whiffen-cann/glyco_msslash

Introduction

GlycoSLASH is software developed based on msSLASH (standing for mass spectral Searching using LocAlity Sensitive Hashing) was developed by Sujun Li and Haixu Tang, specifically for glycopeptides identification based on the pre-constructed glycopeptides library.

Prerequisites

msSLASH

Installation

git clone [email protected]:whiffen-cann/Glyco_MsSLASH.git
cd  GlycoSLASH/msSLASH/
bash install.sh

Usage

1. Create an folder contains all the mgf files for glycopeptides identification. For example:

   mkdir Test
   cp test.mgf Test
   

   In our repository, we already place a test mgf in the Test folder and a test mgf in the folder as well.

2. Create a list file for mgf list files one mgf file per line.

   vi test.list
   

   For example , content in file <test.list> in this repository as belove:

   Test/nash96_r2_90min_22feb.mgf

3. Run:

   GlycoSLASH test.list
   

4. Check the results at the Test folder. You will find results ending with ".GlycoSLASH.tsv"

5. Summarize the results, Run:

   GlycoSLASHParser.py Test
   

   The output will be :

   Filename	UniqueID	Total Spectra	Spectra ID number	Ratio of ID
   nash96_r2_90min_22feb.mgf.GlycoSLASH.tsv	222	3616	350	0.096792035398

   
   

   Questions

   Please contact Sujun Li ([email protected] ),Can Wang ([email protected])

   Acknowledgement

   The paper is partially supported by National Institutes of Health (Grant No: 1U01CA225753-01 and 1R01GM130091-01A1).