MS/MS pipeline analysis schema. Developed by ISB proteome center. Summary of analysis subjected to run(s) Wildcard for summary info customized for a particular analysis Time analysis complete (unique id) Name of analysis program Release Source and filtering criteria used to generate dataset filtering criteria applied to data Search results for LC/MS/MS run Defines the net cleavage specificity of an enzyme, chemical reagent, or a mixture of these, for mass spectrometry purposes Component cleavage specificity. Must be at least one specificity unless enzymeType:fidelity is nonspecific Defines whether cleavage occurs on the C-terminal or N-terminal side of the residue(s) listed in cut minimum separation between adjacent cleavages One or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site Zero or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site Controlled code name for the enzyme that can be referred to by applications Free text to describe alternative names, special conditions, etc. Semispecific means that at least one end of a pepide must conform to the cleavage specificity, (unless the peptide was at the terminus of the parent sequence). Nonspecific means that neither end of a peptide must conform to the cleavage specificity. If there are multiple specificities and independent is true, then a single peptide cannot exhibit one specificity at one terminus and a different specificity at the other. If independent is false, then a single peptide can exhibit mixed specificities. Database search settings Full path address of database on local computer Database type (AA=amino acid, NA=nucleic acid) Required peptide termini Maximum number of enzyme cleavage sites allowable within peptide Minimum number of termini compatible with enzymatic cleavage Required amino acid string Required amino acid string Modified aminoacid, static or variable Mass difference with respect to unmodified aminoacid, must begin with either + (nonnegative) or - [e.g. +1.05446 or -2.3342] Mass of modified aminoacid Y if both modified and unmodified aminoacid could be present in the dataset, N if only modified aminoacid can be present whether modification can reside only at protein terminus (specified 'n', 'c', or 'nc') Special symbol used by search engine to designate this modification Y if each peptide must have only modified or unmodified aminoacid, N if a peptide may contain both modified and unmodified aminoacid Modification to the N or C terminus, static or variable n for N-terminus, c for C-terminus Mass difference with respect to unmodified terminus Mass of modified terminus Y if both modified and unmodified terminus could be present in the dataset, N if only modified terminus can be present Special symbol used by search engine to designate this modification whether modification can reside only at protein terminus (specified n or c) Full path location of mzXML file for this search run (without the .mzXML extension) SEQUEST, Mascot, COMET, etc average or monoisotopic average or monoisotopic Format of file storing the runner up peptides (if not present in pepXML) runner up search hit data type extension (e.g. .tgz) matches id in search hit Reference for analysis applied to current run (time corresponds with analysis_summary/@time, id corresponds with analysis_result/@id) Wildcard for timestamp info customized for a particular analysis Date of analysis Analysis name Unique identifier for each type of analysis MS/MS spectrum, precursor ion charge and mass Peptide assignment Other protein in search database that contains peptide Positions and masses of modifications modified aminoacid position in peptide [ranging from 1 to peptide length] modified mass of aminoacid Mass of modified N terminus Mass of modified C terminus Peptide sequence (with indicated modifications) Wildcard for result info customized for a particular analysis Peptide aminoacid sequence (with no indicated modifications) Aminoacid preceding peptide (- if none) Aminoacid following peptide (- if none) Number of unique proteins in search database containing peptide Number of peptide fragment ions found in spectrum Number of peptide fragment ions predicted for peptide Mass(precursor ion) - Mass(peptide) Number of peptide termini consistent with cleavage by sample enzyme Number of sample enzyme cleavage sites internal to peptide Potential use in future for user manual validation (0 or 1) Extracted from search database Unique identifier to search summary first scan number integrated into MS/MS spectrum last scan number integrated into MS/MS spectrum Precursor ion charge used for search Search constraint applied specifically to this query Unique identifier full path file name of mzXML (minus the .mzXML) raw data type extension (e.g. .mzXML) raw data type extension (e.g. .mzXML) Manufacturer of MS/MS instrument Instrument model (cf mzXML) Instrument model (cf mzXML) Ion trap, etc (cf mzXML) EMT, etc(cf mzXML) Summary name (currently not used) Date pepXML file was written Full path self reference Validation of search results Filter threshold Predicted sensitivity Predicted false positive error rate Predicted number of correct results passing filter Predicted number of incorrect results passing filter Predicted false positive error rate Filter threshold Predicted number of correct results passing filter Predicted number of incorrect results passing filter Discriminant Score (fval) bin Number of 1+ spectra Inferred number of correct 1+ spectra Inferred number of incorrect 1+ spectra Number of 2+ spectra Inferred number of correct 2+ spectra Inferred number of incorrect 2+ spectra Number of 3+ spectra Inferred number of correct 3+ spectra Inferred number of incorrect 3+ spectra Fraction of results inferred to be correct Number of input spectra Number of EM interations prior to convergence Min probability to be included in output User specified run options Total inferred number of correct results Quantitation Elution order of light vs heavy labeled peptide Aminoacids and termini that are differentially labeled for quantitaiton Y if dataset is all light or heavy labeled, N if dataset is mixed heavy and light labeled Quantitation Validation Quantitation Quantitation Combined datasets