mspire library supporting in-silico calculations for mass spec data (protein digestion, peptide fragmentation, etc.)
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README.rdoc

Ms-InSilico

An Mspire library supporting in-silico calculations for mass spec data.

Description

Ms-InSilico provides the following modules:

  • Ms::InSilico::Digester (protein digestion)

  • Ms::InSilico::Spectrum (peptide fragmentation)

Corresponding Tap tasks are also provided.

Usage

require 'ms/in_silico/digester'
require 'ms/in_silico/spectrum'
include Ms::InSilico

trypsin = Digester['Trypsin']
peptides = trypsin.digest('MIVIGRSIVHPYITNEYEPFAAEKQQILSIMAG')
# => [
# 'MIVIGR',
# 'SIVHPYITNEYEPFAAEK',
# 'QQILSIMAG']

spectrum = Spectrum.new(peptides[0])
spectrum.parent_ion_mass    
# => 688.417442373391

spectrum.series('b')
# => [
# 132.047761058391,
# 245.131825038791,
# 344.200238954991,
# 457.284302935391,
# 514.305766658991,
# 670.406877687091]

Installation

Ms-InSilico is available as a gem on RubyForge. Use:

% gem install ms-in_silico

Info

Copyright © 2008-2009, Regents of the University of Colorado.

Developer

Simon Chiang, Biomolecular Structure Program, Hansen Lab

Support

CU Denver School of Medicine Deans Academic Enrichment Fund

Licence

MIT-Style