title: Proteomics Tutorial summary: Short introduction to proteomics authors: Louis L. du Preez date: 2022-07-04 url : https://docs.hpc.ufs.ac.za copyright: Vaudel et al.: Shedding light on black boxes in protein identification. Proteomics. 2014 May;14(9):1001-5.

Proteomics Tutorial - Peptide and Protein Identification

The following Tutorial will detail the steps involved in:

Retrieving and Generating a database to search against
Converting raw output from the MS instrument into an open format
Processing MS/MS spectra into peak lists
Searching the peak lists against the generated sequence database using one or more search engines
Identifying the peptides and proteins
Validating the detected peptides and proteins

This tutorial is derived from the tutorial series by the Compomics group headed by Prof. Dr. Lennart Martens at the University of Ghent in Belgium [1]. Note that there are more tutorials on the site itself if you are interested in exploring the field of Proteomics further.

This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

Preparation

To retrieve the data used in the tutorial and to set-up the initial directory structure, follow these steps:

Open a terminal and navigate to your home directory (if not there already):
```
$ cd ~
```

Download this script:

$ wget http://docs.hpc.ufs.ac.za/training/proteomics_tutorial/data/config_transcript_tut.sh

Make the script executable:
```
$ chmod +x config_gen_tut.sh
```
Execute the script to set-up the tutorial directory ~/proteomics_tutorial and download the tutorial data:
```
$ ./config_gen_tut.sh
```

This ~/proteomics_tutorial will be the base working directory for all the exercises below. We'll create other subdirectories here and move back and forth to our various workspaces that we generate along the way.

Below, we refer to $ as the terminal command prompt

Tutorial Instructions

The tutorial instructions are contained in the PDF documents below:

References

Vaudel, M., Venne, A. S., Berven, F. S., Zahedi, R. P., Martens, L., & Barsnes, H. (2014). Shedding light on black boxes in protein identification. Proteomics, 14(9), 1001-1005.