{"id":1457,"date":"2011-12-16T14:43:35","date_gmt":"2011-12-16T19:43:35","guid":{"rendered":"https:\/\/www.bumc.bu.edu\/msr\/?page_id=1457"},"modified":"2020-06-07T08:38:58","modified_gmt":"2020-06-07T12:38:58","slug":"software","status":"publish","type":"page","link":"https:\/\/www.bumc.bu.edu\/msr\/software\/","title":{"rendered":"Glycoscience mass spectrometry software"},"content":{"rendered":"<p><strong>The MSR has developed \u00a0tools for processing and analysis of proteomics, glycomics and glycoproteomics data spectral data. <\/strong><br \/>\nThe 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<\/p>\n<p><a href=\"https:\/\/github.com\/BostonUniversityCBMS\">Boston University MSR\/CBMS GitHub repository<\/a><\/p>\n<p><a title=\"GlycReSoft\" href=\"https:\/\/www.bumc.bu.edu\/msr\/glycresoft\/\">GlycReSoft<\/a> includes an algorithm for constructing combinatorial hypotheses glycan composition rules and combinations for <em>N<\/em>-linked and <em>O<\/em>-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 <a href=\"\/msr\/files\/2017\/06\/170501_GlycReSoft_workflow_IAV.pdf\">GlycReSoft tutorial<\/a>. Here is a link to our publicly available <a href=\"https:\/\/www.bumc.bu.edu\/msr\/glycoproteomics-test-data\/\">glycoproteomics data<\/a><\/p>\n<ul>\n<li>Klein, J. A.; Zaia, J. Assignment of coronavirus spike protein site-specific glycosylation using GlycReSoft. <em>bioRxiv<\/em> <strong>2020<\/strong>, <em><\/em>, 2020.05.31.125302.<A HREF=\"https:\/\/www.biorxiv.org\/content\/biorxiv\/early\/2020\/05\/31\/2020.05.31.125302.full.pdf\" target = \"blank\"><font color=\"#3300ff\"> Pubmed Link<\/font><\/A><\/li>\n<li>Klein, J.; Zaia, J. Relative Retention Time Estimation Improves N-Glycopeptide Identifications By LC-MS\/MS. <em>J Proteome Res<\/em> <strong>2020<\/strong>, <em>19<\/em>, 2113-2121.<A HREF=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/32223173\" target = \"blank\"><font color=\"#3300ff\"> Pubmed Link<\/font><\/A><\/li>\n<li>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. <em>Mol Cell Proteomics<\/em> <strong>2018<\/strong>, <em>17<\/em>, 1578-1590.<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/29773674\" target=\"blank\"><span style=\"color: #3300ff;\"> Pubmed Link<\/span><\/a><\/li>\n<li>Klein, J.; Carvalho, L.; Zaia, J. Application of Network Smoothing to Glycan LC-MS Profiling. <em>Bioinformatics<\/em> <strong>2018<\/strong>, <em>34<\/em>, 3511-3518.<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/29790907\" target=\"blank\"><span style=\"color: #3300ff;\"> Pubmed Link<\/span><\/a><\/li>\n<li>Khatri, K.; Klein, J. A.; Zaia, J. Use of an informed search space maximizes confidence of site-specific assignment of glycoprotein glycosylation. <em>Anal Bioanal Chem<\/em> <strong>2017<\/strong>, <em>409<\/em>, 607-618.<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/27734143\" target=\"blank\"><span style=\"color: #3300ff;\"> Pubmed Link<\/span><\/a><\/li>\n<li>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. <em>Mol Cell Proteomics<\/em> <strong>2016<\/strong>, <em>15<\/em>, 1895-912.<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/26984886\" target=\"blank\"><span style=\"color: #3300ff;\" color=\"#3300ff\"> Pubmed Link<\/span><\/a><\/li>\n<li>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. <em>PLoS ONE<\/em> <strong>2012<\/strong>, <em>7<\/em>, e45474.