Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis

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Kawahara, Rebeca ^[1] ; Chernykh, Anastasia ^[1] ; Alagesan, Kathirvel ^[2] ; Bern, Marshall ^[3] ; Cao, Weiqian ^{[4, 5]} ; Chalkley, Robert J. ^[6] ; Cheng, Kai ^[7] ; Choo, Matthew S. ^[8] ; Edwards, Nathan ^{[9, 10]} ; Goldman, Radoslav ^{[11, 9, 10]} ; Hoffmann, Marcus ^[12] ; Hu, Yingwei ^[13] ; Huang, Yifan ^[14] ; Kim, Jin Young ^[15] ; Kletter, Doron ^[3] ; Liquet, Benoit ^{[16, 17]} ; Liu, Mingqi ^{[4, 5]} ; Mechref, Yehia ^[14] ; Meng, Bo ^[18] ; Neelamegham, Sriram ^[7] ; Nguyen-Khuong, Terry ^[8] ; Nilsson, Jonas ^[19] ; Pap, Adam ^{[20, 21]} ; Park, Gun Wook ^[15] ; Parker, Benjamin L. ^[22] ; Pegg, Cassandra L. ^[23] ; Penninger, Josef M. ^{[24, 25]} ; Phung, Toan K. ^[23] ; Pioch, Markus ^[12] ; Rapp, Erdmann ^{[12, 26]} ; Sakalli, Enes ^[24] ; Sanda, Miloslav ^{[11, 9]} ; Schulz, Benjamin L. ^[23] ; Scott, Nichollas E. ^[27] ; Sofronov, Georgy ^[16] ; Stadlmann, Johannes ^[24] ; Vakhrushev, Sergey Y. ^[28] ; Woo, Christina M. ^[29] ; Wu, Hung-Yi ^[29] ; Yang, Pengyuan ^{[4, 5]} ; Ying, Wantao ^[18] ; Zhang, Hui ^[13] ; Zhang, Yong ^[18] ; Zhao, Jingfu ^[14] ; Zaia, Joseph ^[30] ; Haslam, Stuart M. ^[31] ; Palmisano, Giuseppe ^[32] ; Yoo, Jong Shin ^{[15, 33]} ; Larson, Goran ^[34] ; Khoo, Kai-Hooi ^[35] ; Medzihradszky, Katalin F. ^{[6, 20]} ; Kolarich, Daniel ^[2] ; Packer, Nicolle H. ^{[1, 36, 2]} ; Thaysen-Andersen, Morten ^{[1, 36]}

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^[1] Macquarie Univ, Dept Mol Sci, Sydney, NSW - Australia

^[2] Griffith Univ, Inst Glyc, Gold Coast Campus, Southport, Qld - Australia

^[3] Prot Metr Inc, Cupertino, CA - USA

^[4] Fudan Univ, Inst Biomed Sci, Shanghai - Peoples R China

^[5] Fudan Univ, NHC Key Lab Glycoconjugates Res, Shanghai - Peoples R China

^[6] UCSF, Dept Pharmaceut Chem, Sch Pharm, San Francisco, CA - USA

^[7] SUNY Buffalo, Buffalo, NY - USA

^[8] Agcy Sci Technol & Res, Bioproc Technol Inst, Analyt Grp, Singapore - Singapore

^[9] Georgetown Univ, Clin & Translat Glycosci Res Ctr CTGRC, Washington, DC - USA

^[10] Georgetown Univ, Dept Biochem & Mol & Cellular Biol, Washington, DC - USA

^[11] Georgetown Univ, Dept Oncol, Washington, DC - USA

^[12] Max Planck Inst Dynam Complex Tech Syst, Bioproc Engn, Magdeburg - Germany

^[13] Johns Hopkins Univ, Dept Pathol, Baltimore, MD - USA

^[14] Texas Tech Univ, Dept Chem & Biochem, Lubbock, TX 79409 - USA

^[15] Korea Basic Sci Inst, Res Ctr Bioconvergence Anal, Daejeon - South Korea

^[16] Macquarie Univ, Dept Math & Stat, Sydney, NSW - Australia

^[17] UPPA, CNRS, Lab Math & Leurs Applicat PAU, E2S, Pau - France

^[18] Beijing Inst Life, Natl Ctr Prot Sci Beijing, Beijing Proteome Res Ctr, State Key Lab Prote, Beijing - Peoples R China

