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ModST Introduction

Welcome to ModST (pronounced "modest") pipeline for Blind PTM searches using the MODa tool.

ModST can be downloaded from here. Please find the latest version and download from the above link.

Background

Post-translational Modifications (PTMs) are the covalent or enzymatic modifications attached to the proteins co or post-translationally. they are required to regulate biological functions of a protein. for information on some widely studied modifications read here.

Installation

Detailed instructions are provided with downloaded documentation for version specific installation. This will require-
1. Perl
2. MODa
3. Java
4. Parallel::ForkManager from cpan

Documentation

Docmentation can be found here or with the downloaded software.

Advantages

There are several advantages of ModST apart from the speed and configurable features:
• It is platform independent (since both Perl & Java are platform independent) and can run on any operating system.
• It integrates MODa results for ease of analysis for individual sites of modifications and statistical analysis from complete set of results.
• It compiles protein level information, which helps in analyzing the fraction of modified peptides for every protein in the sample.
• Using the corrected PTM masses, users can annotate modifications unambiguously using any PTM database like RESID, DeltaMass or Unimod with better accuracy.
• With better PTM annotation, the localization errors can also be corrected as the known PTMs have specific amino acid sites of occurrence.
• Using the newly corrected PTM table frequencies, users can make better biological interpretations of the masses present.
• This pipeline also provides tabulated results for MODa output file which can be used to find the peptide or modification of interest in complete set of results.
• For FDR corrected identification files from analmod program, results are tabulated to ID_SITES and ID_PSMS which help in in-depth analysis and data provenance for sites and modified peptides of interest.

Quick start guide

Input/output

Limitations

As all good things have some bad qualities so do ModST has.
1. ModST can be run for only mgf files. since the package is written for mgf files only. though in future it will be extended for other formats read by MODa.
2. On machines with only 1 core it can give only automation and no parallezation. but in this age of technology boom, 1 core systems hardly exist.

Help

For any help, please email amit.yadav@thsti.res.in, suruchi@thsti.res.in or post in our support forum.

Bug reports

For Bug reports, use the ticket system.