Software

The MSR is developing  tools for processing and analysis of proteomics and PTM data, glycan and glycopeptide mass spectral data and tools for middle-down and top down protein analysis.

GlycReSoft includes an algorithm for constructing combinatorial hypotheses from simple composition rules for glycans and combinations for N-Linked glycopeptidesWe also provides an interface to glycomics databases such as Glycome-DB and GlyTouCan for constructing large naive hypotheses using the GlyPy library.  It also provides an interface to glycomics databases including Glycome-DB and GlyTouCan for constructing large naive hypotheses using the GlyPy library.

  • Khatri, K.; Klein, J. A.; Zaia, J. Use of an informed search space maximizes confidence of site-specific assignment of glycoprotein glycosylation. Anal Bioanal Chem 2016, . Pubmed Link
  • Maxwell, E.; Tan, Y.; Tan, Y.; Hu, H.; Benson, G.; Aizikov, K.; Conley, S.; Staples, G. O.; Slysz, G. W.; Smith, R. D.; Zaia, J. GlycReSoft: A Software Package for Automated Recognition of Glycans from LC/MS Data. PLoS ONE 2012, 7, e45474. Pubmed Link

BrainPy is a Python implementation of the Baffling Recursive Algorithm for Isotope distributioN calculations (BRAIN) algorithm.

  • The original reference for BRAIN is Dittwald, P. et al. Anal. Chem. 2013, 85, 1991-4. Pubmed Link

GlyPy is a glycan analysis and glycominformatics library for the Python programming language.

Mzidentml_writer is a Python package to create MzIdentML files following the HUPO Standard.

MS_peak_picker is a small library to provide peak picking for software processing mass spectrometry data.

MS_deisotope is an experimental union of brainpy and ms_peak_picker.

GAGdecon is an isotopic pattern database approach to deconvolution of high resolution mass spectra generated on low molecular weight heparins.

  • Zaia, J.; Khatri, K.; Klein, J. A.; Shao, C.; Sheng, Y.; Viner, R. Complete Molecular Weight Profiling of Low Molecular Weight Heparins Using Size Exclusion Chromatography-Ion Suppressor-High Resolution Mass Spectrometry. Anal. Chem. 2016, Oct. 6 [Epub ahead of print]. Pubmed Link

STRAP (Software Tool for Rapid Annotation of Proteins) is a software program which automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques.

  • Bhatia, V. N.; Perlman, D. H.; Costello, C. E.; McComb, M. E. Software tool for researching annotations of proteins: open-source protein annotation software with data visualization. Anal. Chem. 2009, 81, 9819-23. Pubmed Link

STRAP PTM (Software Tool for Rapid Annotation of Proteins: Post-Translational Modification edition) is a software program which uses spectral counting and a novel scoring algorithm to accelerate the identification of differential PTMs through easy-to-use GUIs for setup and analysis.

  • Spencer, J. L.; Bhatia, V. N.; Whelan, S. A.; Costello, C. E.; McComb, M. E. STRAP PTM: Software Tool for Rapid Annotation and Differential Comparison of Protein Post-Translational Modifications. Curr Protoc Bioinformatics 2013, 13, 13 22 1-13 22 36. Pubmed Link

BUPID (Boston University Protein Identifier) Top-Down is a web-based platform which provides the means to analyze top-down MS/MS spectra obtained with a number of fragmentation methods, including CID, ECD, and ETD.

  • Bourgoin-Voillard, S.; Leymarie, N.; Costello, C. E. Top-down tandem mass spectrometry on RNase A and B using a Qh/FT-ICR hybrid mass spectrometer. Proteomics 2014, 14, 1174-84. Pubmed Link