#GPTMD
Software to augment a UniProt XML database with PTMs discovered using Morpheus
##General Overview
G-PTMD is a tool used to expand the scope of peptide identification to include specific post-translational modifications. Currently, identifying peptides with post-translational modifications relies on the variable toggling of modifications on all the residues that can be modified or the documentation of a specific modification in a database. The first method is computationally expensive and wasteful while databases are often incomplete. Thus, G-PTMD addresses the weaknesses of both methods to improve protein idenfication results.
The purpose of G-PTMD is to build a new proteome reference .xml database by annotating an existing reference database using a set of peptide spectral matches (PSMs). The PSMs are obtained by running a Morpheus search on a .raw or .mzml file of the experimentally obtained mass spectrometry data. The program identifies the peptide spectral matches that have a mass shift indicative of certain post-translational modifications. For example, if the peptide “PEPTIDE” was identified in the PSMs file with a mass shift of 79.966 Da, the corresponding protein entry in the reference .xml database would be granted a new feature consisting of a phosphorylated threonine at the appropriate position because 79.966 Da is exactly the change in mass of a peptide when one residue is phosphorylated.
Now, when the original .raw or .mzml file is run against this new database in an open search, if the phosphorylation on the threonine is present in the sample, the computer will be able to recognize and identify it. Phosphorylation is just one example, and this technique extends to other post-translational modifications. The user can add or remove modifications to the list of post-translational modifications as needed. This effectively allows for variable post-translational modifications at targeted positions in the protein leading to better search results upon the second pass without incurring huge data costs associated with blindly adding variable modifications.
##General Requirements
The following files must be present in the folder with the executable. If not, they are automatically downloaded (to update a file to a newer version, delete it, and the application will download a new version). This is the only network usage by the application.
-
uniprot.xml: A UniProt reference database in .xml format
-
ptmlist.txt: A PTM library
##Operating System Requirements and Usage
###Windows Perl Version ####System ####Usage
###Windows C# Version ####System
###Linux Python Version ####System
- 8 GB of RAM is recommended
- python v2.7.10 (64 bit) See https://www.python.org/downloads/ for installation instructions. This includes the "pip" package manager.
- This program uses lxml, a package for interpreting XML databases. lxml can be installed using the command: pip install lxml. See http://lxml.de for additional installation instructions.
- If you encounter errors installing lxml, we recommend trying an alternate package manager, such as Canopy, which can be found here.
####Usage
Options:
-h, --help show this help message and exit
-x REFERENCE_XML, --reference_xml=REFERENCE_XML
The reference UniProt-XML file. New PTM features are
appended to this database to generate the output
UniProt-XML protein database.
-t PTM_DATABASE, --ptm_database=PTM_DATABASE
Slightly modified database of UniProt PTMs. This file
determines which types of PTMs are included.
-s PSMS, --psms=PSMS Peptide spectral matches tab-separated. This file is
from first-pass open search and contains the mass
shifts that correspond to PTMs.
-o OUTPUT, --output=OUTPUT
Output file path. Outputs a UniProt-XML file.
Example Command Line:
\Dir>bpython gptmd.py -x ../uniprot.xml -t ../sub_ptmlist_regular.txt -s ../PSMs.tsv -o ../test_output.xml
###Relevant Manuscripts
The software is currently released under the GNU GPLv3.
Copyright 2016 Lloyd M. Smith Group.
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