MS-GF pipeline

MS-GF specifications


Unique identifier OMICS_21812
Name MS-GF
Alternative name MS GeneratingFunction
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A peptide-spectrum match.
Output data A p-values (spectral probabilities) of spectral interpretations.
Output format MGF
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Requirements JRE
Maintained Yes



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  • person_outline Pavel Pevzner <>
  • person_outline Sangtae Kim <>

Publication for MS GeneratingFunction

MS-GF IN pipelines

PMCID: 4843095
PMID: 27200004
DOI: 10.3389/fpls.2016.00517

[…] ppm and fragmentation tolerance for hcd (higher energy collisional dissociation) was 0.05 da. all peptides were identified with < 1% false discovery rate by using an ms-generating function score (ms-gf) < 1e-10 and a decoy database searching strategy (kim et al., 2008, 2010; granholm et al., 2014). modifications were searched looking for static alkylation on cysteine and 8 plex itraq […]

PMCID: 4638048
PMID: 26269333
DOI: 10.1074/mcp.O115.048777

[…] gio., searching the acquired ms/ms data against a fasta file concatenated from the complete uniprot proteomes of human (including isoforms) and adenovirus type 5, 26,401 peptides were found by ms-gf+, which mapped to 3,015 proteins (2997 human and 18 human adenovirus). these figures (provided in table i), and the list of identified proteins that they represent, are comparable […]

PMCID: 3759415
PMID: 24023794
DOI: 10.1371/journal.pone.0072939

[…] m/z 400. mass spectra were processed with xcalibur 2.0.7 (thermo fisher scientific) and peak lists were generated with msconvert (version 3.0.4388) [59]. fragment ion mass spectra were searched with ms-gf+ (ms-gfdb v7747) against a sequence database consisting of 7,258 b. cenocepacia strain h111 proteins (accession cafq00000000.1) and 259 common contaminants (e.g. human keratin, trypsin). […]

MS-GF institution(s)
Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA; Bioinformatics Program, University of California San Diego, La Jolla, CA, USA
MS-GF funding source(s)
Supported by National Institutes of Health Grant NIGMS 1-R01-RR16522; and by Howard Hughes Medical Institute Professor Award.

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