PeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data!
PeptideShaker currently supports nine different analysis tasks:
Figure 2: The PeptideShaker overview tab, showing all proteins in the data set, along with the peptides and peptide-to-spectrum matches for the selected protein and peptide. PeptideShaker further processes PSM information from SearchGUI. This processing includes PSM quality control, statistical analysis and FDR estimation, post-translational modification localization scoring, protein inference from PSMs, as well as organization and annotation for viewing of the output. 【6】蛋白质组学鉴定定量软件之MaxQuant 1.简介. 2016年，德国马普所的Cox和蛋白质组学领域巨擘Matthias Mann合作开发了MaxQuant软件（MQ），并发表在nbt上，protocol也相应发表在nature protocols上。.
- Overview: get a simple yet detailed overview of all the proteins, peptides and PSMs in your dataset.
- Spectrum IDs: compare the search engine performance and see how the search engine results are combined.
- Fractions: inspect from which fractions proteins and peptides are likely to come from.
- Modifications: get a detailed view of the post-translational modifications in the dataset.
- 3D Structure: map the detected peptides and modifications onto corresponding PDB structures.
- GO Enrichment: perform GO enrichment and find enriched GO terms in your dataset.
- Validation: inspect and fine tune the validation process.
- QC Plots: examine the quality of the results with Quality Control plots.
- Reshake PRIDE: re-analyze public datasets in PRIDE as if they were your own.
All data can also easily be exported for follow up analysis in other tools.
After 3 years of work, SearchGUI (SG),a tool that performs protein identification using various search engines, and PeptideShaker (PS) for protein identification (which uses SearchGUI results) have been deeply updated and released in new major versions: 4.0.7 and 2.0.5, respectively.Furthermore, two new utility tools have been added to make the overall workflow more flexible: Brew list packages.
- Identification parameters for creating parameter files reusable by both SG and PS.
- FastaCLI, which appends decoy sequences to a FASTA file in a format readable by SG and PS.
The number of changes and improvements made is large, a few highlights:
SearchGUI
- Support for spectrum files in mzML format.
- Search engines updated to the most recent versions. Options updated accordingly.
- FASTA file is now out of the search parameters.
- Many more supported search engines parameters.
- More detailed release notes.
PeptideShaker
Peptide Shaker Software
- Support for spectrum files in mzML format.
- Internal refactoring, new internal database and more efficient data management.
- Reduced file sizes and memory load.
- More detailed release notes.
Peptideshaker Cli
Thanks, Carlos Horro Marcos for your awesome work on the Galaxy integration.