For better experience, turn on JavaScript!

PeptideShaker
Home » Tools » Proteomics tools and software » PeptideShaker

PeptideShaker

PeptideShaker is a tool to interpret, validate, map, GO enrich, plot, and re-analyze results from peptide identification platform tools, such as X!Tandem, MS Amanda, MS-GF+, MyriMatch, Andromeda, Comet, Tide, Mascot, OMSSA, and mzIdentML. The PeptideShaker algorithm has functions for
1. Detailed overview,
2. Comparison of search tools performance,
3. Inspection of originating fractions,
4. view post-translational modifications,
5. Mapping peptides to PDB structures,
6. Finding GO terms,
7. Finetuning the validation,
8. QC plotting,
9. Re-analyze public datasets in PRIDE.



PeptideShaker

PeptideShaker is a tool to interpret, validate, map, GO enrich, plot, and re-analyze results from peptide identification platform tools, such as X!Tandem, MS Amanda, MS-GF+, MyriMatch, Andromeda, Comet, Tide, Mascot, OMSSA, and mzIdentML. The PeptideShaker algorithm has functions for
1. Detailed overview,
2. Comparison of search tools performance,
3. Inspection of originating fractions,
4. view post-translational modifications,
5. Mapping peptides to PDB structures,
6. Finding GO terms,
7. Finetuning the validation,
8. QC plotting,
9. Re-analyze public datasets in PRIDE.

Topic

Proteomics; Proteomics experiment; Proteome

Details

  • Operation: Mass spectrum visualisation; Label-free quantification; Protein quantification; Target-Decoy
  • Input: FASTA; Peptide identification mzIdentML; Mass spectrometry data MGF
  • Output: Protein structure image JPG, SVG; GO-term enrichment data Txt; Sequence image; Protein report TSV
  • Software interface: Command-line user interface; Graphical user interface
  • Language: Java
  • Operating system: Linux; Mac OS X
  • License: Apache License v2
    • Cost: Free
  • Version name: 1.16.45
    • Maturity: Mature
  • Credit: The Ministerium für Innovation, Wissenschaft und Forschung des Landes Nordrhein-Westfalen, the Bundesministerium für Bildung und Forschung Ghent University, the European Union 7th Framework Program, the Research Council of Norway, the Kristian Gerhard Jebsen Foundation.
  • Contact: lennart.martens _at_ UGent.be
  • Collection: -

Publications

Vaudel M, Burkhart JM, Zahedi RP, Oveland E, Berven FS, Sickmann A, Martens L, Barsnes H "PeptideShaker enables reanalysis of MS-derived proteomics data sets." Nat Biotechnol, 2015 https://doi.org/10.1038/nbt.3109
PMID: 25574629


Download and documentation







If you find errors, please report here.

SECTIONS

Tutorials
In-house software
Blog
News
Find Jobs
History
Definition of Bioinformatics
ENCYCLOPEDIA
COVID-19
⚬ Timeline of outbreak
⚬ Blog
⚬ Scientific Facts
⚬ Daily statistics
⚬ News


TOOLS


1. SNP Tools
2. GWAS Tools
3. Genotype Imputation Tools
4. MSA tools
5. CNV tools
6. WGA tools
7. RNA-seq tools
8. Proteomics Tools
9. Nucleic Acid Structure Analysis Tools
10. Nucleic Acid Sequence Analysis Tools
11. Sequence Logo Tools
12. In-house Software Tools

Find thousands of Bioinformatics and Life Science software tools and databases in the newly launched




Ads