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 | Protein ratio is the weighted average of the peptide ratios |
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 |
| % | % |
