mspire - ‘Mass Spectrometry Proteomics in Ruby’ is a collection of tools for working with MS proteomics data in ruby. It seeks to provide support for open standards (e.g., parsers for mzData, mzXML, Peptide/Protein Prophet and the TPP) and contribute other useful functionality for working with mass spectrometry data in ruby.

Current Focus

The project is currently focusing on the following:

  • SEQUEST data (particularly the output of Bioworks 3.2-3.3)

  • mzXML

  • mzData

  • ProteinProphet

  • Preparation of files for [obiwarp](obi-warp.sourceforge.net/)

Features

  • mzXML (version 1, 2, and 3) parsing

  • mzData parsing

  • bioworks .srf (binary files) reader

  • read/write .sqt files

  • bioworks to PeptideProphet input (pepXML files)

  • lightweight APEX values parser

  • histogram protein probabilities

  • protein summary views with custom false ID cutoff values

  • conversion to OBI-Warp input files

  • portable: works across platforms

Validation by:

* Various Decoy Database search options: Reverse/Shuffle, concatenated/separate, with various hashing options (e.g., by amino acid sequence + charge)
* Amino acid (e.g., search for unblocked cysteines)
* Transmembrane prediction (Phobius or TopPred)
* Generic sample bias (e.g., low abundance/high abundance proteins)
* Defined sample

Spectra and Spectra Identification

The [MS](ms/index.html) namespace contains objects for working with mass spectra and associated file formats.

The [SpecID](spec_id/index.html) namespace contains objects for working with spectral identifications.

Tutorials

  • [Database Searching Tutorial](tutorial/database_searching/index.html) -

Demonstrates two methods for running and analysing Bioworks output to obtain false positive rates using mspire executables.

Warning

This is an experimental package. As such, all versions prior to version 1.0 may contain interface changes on minor revisions (major.minor.build) (e.g., 0.4.0 may contain interface change from 0.3.9). Beyond version 1.0, the versioning scheme will be strictly adhered to (no interface changes except on major revisions).

Installation

see [Install](install/index.html)