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PeptideShaker: Advanced Proteomics Analysis Made Easy and Accessible

PeptideShaker is a free, open-source, and platform-independent software designed for user-friendly proteomics analysis. It allows researchers to identify spectra with SearchGUI while accessing data in a simple graphical interface. With integrated tables, plots, and graphics, users can effortlessly explore proteins, peptides, and spectrum data, facilitating a complete analysis cycle. Features include mapping peptide to protein structures, Gene Ontology analysis, and easy data export to tools like Excel or PDF. Collaborate and share projects seamlessly, with facilities to reanalyze public PRIDE data.

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PeptideShaker: Advanced Proteomics Analysis Made Easy and Accessible

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  1. PeptideShaker Overview What makes PeptideShaker special? Free, open-source and platform independent! Focus on user-friendliness and visualization! Completes the proteomics analysis cycle! - proteomics: shaken, not stirred!

  2. PeptideShaker Overview Use SearchGUI to identify your spectra! Search OMSSA and X!Tandem … … with the same settings … … in a simple graphical user interface. Click here to download SearchGUI

  3. PeptideShaker Overview Get an overview of all proteins, peptides and spectra! Proteins Peptides Spectrum PSMs* Coverage * Peptide-Spectrum Match

  4. PeptideShaker Overview All tables, plots and graphics are linked! Selecting a protein … 1 … displays the peptides … … which opens the spectrum … 2 4 … and then the PSMs … 3 … and updates the sequence coverage. 5

  5. PeptideShaker Overview Easily export specific features to other tools! Export features

  6. PeptideShaker Overview Or export directly from the table or plot! Export to Excel Export to PDF

  7. PeptideShaker Overview Get help for each table, plot and feature! Help

  8. PeptideShaker Overview Specific tabs for specific tasks! Peptide to Protein Structure Mapping Gene Ontology Analysis Custom Peptide and Protein Validation Plus: Spectrum ID analysis, PTM analysis, Protein Annotation, QC Plots …

  9. PeptideShaker Overview Easy sharing of projects with collaborators! Export project

  10. PeptideShaker Overview Straightforward export to PRIDE! PRIDE Export

  11. PeptideShaker Overview Easy reanalysis of public PRIDE data! Find the desired project … … inspect the project details …. … and start re-analyzing the data!

  12. PeptideShaker Overview Now open a PeptideShaker example dataset! Click to open an example dataset* *Data kindly provided by the Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany.

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