Project Descriptions
Informed-Proteomics is an open-source suite written in C# for top-down proteomics analysis. The software package is composed of multiple modules including data structures and algorithms for analysis of proteomics data, unit tests, and command-line tools for running LC-MS feature finding algorithm (ProMex), and a new database search algorithm (MSPathFinder). Source codes and compiled binary files are available on GitHub at https://github.com/PNNL-Comp-Mass-Spec/Informed-Proteomics. An interactive results viewer, named LcMsSpectator is also available at https://github.com/PNNL-Comp-Mass-Spec/LCMS-Spectator.
Base elements for processing proteomics data
- Read/write mass-spectrometry data in different formats
- Extract spectrum and chromatogram
- Handle protein sequence database in Fasta format
- Predict theoretical isotopomer envelope
- Data structures for atom, composition, amino acid, sequence, and modification
- Sequence graph for modification search
LC-MS feature finding algorithm (ProMex)
- Data structures for LC-MS feature
- Likelihood ratio scoring model
- Align LC-MS features across multiple runs
Top-down proteomics specific data structures and algorithms
- Scoring models for proteoform-spectrum matches
- Sequence tag finding algorithm
- Sequence tag-based search algorithm for multiply cleaved proteoforms
Generating function approach for computing statistical significance of proteoform- or peptide-spectrum matches
External library for induced sorting based suffix array construction algorithms
- Ge Nong, Sen Zhang & Wai Hong Chan. Two Efficient Algorithms for Linear Time Suffix Array Construction. IEEE Trans. Comput. 60, 1471–1484 (2011)
Command line tool for database search algorithm for top-down proteomics
- Executable MSPathFinder for top-down proteomics data
Command line tool for generating PBF files from LC-MS data in Thermo RAW or MZML format
Command line tool for LC-MS feature finding