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
File from which derived
filtering criteria applied to data
number preceding filter generations
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
analysis and id must be unique within a search_hit
Unique identifier to search summary
first scan number integrated into MS/MS spectrum
last scan number integrated into MS/MS spectrum
retention time associated with start_scan
Precursor ion charge used for search
Search constraint applied specifically to this query
Unique identifier
search_id must be unique within each msms_run_summary
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)
analysis_timestamp analysis and time must be unique within each msms_run_summary
search_id within each search_hit must correspond with that of a search_summary
analysis and id in analysis_result must correspond with those in an analysis_timestamp element
Summary name (currently not used)
Date pepXML file was written
Full path self reference
time and analysis within timestamp must correspond with those within analysis_summary element
search_summary base_name (mzXML file) must be unique within document
spectrum_query index must be unique in document
Summary information for PeptideProphet analysis
Input file
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
PeptideProphet validation results for search hit
ASAPRatio quantitation results for search hit
minimum number of termini compaitble with enzyme used (should correspond with search enzyme constraint)
Quantitation
Combined datasets
Input file
Self reference
Directory of self
libra quantitation for search hit
integrated mass intensity
mass channel number
mass of channel
absolute integrated intensity
normalized integrated intensity (normalization channel stored in libra_summary)
whether or not to reject this ratio as valid
whether or not to reject this ratio as valid
channel number must be unique
summary info for libra quantitation analysis
quantitation channel
channel number
channel mass
mass offset from mz value
isotopic contributions from one channel to others
channel donor
channel recipient
channel number
fraction of affected channel due to contributing
channel number
channel mass width
channel used as denominator for normalized integrated intensities (0 means use channel with strongest absolute integrated intensity)
concatenated channel masses (used as signature for defined channel masses)
contributing channel numbers must correspond with defined channels
contributing channel numbers must correspond with defined channels