan spectra across the target or
qualifier chromatographic peak. This averaged spectrum does take into account saturation if
SpectrumPercentSaturationThreshold is specified. A poor Mass Accuracy metric indicates a mass
drift which can arise from tune, or other effects.

The acceptable mass accuracy is defined as within the MassAccuracyLimit.

MassAccuracy is calculated as the difference between the expected MZ and the most
abundant MZ peak found within the range [MZ – MZExtractionWindowFilterLeft,
MZ+MZExtractionWindowFilterRight], it is measured in units as determined by the
MZExtractionWindowUnits setting (Thomason, PPM, Percent).
The outlier is set too High if

𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀 > +𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀

The outlier is set too Low if

𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀 < −𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑚𝑚𝑚𝑚𝑚𝑚

When the outlier is set, the MassAccuracy column of the Target Compound table is
highlighted.
For the outlier to activate, the following columns must be set in the Quantitation Method Editor:

232 Quantitative Analysis Quantitation DataSet

 Outliers

• MassAccuracyLimit

Mass Match Score

This outlier metric is a measure of the probability that the observed isotope spectrum pattern
matches the synthesized isotope pattern. This outlier applies to the primary peak of all
compound types and all sample types.

Mass match score is defined as weighted aggregate of the three individual

metrics including mass accuracy score, mass abundance score and mass
spacing score. In this computation, the weighting factors are taken from the
accurate mass metrics parameters configuration file
AccuMassMetricsParams.xml, which is located under the bin directory. The
default values are

𝑊𝑊𝑚𝑚𝑚𝑚𝑚𝑚𝑚𝑚 = 100.0

𝑊𝑊𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎 = 60.0

𝑊𝑊𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠 = 50.0

The equation for computing the overall score is then

𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀ℎ𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆
𝑊𝑊𝑚𝑚𝑚𝑚𝑚𝑚𝑚𝑚 ∗ 𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀 + 𝑊𝑊𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎 ∗ 𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀 + 𝑊𝑊𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠 ∗ 𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀
=
𝑊𝑊𝑚𝑚𝑚𝑚𝑚𝑚𝑚𝑚 + 𝑊𝑊𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎𝑎 + 𝑊𝑊𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠

Quantitative Analysis Quantitation DataSet 233

Outliers

The outlier is set too Low if

𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀ℎ𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆 < 𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀𝑀ℎ𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆

When the outlier is set, the MassMatchScore column of the Peak table is highlighted.
For the outlier to activate, the following columns must be set in the Quantitation Method Editor:

• MassMatchScoreMininum

Alternative Peak
This outlier metric is a measure of goodness of fit of the primary peak against certain
creteria AlternativePeakCriteria. When the AlternativePeakCriteria is
DeconvolutedLibraryMatchScore, component spectrum of each alternative peak is
compared against the reference library, and library match scores are calculated. If any
alternative peak has better matched component, AlternativePeakRTDiff is calculated
as the RT difference between the primary peak and the alternative peak.
The outlier is set to High if
𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴 > 0

234 Quantitative Analysis Quantitation DataSet

 Outliers

Which indicates the alternative peak with better library match score is on the right
side of the current primary peak.
And the outlier is set to Low if
𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴𝐴 < 0
Which indicates the alternative peak with better library match score is on the left side
of the current primary peak.

For the outlier to activate, the following columns must be set in the Quantitation
Method Editor:
• AlternativePeakCriteria

Saturation Recovery
This outlier metric is an indicator of wheather an accurate mass signal is recovered
successfully or not by Feature Detection aka “SureMass extrapolation”. Feature
Detection offers extended dynamic range by signal processing. In some boundary
condition cases, the existing signal is not sufficient to recover, so we need to notify the
analyst. Notifying the analyst of a possible false negative often results in re-injecting
the sample with dilution in order to see a signal which is within the limits.
The outlier is computed by comparing the ratio of the restored feature peak height to
the original feature peak height. The feature peak and recovery of feature peak are
determined by the feature detection algorithm for accurate mass data.
SaturationRecoveryRatio indicates the status of feature recovery:

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Outliers

Saturation Recovery Ratio Recovery Status

Null Feature is not saturated

0 Feature is saturated and not

recovered

>0 Feature is saturated but recoverd

The outlier is set to High if feature is saturated and not recovered, i.e.
𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆𝑆 = 0
Saturation Recovery outlier is automatically enabled when SureMass global is set.

Custom
This set of outliers are grouped together to handle exceptions related to Custom
Calculations.

Custom Calculation
This outlier metric is a measure of whether the result of a user custom calculation falls within
the user-defined limits This outlier applies to all target compounds in all sample types.

This outlier metric is determined by comparing the value of the

UserCustomCalculation column in the Target Compound table, treated as a double-
precision floating-point number, against the user-defined limits
UserCustomCalculationLimitLow and UserCustomCalculationLimitHigh.
The outlier is set too High if
UserCustomCalculation > UserCustomCalculationLimitHigh

The outlier is set too Low if

UserCustomCalculation < UserCustomCalculationLimitLow

236 Quantitative Analysis Quantitation DataSet

 Outliers

When the outlier is set, the UserCustomCalculation column of the Target Compound
table is highlighted.
For the outlier to activate, the following columns must be set in the Quantitation Method Editor:

• UserCustomCalculationLimitLow
• UserCustomCalculationLimitHigh

Quantitative Analysis Quantitation DataSet 237