Description: Simulates MS runs given amino acid FASTA files. Outputs a .mzML file.
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)
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
$ 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
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.
See LICENSE.txt for further details.