<a href=\"http:\/\/dx.doi.org\/10.1371%2Fjournal.pone.0045474\" target=\"blank\"><span style=\"color: #3300ff;\" color=\"#3300ff\"> Pubmed Link<\/span><\/a><\/li>\n<\/ul>\n<p><a href=\"https:\/\/github.com\/BostonUniversityCBMS\/glypy\">GlyPy<\/a> library.\u00a0 We also provide interfaces to glycomics databases including Glycome-DB and GlyTouCan for constructing large naive hypotheses using the <a href=\"https:\/\/github.com\/BostonUniversityCBMS\/glypy\">GlyPy<\/a> library.<\/p>\n<p><a title=\"BrainPy\" href=\"https:\/\/github.com\/BostonUniversityCBMS\/brainpy\/\">BrainPy<\/a> is a Python implementation of the Baffling Recursive Algorithm for Isotope distributioN calculations (BRAIN) algorithm.<\/p>\n<ul>\n<li>The original reference for BRAIN is Dittwald, P. et al. <em>Anal. Chem.<\/em> <strong>2013<\/strong>, <em>85<\/em>, 1991-4.<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/23350948\" target=\"blank\"><span style=\"color: #3300ff;\" color=\"#3300ff\"> Pubmed Link<\/span><\/a><\/li>\n<\/ul>\n<p><a title=\"GlyPy\" href=\"https:\/\/github.com\/BostonUniversityCBMS\/glypy\">GlyPy<\/a> is a glycan analysis and glycominformatics library for the Python programming language.<\/p>\n<p><a href=\"https:\/\/github.com\/jdhogan\/gagfinder\/releases\" target=\"_blank\" rel=\"noopener\">GAGfinder<\/a> 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.<\/p>\n<ul>\n<li>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. <em>Mol Cell Proteomics<\/em> <strong>2018<\/strong>, <em>17<\/em>, 1448-1456.<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/29615495\" target=\"blank\"><span style=\"color: #3300ff;\"> Pubmed Link<\/span><\/a><\/li>\n<\/ul>\n<p><a href=\"https:\/\/github.com\/jdhogan\/gagrank\">GAGrank<\/a> is an algorithm for assigning GAG sequence from ExD tandem mass spectra processed using GAGfinder.<\/p>\n<p><a href=\"https:\/\/github.com\/BostonUniversityCBMS\/psims\">psims<\/a> is a Python package to create mzML and mzIdentML files compliant with the PSI-HUPO Standard.<\/p>\n<p><a title=\"ms_peak_picker\" href=\"https:\/\/github.com\/BostonUniversityCBMS\/ms_peak_picker\">MS_peak_picker<\/a> is a small library to provide peak picking for software processing mass spectrometry data.<\/p>\n<p><a title=\"ms_deisotope\" href=\"https:\/\/github.com\/BostonUniversityCBMS\/ms_deisotope\">MS_deisotope<\/a> is an experimental union of brainpy and ms_peak_picker.<\/p>\n<p><a title=\"GAGdecon\" href=\"https:\/\/github.com\/BostonUniversityCBMS\/gagdecon\">GAGdecon<\/a> is an isotopic pattern database approach to deconvolution of high resolution mass spectra generated on low molecular weight heparins.<\/p>\n<ul>\n<li>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. <em>Anal. Chem.<\/em> <strong>2016<\/strong>, <em>88<\/em>, 10654-10660.<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/27709905\" target=\"blank\"><span style=\"color: #3300ff;\" color=\"#3300ff\"> Pubmed Link<\/span><\/a><\/li>\n<\/ul>\n<p><a href=\"https:\/\/github.com\/hongpengyu\/GlycoDeNovo\">GlycoDeNovo<\/a> is an algorithm for efficient reconstruction of glycan topology from tandem mass spectra.<\/p>\n<ul>\n<li>Hong, P.; Sun, H.; Sha, L.; Pu, Y.; Khatri, K.; Yu, X.; Tang, Y.; Lin, C. GlycoDeNovo &#8211; an Efficient Algorithm for Accurate de novo Glycan Topology Reconstruction from Tandem Mass Spectra. <em>J Am Soc Mass Spectrom<\/em> <strong>2017<\/strong>, <em>28<\/em>, 2288-2301.