1. Summary

Bottom-up proteomics is a technique for studying proteins that involves digesting proteins to fragment peptides prior to identification using mass spectrometry. Masses of digested peptides are compared with those predicted from a sequence database to identify peptides. Proteins are then identified by analyzing peptides present in the sample. This two-part module will be an introduction to peptide and protein identification using MS/MS data on the Galaxy-P platform. Galaxy-P is an extension of Galaxy , a platform developed to enable reproducible data intensive research by providing complex computational software that often requires advanced computer skills via a web-interface. Part one of the module will be a brief introduction to the Galaxy framework. Part two of the module will be an overview of peptide and protein identification using MS/MS data.

2. Presentation Materials

Click here.

3. Hands-on Exercise(s)

Click here.

4. Associated Materials/Files

Mo_Tai_Trimmed_mgfs__Mo_Tai_iTRAQ_f9.mgf

Protein_Database_uniprot.fasta

5. Program/Software requirements

Java JRE: https://www.java.com/en/download/

SearchGui: http://compomics.github.io/projects/searchgui.html

PeptideShaker: http://compomics.github.io/projects/peptide-shaker.html

6. Advanced Material

https://galaxyproject.org/learn/

https://compomics.com/bioinformatics-for-proteomics/identification/

https://compomics.com/bioinformatics-for-proteomics/quantification/

7. Instructor Notes

These materials will be uploaded later.