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 Protein ratio is the weighted average of the peptide ratios 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. 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