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

Autor: Robert J. Chalkley, Kai Hooi Khoo, Daniel Kolarich, Erdmann Rapp, Yong Zhang, Hung Yi Wu, Miloslav Sanda, Jonas Nilsson, Enes Sakalli, Gun Wook Park, Doron Kletter, Kathirvel Alagesan, Katalin F. Medzihradszky, Rebeca Kawahara, Nathan Edwards, Radoslav Goldman, Nicolle H. Packer, Yehia Mechref, Wantao Ying, Joseph Zaia, Sriram Neelamegham, Bo Meng, Sergey Y. Vakhrushev, Benjamin L. Schulz, Markus Pioch, Benoit Liquet, Jin Young Kim, Johannes Stadlmann, Benjamin L. Parker, Terry Nguyen-Khuong, Jong Shin Yoo, Adam Pap, Nichollas E. Scott, Mingqi Liu, Marcus Hoffmann, Morten Thaysen-Andersen, Jingfu Zhao, Yingwei Hu, Göran Larson, Matthew S F Choo, Pengyuan Yang, Josef M. Penninger, Marshall Bern, Christina M. Woo, Weiqian Cao, Toan K. Phung, Giuseppe Palmisano, Kai Cheng, Anastasia Chernykh, Stuart M. Haslam, Yifan Huang, Hui Zhang, Cassandra L. Pegg, Georgy Sofronov
Rok vydání: 2021
Předmět:
Zdroj: Nature Methods
Repositório Institucional da USP (Biblioteca Digital da Produção Intelectual)
Universidade de São Paulo (USP)
instacron:USP
Nature methods, vol 18, iss 11
Kawahara, R, Chernykh, A, Alagesan, K, Bern, M, Cao, W, Chalkley, R J, Cheng, K, Choo, M S, Edwards, N, Goldman, R, Hoffmann, M, Hu, Y, Huang, Y, Kim, J Y, Kletter, D, Liquet, B, Liu, M, Mechref, Y, Meng, B, Neelamegham, S, Nguyen-Khuong, T, Nilsson, J, Pap, A, Park, G W, Parker, B L, Pegg, C L, Penninger, J M, Phung, T K, Pioch, M, Rapp, E, Sakalli, E, Sanda, M, Schulz, B L, Scott, N E, Sofronov, G, Stadlmann, J, Vakhrushev, S Y, Woo, C M, Wu, H Y, Yang, P, Ying, W, Zhang, H, Zhang, Y, Zhao, J, Zaia, J, Haslam, S M, Palmisano, G, Yoo, J S, Larson, G, Khoo, K H, Medzihradszky, K F, Kolarich, D, Packer, N H & Thaysen-Andersen, M 2021, ' Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis ', Nature Methods, vol. 18, no. 11, pp. 1304-1316 . https://doi.org/10.1038/s41592-021-01309-x
ISSN: 1548-7105
1548-7091
DOI: 10.1038/s41592-021-01309-x
Popis: 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.
Databáze: OpenAIRE
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