Glycoscience mass spectrometry software
The MSR has developed tools for processing and analysis of proteomics, glycomics and glycoproteomics data spectral data.
The source code have been published under the Apache Common License, making the codebase legally compatible with both open source and commercial efforts. All software developed in the proposed work will be open source and publically available through the
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.; Zaia, J. Assignment of coronavirus spike protein site-specific glycosylation using GlycReSoft. bioRxiv 2020, , 2020.05.31.125302. Pubmed Link
- Klein, J.; Zaia, J. Relative Retention Time Estimation Improves N-Glycopeptide Identifications By LC-MS/MS. J Proteome Res 2020, 19, 2113-2121. Pubmed Link
- 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, 34, 3511-3518. 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 2017, 409, 607-618. 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
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
GAGrank is an algorithm for assigning GAG sequence from ExD tandem mass spectra processed using GAGfinder.
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.