Configuration file for Mascot quantitation methods
How to calculate a ratio for a protein
Protein ratio is the median of the peptide ratios
Protein ratio is the unweighted average of the peptide ratios
For each component, the intensity values are summed over the set of peptides and the protein ratio is calculated from the summed values
Data for individual peak
Reporter ion m/z
Can be variable or exclusive, with maximum of one exclusive group
Element for non-SILAC metabolic labelling. Applies to residues only.
Data file identifier (replicate)
Isotope and impurity correction factors for this component
Modification group that defines satellite peaks to be summed into the heaviest component to correct for Arg-Pro conversion of SILAC label.
Used to identify this component in the expression for a ratio
Specifies which element should be substituted by which isotope. Empty element means "no substitutions".
Isotope to be replaced, usually the most abundant natural isotope of the element
Isotopic label
Unimod composition
Chemical element reference
Isotope correction factor
Percentage isotopic impurities for each reagent as tabulated on a Certificate of Analysis.
Mass dependent isotope overlap. Isotope purity specified using element attribute of correction
Isotope under-enrichment
symbols for elements
Integration method
No integration
Numerical integration using Simpsons rule
Numerical integration using the trapezium rule
Symbols for sequence ion series
a series fragment ions
b series fragment ions
c series fragment ions
x series fragment ions
y series fragment ions
z series fragment ions
Composition based modification definition
Unimod style specificity
The modification delta defined as a composition
Artefact peaks associated with this modification
Name conforming to Mascot modification naming rules
Schema minor version number
Specificity for a group of modifications
Quantitative modification
Non-quantitative modification
A given peptide may carry one or the other set of modifications, but never a mixture of both
normalisation method
No normalisation
(Reporter protocol only) The total intensity of each reporter ion, summed across all MS/MS spectra, is made equal
For each ratio, the geometric mean of all reported values for peptide matches is made unity
For each ratio, the median of all reported values for peptide matches is made unity
method of detecting outliers
No outlier removal
Detect and remove outliers using Dixon's method
Detect and remove outliers using Dixon's method or Rosner's method according to the number of values
Detect and remove outliers using Grubb's method
Detect and remove outliers using Rosner's method
Parameter name and value pair
Name and value pair
Unimod position
Unrestricted
Modification only if residue or terminus is at peptide N-term
Modification only if residue or terminus is at peptide C-term
Modification only if residue or terminus is at N-term of intact protein
Modification only if residue or terminus is at C-term of intact protein
Mascot protein score method
Use Mascot standard protein scoring
Use Mascot mudpit protein scoring
A ratio to be reported
Each component has a coefficient to allow linear combinations to be specified.
Each component has a coefficient to allow linear combinations to be specified.
Descriptive label suitable for use in a report, e.g. 117/114. Must be unique
Data source for integration
Precursor peak area from survey scan
Precursor peak area from zoom scan
XIC value taken from file header
Sum of fragment peak areas from MS/MS scan
Multiple reaction monitoring
Unimod site
Alanine
Cysteine
Aspartic acid
Glutamic acid
Phenylalanine
Glycine
Histidine
Isoleucine
Unassigned
Lysine
Leucine
Methionine
Asparagine
Unassigned
Proline
Glutamine
Arginine
Serine
Threonine
Selenocysteine
Valine
Tryptophan
Tyrosine
Amino terminus
Carboxy terminus
Significance threshold for peptide matches
Significance threshold for peptide matches is a minimum score
Significance threshold for peptide matches is a maximum expectation value
Significance threshold for peptide matches is score at or above identity threshold
Significance threshold for peptide matches is score at or above homology threshold
time units
seconds
minutes
Fraction expressed as parts per 100
Fraction expressed as parts per million
Type created to simplify xml validation
Number of peptides per protein to be used for Average protocol quantitation
Whether to require the peptides to be used for quantitation to be unique sequences, or to accept different modification states of same sequence (unique_mr), or even accept peptides with same sequence and modifications in different charge states (unique_mz).
Database accession for reference protein.
Name of database of reference protein.
Amount of reference protein.
List of allowed values for selection-attribute
Peptides to be used for quantitation are required to be unique sequences
Accept different modification states of same sequence
Accept peptides with same sequence and modifications in different charge states
Type created to simplify xml validation
Type created to simplify xml validation
Type created to simplify xml validation
Used with type=AB certificate, e.g -1
Type of isotope correction
Used with type=impurity, e.g. 18O
Modification group that defines satellite peaks to be summed into the heaviest component to correct for Arg-Pro conversion of SILAC label.
Variable only
Type created to simplify xml validation
Symbol for element or isotope
Count for this element or isotope. Can be negative
Type created to simplify xml validation
Type created to simplify xml validation
Type created to simplify xml validation
Integration algorithm
Scan type containing data to be integrated
True to allow the components in a ratio to have shifted elution times
Maximum elution time difference allowed when trying to pair up components
Units for elution_time_delta
Threshold on the standard error for a straight line fit of the component intensities from each of the scans in the XIC peak.
Threshold on the correlation coefficient between the predicted and observed precursor isotope distributions.
The start and end of an XIC peak are where the intensity drops to this fraction of the intensity of the XIC peak maximum.
Upper limit on the number of survey scans in an XIC peak
XIC peak is smoothed by a set of 2n+1 Savitzky-Golay convolution integers, where n is this value, (0 corresponds to no smoothing).
