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PTM select

PTMselect is a software to computationally identify the best protease combinations for optimal coverage of any global or targeted protein post-translational modification (PTM), from one or several proteins.

PTMselect was optimized to eliminate the tedious work of manually sorting and selecting peptides to choose digestion settings before performing any MS-driven PTM analysis. This software is designed for :
(1) optimization of global coverage of proteinPTM sites, 
(2) optimization of protein PTM sites coverage with the highest probability to be modified and 
(3) optimization oftarget PTM positions coverage.

PTM select allows to quickly discard a large number of inappropriate protease combinations in PTMs studies by MS.

If you enjoy using PTM select and find it useful, then please cite Fred'Softwares address and "PTMselect : optimization of protein modifications discovery by mass spectrometry. Scientific Reports volume 9, Article number: 4181 (2019)".

change log :
2020-05-25 : PTMselect has been updated to v100 : compatibility update with Julia 1.4.1 and Julia 1.4.2 and manual improvements.
2020-02-14 : PTMselect has been updated to v099 : minor code cleaning + unit tests + packages versionning + manual improvements
2019-12-10 : PTMselect has been updated to v098 to be compatible with Combinatorics v1.0.0 (Julia 1.3)
2019-11-27 : compatibility check of PTMselect v0.97  with Julia 1.3 : passed
2019-08-20 : compatibility check of PTMselect v0.97  with Julia 1.2 : passed
2019-07-19 : compatibility update with Julia 1.1.1 and DataFrames 0.19 PTMselect v0.97 
2019-05-23 : compatibility update with Julia 1.1.1 PTMselect v0.96 

Quick Start (the detailed manual is available in PDF file with the software code)

1- install Julia v1.4.1 free programming language, start Julia and install packages by pressing the "]"  key:
DataFrames     :  add DataFrames 
Combinatorics :  add Combinatorics 
CSV                 :  add CSV
DelimitedFiles  :  add DelimitedFiles

PTM select v100 is compatible with Julia v 1.4.1 and later :
[336ed68f] CSV v0.6.2
[861a8166] Combinatorics v1.0.2
[a93c6f00] DataFrames v0.21.1

For windows 7 users, it is recommended to install Microsoft "Easy Fix" to download packages from GitHub.
It is also possible to avoid manual packages installation with JuliaPro v1.4.1. We found that Julia installation was easier on windows 10 than on windows 7.

2- unzip the software
3- copy your FASTA files in the “fasta” directory
4- With a text editor, edit config/config.txt to set PTM target amino acids. 
Edit config/proteases.tsv to set your digestion settings. 
(on windows avoid the notepad to edit config files, we recommend notepad++)
5- execute the software by the command : julia PTMselect_xx.jl or double click on the PTMselect_xx.jl file after associating .jl files with Julia executable file.
If the program does not start on windows, alternative methods are here.
6- processed file is in the “results”, "scores" and "html" directories.

tips : 
1- we recommend to always use trypsin in protease combinations to ensure large sequence coverage.
2- perform a first simulation without missed cleavages for minimal false positives
3-  perform a second simulation with missed cleavages (we found that good parameters are 2 MC for chymotrypsin and 1 MC for V8) for minimal false negatives
4- based on the last simulation, the very low false rate of results allows to quickly discard inappropriate protease combinations.
Frédéric PONT,
May 25, 2020, 1:46 AM