MS-GFDB protocols

MS-GFDB specifications


Unique identifier OMICS_02465
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data It takes a set of spectra (CID, ETD, or CID/ETD pairs) and a protein database as an input and outputs peptide matches. If the input is a set of CID/ETD pairs, it outputs the best scoring peptide matches and their p values (1) using only CID spectra, (2) using only ETD spectra, and (3) using combined spectra of CID/ETD pairs.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for MS-GFDB

MS-GFDB IN pipeline

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

[…] 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). spectra […]

MS-GFDB institution(s)
Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA

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