MS-GFDB protocols
MS-GFDB specifications
Information
| Unique identifier | OMICS_02465 |
|---|---|
| Name | MS-GFDB |
| 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
library_books
The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search.
2010 Mol Cell Proteomics
PMCID: 3101864
PMID: 20829449
DOI: 10.1074/mcp.M110.003731
MS-GFDB IN pipeline
2013
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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