^[19] Univ Gothenburg, Sahlgrenska Acad, Prote Core Facil, Gothenburg - Sweden

^[20] BRC, Lab Prote Res, Szeged - Hungary

^[21] Univ Szeged, Fac Sci & Informat, Doctoral Sch Biol, Szeged - Hungary

^[22] Univ Melbourne, Dept Anat & Physiol, Melbourne, Vic - Australia

^[23] Univ Queensland, Sch Chem & Mol Biosci, Brisbane, Qld - Australia

^[24] Austrian Acad Sci, IMBA, Inst Mol Biotechnol, Vienna - Austria

^[25] Univ British Columbia, Life Sci Inst, Dept Med Genet, Vancouver, BC - Canada

^[26] glyXera GmbH, Magdeburg - Germany

^[27] Univ Melbourne, Dept Microbiol & Immunol, Melbourne, Vic - Australia

^[28] Univ Copenhagen, Copenhagen Ctr Glyc, Dept Cellular & Mol Med, Copenhagen - Denmark

^[29] Harvard Univ, Dept Chem & Chem Biol, Cambridge, MA 02138 - USA

^[30] Boston Univ, Dept Biochem, Med Campus, Boston, MA - USA

^[31] Imperial Coll London, Dept Life Sci, London - England

^[32] Univ Sao Paulo, Inst Ciencias Biomed, Dept Parasitol, Sao Paulo, SP - Brazil

^[33] Chungnam Natl Univ, Grad Sch Analyt Sci & Technol, Daejeon - South Korea

^[34] Univ Gothenburg, Sahlgrenska Acad, Dept Lab Med, Gothenburg - Sweden

^[35] Acad Sinica, Inst Biol Chem, Taipei - Taiwan

^[36] Macquarie Univ, Biomol Discovery Res Ctr, Sydney, NSW - Australia

• Tipo de documento: Artigo Científico
• Fonte: NATURE METHODS; v. 18, n. 11, p. 1304+, NOV 2021.
• Citações Web of Science: 2

Resumo

Glycoproteomics is a powerful yet analytically challenging research tool. Software packages aiding the interpretation of complex glycopeptide tandem mass spectra have appeared, but their relative performance remains untested. Conducted through the HUPO Human Glycoproteomics Initiative, this community study, comprising both developers and users of glycoproteomics software, evaluates solutions for system-wide glycopeptide analysis. The same mass spectrometrybased glycoproteomics datasets from human serum were shared with participants and the relative team performance for N- and O-glycopeptide data analysis was comprehensively established by orthogonal performance tests. Although the results were variable, several high-performance glycoproteomics informatics strategies were identified. Deep analysis of the data revealed key performance-associated search parameters and led to recommendations for improved `high-coverage' and `high-accuracy' glycoproteomics search solutions. This study concludes that diverse software packages for comprehensive glycopeptide data analysis exist, points to several high-performance search strategies and specifies key variables that will guide future software developments and assist informatics decision-making in glycoproteomics. This analysis presents the results of a community-based evaluation of existing software for large-scale glycopeptide data analysis. (AU)

• Processo FAPESP: 18/15549-1 - Modificações pós-traducionais nos processos biológicos e no diagnóstico da Doença de Chagas: novas abordagens metodológicas e implicações biológicas
• Beneficiário: Giuseppe Palmisano
• Modalidade de apoio: Auxílio à Pesquisa - Jovens Pesquisadores - Fase 2