True to extend the mass and time matching to cover contiguous charge states
When all_charge_states is true, additional contiguous charge states are included in quantitation if their intensity exceeds this fraction of the the most intense charge state for which there is a database match.
If true, calculate ratio from integrated areas. If false, ratio is gradient of straight line fit to areas from individual spectra
Type created to simplify xml validation
Type created to simplify xml validation
Type created to simplify xml validation
Can be fixed or variable, but not exclusive
Identifies a component used to calculate a ratio.
Ratio to be reported
Exclude peptides from quantitation if they contain modifications from this group
Sequence qualifier in Mascot notation, e.g. *-TSL
Composition qualifier in Mascot notation, e.g. *[C]
Quality thresholds for selecting individual spectra or matches
Method and parameters to be used to integrate precursor over time. If missing, no integration is performed
Method and parameters to be used to remove outliers. If missing, no outlier removal is performed
Method of normalising ratios for a complete data set. If missing, no normalisation is performed
How the quantitative information is obtained
Descriptive name that will appear in drop down lists, etc.
If any modification group specifies exclusive mode, then apply this constraint during the search so that only matches that can be used for quantitation will be returned.
Method of calculating the ratio for the protein from the individual peptide ratios.
Whether to display quantitation results at the peptide match level
Minimum number of peptide matches for reporting quantitation at protein level
standard or mudpit
Mascot score significance threshold as a probability
Whether to show proteins which contain a sub-set of peptide matches
Only show proteins that contain a least one "bold red" peptide match
Free text string for description
Type created to simplify xml validation
Type created to simplify xml validation
Type created to simplify xml validation
A Mascot modification name
Unimod style specificity for an unmodified residue or terminus
A complete modification definition
Used to identify the modification group in an exclusion element
One of fixed, variable or exclusive. Applies to all the modifications in the group
Modification required for a peptide to be assigned to a component.
Type created to simplify xml validation
Monoisotopic m/z
Average m/z
Type created to simplify xml validation
Fragment ion series (multiplex)
Label allowed at terminus only
Fragment ion intensity threshold as fraction of base peak
Exclude fragment ions which have a potential isobaric interferences
Minimum number of fragment ion pairs required before a peptide match is used for quantitation
Type created to simplify xml validation
If false, neutral loss peaks can be used for Mascot scoring. If true, neutral loss peaks are weak satellite peaks that should not be used for scoring the match
Choice of lists of peptide sequences or protein accessions. If an element of either is defined, then normalisation is based on the specified peptide(s) or protein(s) rather than complete dataset. For example, if protein was set to ALBU_BOVIN, and this was found in the search, then normalisation would ensure that the protein ratio for this protein was 1. Cannot have both peptides and proteins, only one list can be populated. If peptide or protein not in report, then no normalisation.
Peptide sequence(s) to be used for normalisation
Protein accession(s) to be used for normalisation
Name of normalisation procedure. Sum only available for reporter protocol; average and median may only available when all protein hits are processed
Peptide sequence(s) to be used for normalisation
A peptide sequence to be used for normalisation
Protein accession(s) to be used for normalisation
A protein accession to be used for normalisation
Type created to simplify xml validation
Peptide sequence
Type created to simplify xml validation
Protein accession
Type created to simplify xml validation
component name
Coefficient used to form linear combination of values
Type created to simplify xml validation
Outlier detection algorithm
Type created to simplify xml validation
Type created to simplify xml validation
Name of the parameter
Free text description of this parameter
Type created to simplify xml validation
True if this is a required neutral loss
Type created to simplify xml validation
If false, we only report a ratio if we have peptide matches to both components. Also, if false, then all_charge_states treated as false, even if true in method. Should usually be set true.
Type created to simplify xml validation
No quantitation
Use intensities of specific reporter ion fragment peaks within an MS/MS spectrum
Use intensities of precursors within a single dataset
Use intensities of sequence ion fragment peaks within an MS/MS spectrum
Use intensities of precursors from multiple datasets
Use average intensities of precursors in a database search result
Type created to simplify xml validation
Unsigned integer, corresponding to abs(charge)
Determines whether to perform test for matched_fraction.
Hsu, J. L., et al., Beyond quantitative proteomics: Signal enhancement of the a(1) ion as a mass tag for peptide sequencing using dimethyl labeling, Journal of Proteome Research 4 101-108 (2005)
Type of significance threshold for peptide matches
Value of significance threshold for peptide matches (only used by certain threshold types)
If true, only report ratios for peptide sequences that are unique to one protein hit (which may be a family containing multiple proteins)
Threshold on the fraction of the peak area in the precursor region accounted for by the components.
Determines whether to perform test for total intensity of fitted peaks across the XIC peak.
Threshold on the total intensity of fitted peaks across the XIC peak.
Type created to simplify xml validation
A complete method, identified by a descriptive name
Major version number
Minor version number
Type created to simplify xml validation
Type created to simplify xml validation
Type created to simplify xml validation
Mass tolerance to be used for matching reporter ion peaks.
Units for reporter_tol (Da ppm mmu %)
Units for reporter_tol
Daltons
ppm
mmu
%
Type created to simplify xml validation
Type created to simplify xml validation
Type created to simplify xml validation
A neutral loss for the sequence ions, e.g. loss of phosphate
A neutral loss from the precursor
Residue code or terminus label
E.g. Anywhere
Type created to simplify xml validation
Residue code or terminus label
E.g. Anywhere