MS-GFDB protocols

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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

MS-GFDB in pipeline

2013
PMCID: 3759415
PMID: 24023794
DOI: 10.1371/journal.pone.0072939

[…] 400. mass spectra were processed with xcalibur 2.0.7 (thermo fisher scientific) and peak lists were generated with msconvert (version 3.0.4388) . 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 […]


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MS-GFDB in publications

 (4)
PMCID: 4842269
PMID: 27107716
DOI: 10.1186/s12864-016-2602-9

[…] medium, [], and in symbiosis with soybean (g. max, []), cowpea (v. unguiculata) or siratro (m. atropurpureum) [] was re-analyzed as follows: fragment ion mass spectra were searched with ms-gf+ (ms-gfdb v9979, []) against a protein database containing sequences of 8317 b. japonicum usda 110 proteins, 2857 shorter orfs and 194 longer orfs, 1391 newly predicted orfs, 5894 protein sequences […]

PMCID: 4012837
PMID: 24742327
DOI: 10.1021/pr4011684

[…] database. we used bioworks/sequest (thermo electron; version 3.3.1 sp1), x!tandem with k-score (version 2009.10.01.1 labkey and isb, included in tpp 4.3.1 package),, inspect (version 20100331), and ms-gfdb (version 06/16/2011) for the database search. we used the same search parameters as described previously except that ms-gfdb was newly added for the current study (with the settings –t 300 […]

PMCID: 4264622
PMID: 24620897
DOI: 10.1021/jf405601e

[…] all tandem ms from each data file were exported as mascot generic files (.mgf) with a peptide isotope model and a maximum charge state of +9., peptide identification was accomplished using both the ms-gfdb (via a command-line interface) and x!tandem (using the downloadable graphical user interface). the human milk library used in both searches was constructed on the basis of a query […]

PMCID: 3489529
PMID: 23176207
DOI: 10.1186/1471-2105-13-S16-S2

[…] come from peptides and typically interpreted using a database search engine. there are numerous database search engines available such as sequest [], mascot [], x!tandem [], omssa [], inspect [] and ms-gfdb []. these engines take a set of spectra and a protein database as the input and output peptide-spectrum matches (psms) by scoring each spectrum against the peptides in the database […]


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

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