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

Value	Description
median	Protein ratio is the median of the peptide ratios
average	Protein ratio is the unweighted average of the peptide ratios
weighted	For each component, the intensity values are summed over the set of peptides and the protein ratio is calculated from the summed values

Type mqm:correctionTypeType

Isotope correction factor
List of values

Value	Description
AB certificate	Percentage isotopic impurities for each reagent as tabulated on a Certificate of Analysis.
averagine	Mass dependent isotope overlap. Isotope purity specified using element attribute of correction
impurity	Isotope under-enrichment

Type mqm:integrationMethodType

Integration method
List of values

Value	Description
none	No integration
simpsons	Numerical integration using Simpsons rule
trapezium	Numerical integration using the trapezium rule

Type mqm:ionSeriesType

Symbols for sequence ion series
List of values

Value	Description
a	a series fragment ions
b	b series fragment ions
c	c series fragment ions
x	x series fragment ions
y	y series fragment ions
z	z series fragment ions
z+1	-
z+2	-

Type mqm:modeType

Specificity for a group of modifications
List of values

Value	Description
fixed	Quantitative modification
variable	Non-quantitative modification
exclusive	A 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

Value	Description
none	No normalisation
sum	(Reporter protocol only) The total intensity of each reporter ion, summed across all MS/MS spectra, is made equal
average	For each ratio, the geometric mean of all reported values for peptide matches is made unity
median	For each ratio, the median of all reported values for peptide matches is made unity

Type mqm:outlierType

method of detecting outliers
List of values

Value	Description
none	No outlier removal
dixons	Detect and remove outliers using Dixon's method
auto	Detect and remove outliers using Dixon's method or Rosner's method according to the number of values
grubbs	Detect and remove outliers using Grubb's method
rosners	Detect and remove outliers using Rosner's method

Type mqm:positionType

Unimod position
List of values

Value	Description
Anywhere	Unrestricted
Any N-term	Modification only if residue or terminus is at peptide N-term
Any C-term	Modification only if residue or terminus is at peptide C-term
Protein N-term	Modification only if residue or terminus is at N-term of intact protein
Protein C-term	Modification only if residue or terminus is at C-term of intact protein

Type mqm:proteinScoreType

Mascot protein score method
List of values

Value	Description
standard	Use Mascot standard protein scoring
mudpit	Use Mascot mudpit protein scoring

Type mqm:scanType

Data source for integration
List of values

Value	Description
survey	Precursor peak area from survey scan
zoom	Precursor peak area from zoom scan
header	XIC value taken from file header
fragments	Sum of fragment peak areas from MS/MS scan
mrm	Multiple reaction monitoring

Type mqm:siteType

Unimod site
List of values

Value	Description
A	Alanine
C	Cysteine
D	Aspartic acid
E	Glutamic acid
F	Phenylalanine
G	Glycine
H	Histidine
I	Isoleucine
J	Unassigned
K	Lysine
L	Leucine
M	Methionine
N	Asparagine
O	Unassigned
P	Proline
Q	Glutamine
R	Arginine
S	Serine
T	Threonine
U	Selenocysteine
V	Valine
W	Tryptophan
Y	Tyrosine
N-term	Amino terminus
C-term	Carboxy terminus

Type mqm:thresholdType

Significance threshold for peptide matches
List of values

Value	Description
minimum score	Significance threshold for peptide matches is a minimum score
maximum expect	Significance threshold for peptide matches is a maximum expectation value
at least identity	Significance threshold for peptide matches is score at or above identity threshold
at least homology	Significance threshold for peptide matches is score at or above homology threshold

Type mqm:timeUnitType

time units
List of values

Value	Description
seconds	seconds
minutes	minutes
%	Fraction expressed as parts per 100
ppm	Fraction expressed as parts per million

Type mqm:averageSelectionType

List of allowed values for selection-attribute
List of values

Value	Description
unique_sequence	Peptides to be used for quantitation are required to be unique sequences
unique_mr	Accept different modification states of same sequence
unique_mz	Accept peptides with same sequence and modifications in different charge states

Type mqm:reporterTolUnitType

Units for reporter_tol
List of values

Value	Description
Da	Daltons
ppm	ppm
mmu	mmu
%	%