InSilicoSpectro is a proteomics Perl open-source project intended to cover common operations in mass list file format conversions, protein sequence digestion, theoretical mass spectra computations, theoretical and experimental MS data matching, text/graphic display, peptide retention time predictions, etc.

The problems of raw data processing, storage and database searching are not addressed by the InSilicoSpectro project. InSilicoSpectro is released under the LGPL license and it is available from this web site or CPAN.

The general design of the modules follows the object oriented programming (OOP) model and most of the modules are class definitions actually. The module that implements most of the theoretical mass computation routines supports a dual OOP and procedural programming model. InSilicoSpectro modules make use of some Perl modules that are not part of the standard Perl distribution, such as Statistics:Regression, XML:Twig, GD, and IA:NNFlex.

We have developed a simple and minimal hierarchy of classes to represent protein sequences and peptides (as digestion product) in a way that, on the one hand, fits the needs of the computations we perform and, on the other hand, stays relatively neutral in its design. Thus it should be possible to combine the latter classes with existing projects at users sites, e.g. via multiple inheritance, or to use them as the basis of more sophisticated objects.

InSilicoSpectro Perl code is documented mainly via pod and a wide collection of simple and focused examples. An introductory explanation is provided here to guide new users and give them an understanding of the library that should be sufficient such that pod and the examples are the only necessary documentation.

Current Version

• Mass list file format conversions.
• Protein modifications.
• Protein sequences digestion with a large choice of possible enzyme types.
• Peptide mass computations with fixed and variable modifications. Match with experimental PMF data.
• Fragment mass computations for modified peptides and with neutral losses. Match with experimental MS/MS data. Possibility to define new types of fragments.
• Text/graphical output in many formats of MS/MS spectra and match with experimental data.
• Peptide HPLC elution time prediction.
• Protein pI estimation.
• Peak/compound filtering.
• Automatic extraction of sets of reliable peptide identifications (from Mascot and Phenyx result files) and manipulation of such sets.

Under development

• Low-quality MS/MS spectra filtering.
• More graphical output for MS/MS and PMF data.
• Atomic composition and isotope relative intensity computation.

Links

• BioPerl, the well known Perl package suite for bioinformatics, mainly oriented towards sequence manipulations
• Phenyx an MS identification platform, using InSilicoSpectro modules for its Perl computations.
• Expasy the Swiss Institute of Bioinformatics proteomics portal

Reference

      Colinge, J., Masselot, A., Carbonell, P, Appel, R.D., "InSilicoSpectro: An open-source proteomics library", J Proteome Res, 2006, 5(3):619-624.
      

Acknowledgments