PeptideShaker
interpretation of proteomics identifications from multiple search engines
PeptideShaker is divided into nine tabs covering different aspects of the analysis:
- Overview: get a simple but detailed overview of the protein and peptide identifications.
- Spectrum IDs: compare search engine performance and see how the search engine results are combined.
- Fractions see how the protein identifications are spread over the different fractions.
- Modifications: get an overview of all the post-translational modifications in the dataset.
- 3D Structure: see how the detected peptides map onto the corresponding protein structure.
- Annotation get simple access to numerous protein annotation resources for each protein.
- GO Analysis do a Gene Ontology enrichment analysis of the detected proteins.
- Validation: inspect and modify all the calculations behind the identifications.
- QC Plots: inspect various aspects of the quality of the identifications.
For how to use PeptideShaker please see our Bioinformatics for Proteomics Tutorials.
At the PeptideShaker home page you will also find a Troubleshooting section dealing with known issues
related to the startup and use of the tool.
If you find any bugs or have any questions please contact the developers. Information on how to do this can be
found on the PeptideShaker home page.
PeptideShaker home page: http://compomics.github.io/projects/peptide-shaker.html.
Please cite PeptideShaker as: Vaudel et al.: Nature Biotechnol. 2015 Jan;33(1):22-24.