Protein Parsimony

This program implements a protein parsimony algorithm for grouping proteins with similar peptides.

The algorithm is based on concepts in the manuscript
"Proteomic Parsimony through Bipartite Graph Analysis Improves Accuracy and Transparency"
by Bing Zhang, Matthew C. Chambers, and David L. Tabb

• J Proteome Res. 2007 Sep; 6(9): 3549-57. doi: 10.1021/pr070230d. Epub 2007 Aug 4.
• Abstract: PMID: 17676885
• Full text: PMCID: 2810678

ProteinParsimony Console

The ProteinParsimony.exe program can be used to manually process a tab-delimited text file with columns Protein and Peptide, or to process data in SQLite database table.

Program syntax #1:

ProteinParsimony.exe InputFilePath.txt [OutputFilePath]

The input file is a tab delimited text file with columns Protein and Peptide (column order does not matter; extra columns are ignored)

If the output file path is not defined, it will be created in the same location as the input file, but with '_parsimony' added to the filename

Program syntax #2:

ProteinParsimony.exe SQLiteDatabase.db3 [TableName]

If the input is a SQLite database file (extension .db, .db3, .sqlite, or .sqlite3), proteins and peptides will be read from the specified table, or from T_Row_Metadata if TableName is not provided. The table must have columns Protein and Peptide.
Results will be written to tables T_Parsimony_Grouping and T_Parsimony_Group_Members

Contacts

Written by Josh Aldrich for the Department of Energy (PNNL, Richland, WA)
E-mail: proteomics@pnnl.gov Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://www.pnnl.gov/integrative-omics

License

The Protein Parsimony library is licensed under the Apache License, Version 2.0; you may not use this file except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/Apache-2.0