Matrix Science header

Fixed values for quantitation.xml
[Mascot configuration files module]

Some attributes and element values in quantitation.xml are restrictions of the string-type and can accept one of the fixed values defined in a special enumeration-list.

Type mqm:calcType

How to calculate a ratio for a protein
List of values

ValueDescription
medianProtein ratio is the median of the peptide ratios
averageProtein ratio is the unweighted average of the peptide ratios
weightedProtein ratio is the weighted average of the peptide ratios

Type mqm:correctionTypeType

Isotope correction factor
List of values

ValueDescription
AB certificatePercentage isotopic impurities for each reagent as tabulated on a Certificate of Analysis.
averagineMass dependent isotope overlap. Isotope purity specified using element attribute of correction
impurityIsotope under-enrichment

Type mqm:integrationMethodType

Integration method
List of values

ValueDescription
noneNo integration
simpsonsNumerical integration using Simpsons rule
trapeziumNumerical integration using the trapezium rule

Type mqm:ionSeriesType

Symbols for sequence ion series
List of values

ValueDescription
aa series fragment ions
bb series fragment ions
cc series fragment ions
xx series fragment ions
yy series fragment ions
zz series fragment ions
z+1-
z+2-

Type mqm:modeType

Specificity for a group of modifications
List of values

ValueDescription
fixedQuantitative modification
variableNon-quantitative modification
exclusiveA given peptide may carry one or the other set of modifications, but never a mixture of both

Type mqm:normaliseType

normalisation method
List of values

ValueDescription
noneNo normalisation
sum(Reporter protocol only) The total intensity of each reporter ion, summed across all MS/MS spectra, is made equal
averageFor each ratio, the geometric mean of all reported values for peptide matches is made unity
medianFor each ratio, the median of all reported values for peptide matches is made unity

Type mqm:outlierType

method of detecting outliers
List of values

ValueDescription
noneNo outlier removal
dixonsDetect and remove outliers using Dixon's method
autoDetect and remove outliers using Dixon's method or Rosner's method according to the number of values
grubbsDetect and remove outliers using Grubb's method
rosnersDetect and remove outliers using Rosner's method

Type mqm:positionType

Unimod position
List of values

ValueDescription
AnywhereUnrestricted
Any N-termModification only if residue or terminus is at peptide N-term
Any C-termModification only if residue or terminus is at peptide C-term
Protein N-termModification only if residue or terminus is at N-term of intact protein
Protein C-termModification only if residue or terminus is at C-term of intact protein

Type mqm:proteinScoreType

Mascot protein score method
List of values

ValueDescription
standardUse Mascot standard protein scoring
mudpitUse Mascot mudpit protein scoring

Type mqm:scanType

Data source for integration
List of values

ValueDescription
surveyPrecursor peak area from survey scan
zoomPrecursor peak area from zoom scan
headerXIC value taken from file header
fragmentsSum of fragment peak areas from MS/MS scan
mrmMultiple reaction monitoring

Type mqm:siteType

Unimod site
List of values

ValueDescription
AAlanine
CCysteine
DAspartic acid
EGlutamic acid
FPhenylalanine
GGlycine
HHistidine
IIsoleucine
JUnassigned
KLysine
LLeucine
MMethionine
NAsparagine
OUnassigned
PProline
QGlutamine
RArginine
SSerine
TThreonine
USelenocysteine
VValine
WTryptophan
YTyrosine
N-termAmino terminus
C-termCarboxy terminus

Type mqm:thresholdType

Significance threshold for peptide matches
List of values

ValueDescription
minimum scoreSignificance threshold for peptide matches is a minimum score
maximum expectSignificance threshold for peptide matches is a maximum expectation value
at least identitySignificance threshold for peptide matches is score at or above identity threshold
at least homologySignificance threshold for peptide matches is score at or above homology threshold

Type mqm:timeUnitType

time units
List of values

ValueDescription
secondsseconds
minutesminutes
%Fraction expressed as parts per 100
ppmFraction expressed as parts per million

Type mqm:averageSelectionType

List of allowed values for selection-attribute
List of values

ValueDescription
unique_sequencePeptides to be used for quantitation are required to be unique sequences
unique_mrAccept different modification states of same sequence
unique_mzAccept peptides with same sequence and modifications in different charge states

Type mqm:reporterTolUnitType

Units for reporter_tol
List of values

ValueDescription
DaDaltons
ppmppm
mmummu
%%
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:51