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MS-GF+ specifications


Unique identifier OMICS_02525
Name MS-GF+
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline Pavel Pevzner

Publication for MS-GF+

MS-GF+ citations


Hookworm Secreted Extracellular Vesicles Interact With Host Cells and Prevent Inducible Colitis in Mice

Front Immunol
PMCID: 5936971
PMID: 29760697
DOI: 10.3389/fimmu.2018.00850
call_split See protocol

[…] is genome (PRJEB511) with the common repository of adventitious proteins (cRAP) appended to it. Database search was performed using Mascot Versions 2.4 (Matrix Science Ltd., London, UK) and X!Tandem, MS-GF+, OMSSA, and Tide search engines using SearchGUI (). The same parameters were used as described in Ref. ().The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consor […]


Profiling plasma extracellular vesicle by pluronic block copolymer based enrichment method unveils features associated with breast cancer aggression, metastasis and invasion

J Extracell Vesicles
PMCID: 5912199
PMID: 29696079
DOI: 10.1080/20013078.2018.1458574
call_split See protocol

[…] een 2 and 7.ProteoWizard [] was used for peak-picking, filtering out peaks with intensity less than 100 and converting the file to mzML format. Protein search and identifications were performed using MS-GF+ [] search engine on Homo sapiens (Uniprot TaxID¬†=¬†9606). For semi-quantification analysis, algorithm was establish according to the previous normalized spectra index algorithm [,] with modifica […]


The NISTmAb tryptic peptide spectral library for monoclonal antibody characterization

PMCID: 5916550
PMID: 29425077
DOI: 10.1080/19420862.2018.1436921

[…] Peptides containing metal ion adducts are common low abundance artifacts in electrospray ionization (ESI). A total of 191 such spectra with sodium, calcium, or iron were identified by MS-GF+, half of them with low scores. The most common such peptide ion adduct was sodium; 59 sodiated ions were identified. Examination of adduct fragmentation behavior showed that the metal atom did […]


Proteomic Analysis of Combined Gemcitabine and Birinapant in Pancreatic Cancer Cells

Front Pharmacol
PMCID: 5827530
PMID: 29520231
DOI: 10.3389/fphar.2018.00084

[…] The individual raw files (.raw) generated by LC-MS analysis were matched to the human database containing 23,306 entries, using the MS-GF+ searching engines (released on May 17, 2013) (). The search parameters set were as follows: (1) precursor ion mass tolerance: 20 ppm; (2) instrument: Q-Exactive; (3) one match per spectrum is a […]


Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy P Framework

PMCID: 5874766
PMID: 29385081
DOI: 10.3390/proteomes6010007

[…] dy deployed in Galaxy, utilizing X!Tandem as the sequence database search algorithm of choice. Although the Galaxy-deployed SearchGUI tool offers the use of multiple database search algorithms (e.g., MS-GF+, Myrimatch, OMSSA, Comet, Myrimatch, MS-Amanda and Novor), X!Tandem was determined to have a balance of speed and sensitivity that made it a good choice, especially for a training resource. The […]


The proteomic response of the reef coral Pocillopora acuta to experimentally elevated temperatures

PLoS One
PMCID: 5792016
PMID: 29385204
DOI: 10.1371/journal.pone.0192001

[…] ts exist []. Given that the actual translation of these mRNAs was not observed, it cannot be known which splice variants were actually translated into proteins. Like Mascot (Matrix Sciences), MS-SCAN/MS-GF+ makes guesses about protein identity based on querying translated transcriptomes; no coral proteomes have been sequenced at present, and only a partial sea anemone proteome (~3,000 proteins fro […]


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MS-GF+ institution(s)
Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA; Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands; Netherlands Proteomics Centre, Utrecht, Netherlands; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
MS-GF+ funding source(s)
This work was supported by National Institutes of Health Grant 1-P41-RR024851 from the National Center for Research Resources.

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