mspire-simulator

Description: Simulates MS runs given amino acid FASTA files. Outputs a .mzML file.

Install

gem install mspire-simulator

Dependencies:

ruby 1.9*
weka 3.6.0 - May need to add to CLASSPATH see: http://weka.wikispaces.com/CLASSPATH+problems
fftw 3.2.2 - Tested in Linux Mint 12 and Ubuntu Oneiric Ocelot and Ubuntu 12.04
SQLite3 3.6.16 or newer (Note: install this first if needed)

Examples

The simplest way to run mspire-simulator is to give it an mzML file with a single centroided elution profile from which the simulator can extract needed parameters including:

• Elution parameters: front, tail, and mu

• Overlap range (for merging signals)

• Sampling rate

• m/z wobble parameters: wobA, wobB

• Intensity variance parameters: jagA, jagB, jagC

  $ mspire-simulator --mzml input.mzml [options] <.fasta file>
  

Alternatively all parameters can be specified on the command line:

$ mspire-simulator -r 3000 -s 1.0 -n false ...

To see all the available options:

$ mspire-simulator --help

Charge State Calculator

$ ruby lib/ms/isoelectric_calc.rb --ph 2 --distribution DRVYIHPFHL DRVYIHPF RVYIHPF VYIHPF

will return:

DRVYIHPFHL @ pH 2.0: 3, 29.040854; 4, 70.959146

DRVYIHPF @ pH 2.0: 2, 29.045885; 3, 70.954115

RVYIHPF @ pH 2.0: 2, 37.364123; 3, 62.635877

VYIHPF @ pH 2.0: 1, 40.341305; 2, 59.658695

To see all the available options:

$ ruby lib/ms/isoelectric_calc.rb --help

TODO

Because of the many options and parameters to specify we will be moving to a .init file format with a .init file editor.

Other improvments to mspire-simulator are also pending.

Copyright

See LICENSE.txt for further details.