Glycoscience mass spectrometry 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 glycan composition rules and combinations for N-linked and O-linked glycopeptides. This version of GlycReSoft is optimized for QTOF CAD or Q-Exactive/Orbitrap HCD data acquired using data-dependent LC-tandem MS. Here is a GlycReSoft tutorial. Here is a link to our publicly available glycoproteomics data

  • Klein, J. A.; Meng, L.; Zaia, J. Deep sequencing of complex proteoglycans: a novel strategy for high coverage and site-specific identification of glycosaminoglycan-linked peptides. Mol Cell Proteomics 2018, 17, 1578-1590. Pubmed Link
  • Klein, J.; Carvalho, L.; Zaia, J. Application of Network Smoothing to Glycan LC-MS Profiling. Bioinformatics 2018, . Pubmed Link
  • 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
  • Khatri, K.; Klein, J. A.; White, M. R.; Grant, O. C.; Leymarie, N.; Woods, R. J.; Hartshorn, K. L.; Zaia, J. Integrated Omics and Computational Glycobiology Reveal Structural Basis for Influenza A Virus Glycan Microheterogeneity and Host Interactions. Mol Cell Proteomics 2016, 15, 1895-912. 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

GlyPy library.  We also provide interfaces to glycomics databases including Glycome-DB and GlyTouCan for constructing large naive hypotheses using the GlyPy library.

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.

GAGfinder is glycosaminoglycan spectrum analysis software written in the Python programming lanuage. It returns a list of peaks with annotations for a GAG composition given its precursor m/z and precursor charge.

  • Hogan, J. D.; Klein, J. A.; Wu, J.; Chopra, P.; Boons, G. J.; Carvalho, L.; Lin, C.; Zaia, J. Software for peak finding and elemental composition assignment for glycosaminoglycan tandem mass spectra. Mol Cell Proteomics 2018, 17, 1448-1456. Pubmed Link

psims is a Python package to create mzML and mzIdentML files compliant with the PSI-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, 88, 10654-10660. Pubmed Link

GlycoDeNovo is an algorithm for efficient reconstruction of glycan topology from tandem mass spectra.

  • Hong, P.; Sun, H.; Sha, L.; Pu, Y.; Khatri, K.; Yu, X.; Tang, Y.; Lin, C. GlycoDeNovo – an Efficient Algorithm for Accurate de novo Glycan Topology Reconstruction from Tandem Mass Spectra. J Am Soc Mass Spectrom 2017, 28, 2288-2301. 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

BUPID-XL (Boston University Protein Identifier – Cross Linking Analysis): Identify sites of chemical cross-linking for determination of protein-protein interaction.

BUPID-PALM (Boston University Protein Identifier – Parallel Acquisition Library Matcher): Glycopeptide Identification by All-ion Fragmentation(AIF) Ion Mobility MS/MS.