<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/28786094\" target=\"blank\"><span color=\"#3300ff\" style=\"color: #3300ff;\"> Pubmed Link<\/span><\/a><\/li>\n<\/ul>\n<p>&nbsp;<br \/>\n<a href=\"https:\/\/jdhogan.shinyapps.io\/peaksviz\">PEAKSviz: a web application for data visualization and statistical analysis of PEAKS proteomics data<\/a><br \/>\n&nbsp;<\/p>\n<p><a title=\"STRAP\" href=\"https:\/\/www.bumc.bu.edu\/msr\/software\/strap\/\">STRAP <\/a>(Software Tool for Rapid Annotation of Proteins) is a software program which\u00a0automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques.<\/p>\n<ul>\n<li>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. <em>Anal. Chem.<\/em> <strong>2009<\/strong>, <em>81<\/em>, 9819-23.<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/19839595\" target=\"blank\"><span style=\"color: #3300ff;\" color=\"#3300ff\"> Pubmed Link<\/span><\/a><\/li>\n<\/ul>\n<p><a title=\"STRAP-PTM\" href=\"https:\/\/www.bumc.bu.edu\/msr\/software\/strap-ptm\/\">STRAP PTM<\/a> (Software Tool for Rapid Annotation of Proteins: Post-Translational Modification edition) is a software program which\u00a0uses spectral counting and a novel scoring algorithm to accelerate the identification of differential PTMs through easy-to-use GUIs for setup and analysis.<\/p>\n<ul>\n<li>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. <em>Curr Protoc Bioinformatics<\/em> <strong>2013<\/strong>, <em>13<\/em>, 13 22 1-13 22 36.<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/25422678\" target=\"blank\"><span style=\"color: #3300ff;\" color=\"#3300ff\"> Pubmed Link<\/span><\/a><\/li>\n<\/ul>\n<p><a title=\"BUPID\" href=\"https:\/\/www.bumc.bu.edu\/msr\/software\/bupid-top-down\/\">BUPID <\/a>(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.<\/p>\n<ul>\n<li>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. <em>Proteomics<\/em> <strong>2014<\/strong>, <em>14<\/em>, 1174-84.<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/24687996\" target=\"blank\"><span style=\"color: #3300ff;\" color=\"#3300ff\"> Pubmed Link<\/span><\/a><\/li>\n<\/ul>\n<p><a href=\"https:\/\/www.bumc.bu.edu\/msr\/bupid-xl\/\">BUPID-XL\u00a0<\/a>(Boston University Protein Identifier &#8211; Cross Linking Analysis): Identify sites of chemical cross-linking for determination of protein-protein interaction.<\/p>\n<p><a href=\"https:\/\/www.bumc.bu.edu\/msr\/bupid-palm\/\">BUPID-PALM <\/a>(Boston University Protein Identifier &#8211; Parallel Acquisition Library Matcher): Glycopeptide Identification by All-ion Fragmentation(AIF) Ion Mobility MS\/MS.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>The MSR has developed \u00a0tools 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 [&hellip;]<\/p>\n","protected":false},"author":1067,"featured_media":0,"parent":0,"menu_order":25,"comment_status":"closed","ping_status":"closed","template":"page-templates\/no-sidebars.php","meta":[],"_links":{"self":[{"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/pages\/1457"}],"collection":[{"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/users\/1067"}],"replies":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/comments?post=1457"}],"version-history":[{"count":50,"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/pages\/1457\/revisions"}],"predecessor-version":[{"id":3633,"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/pages\/1457\/revisions\/3633"}],"wp:attachment":[{"href":"https:\/\/www.bumc.bu.edu\/msr\/wp-json\/wp\/v2\/media?parent=1457"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}