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