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

Rebeca Kawahara; Anastasia Chernykh; Kathirvel Alagesan; Marshall Bern; Weiqian Cao; Robert J. Chalkley; Kai Cheng; Matthew S. Choo; Nathan Edwards; Radoslav Goldman; Marcus Hoffmann; Yingwei Hu; Yifan Huang; Jin Young Kim; Doron Kletter; Benoit Liquet; Mingqi Liu; Yehia Mechref; Bo Meng; Sriram Neelamegham; Terry Nguyen-Khuong; Jonas Nilsson; Adam Pap; Gun Wook Park; Benjamin L. Parker; Cassandra L. Pegg; Josef M. Penninger; Toan K. Phung; Markus Pioch; Erdmann Rapp; Enes Sakalli; Miloslav Sanda; Benjamin L. Schulz; Nichollas E. Scott; Georgy Sofronov; Johannes Stadlmann; Sergey Y. Vakhrushev; Christina M. Woo; Hung Yi Wu; Pengyuan Yang; Wantao Ying; Hui Zhang; Yong Zhang; Jingfu Zhao; Joseph Zaia; Stuart M. Haslam; Giuseppe Palmisano; Jong Shin Yoo; Göran Larson; Kai Hooi Khoo; Katalin F. Medzihradszky; Daniel Kolarich; Nicolle H. Packer; Morten Thaysen-Andersen

doi:10.1038/s41592-021-01309-x

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

Rebeca Kawahara, Anastasia Chernykh, Kathirvel Alagesan, Marshall Bern, Weiqian Cao, Robert J. Chalkley, Kai Cheng, Matthew S. Choo, Nathan Edwards, Radoslav Goldman, Marcus Hoffmann, Yingwei Hu, Yifan Huang, Jin Young Kim, Doron Kletter, Benoit Liquet, Mingqi Liu, Yehia Mechref, Bo Meng, Sriram NeelameghamTerry Nguyen-Khuong, Jonas Nilsson, Adam Pap, Gun Wook Park, Benjamin L. Parker, Cassandra L. Pegg, Josef M. Penninger, Toan K. Phung, Markus Pioch, Erdmann Rapp, Enes Sakalli, Miloslav Sanda, Benjamin L. Schulz, Nichollas E. Scott, Georgy Sofronov, Johannes Stadlmann, Sergey Y. Vakhrushev, Christina M. Woo, Hung Yi Wu, Pengyuan Yang, Wantao Ying, Hui Zhang, Yong Zhang, Jingfu Zhao, Joseph Zaia, Stuart M. Haslam, Giuseppe Palmisano, Jong Shin Yoo, Göran Larson, Kai Hooi Khoo, Katalin F. Medzihradszky, Daniel Kolarich, Nicolle H. Packer, Morten Thaysen-Andersen^*

^*Corresponding author af dette arbejde

Glycomics Program

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

107 Citationer (Scopus)

23 Downloads (Pure)

Abstract

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.

Originalsprog	Engelsk
Tidsskrift	Nature Methods
Vol/bind	18
Udgave nummer	11
Sider (fra-til)	1304-1316
Antal sider	13
ISSN	1548-7091
DOI	https://doi.org/10.1038/s41592-021-01309-x
Status	Udgivet - 2021

Bibliografisk note

Funding Information:
Rosa Viner and Sergei Snovida (Thermo Fisher Scientific) are thanked for providing high-quality LC-MS/MS data. Krishnatej Nishtala is thanked for aiding the data analysis. Catherine Hayes, Julien Mariethoz and Frederique Lisacek are thanked for informatics assistance. RK was supported by an Early Career Fellowship (Cancer Institute NSW ECF181259). DK was supported by an Australian Research Council Future Fellowship (FT160100344). GP was funded by FAPESP (n° 2018/15549-1). MT-A was supported by a Macquarie University Safety Net Grant. DK and NHP were supported by the Australian Research Council Centre of Excellence in Nanoscale Biophotonics (CE140100003).

Publisher Copyright:
© 2021, The Author(s).

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

Citationsformater

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., ... Thaysen-Andersen, M. (2021). Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis. Nature Methods, 18(11), 1304-1316. https://doi.org/10.1038/s41592-021-01309-x

Kawahara, R, Chernykh, A, Alagesan, K, Bern, M, Cao, W, Chalkley, RJ, Cheng, K, Choo, MS, Edwards, N, Goldman, R, Hoffmann, M, Hu, Y, Huang, Y, Kim, JY, Kletter, D, Liquet, B, Liu, M, Mechref, Y, Meng, B, Neelamegham, S, Nguyen-Khuong, T, Nilsson, J, Pap, A, Park, GW, Parker, BL, Pegg, CL, Penninger, JM, Phung, TK, Pioch, M, Rapp, E, Sakalli, E, Sanda, M, Schulz, BL, Scott, NE, Sofronov, G, Stadlmann, J, Vakhrushev, SY, Woo, CM, Wu, HY, Yang, P, Ying, W, Zhang, H, Zhang, Y, Zhao, J, Zaia, J, Haslam, SM, Palmisano, G, Yoo, JS, Larson, G, Khoo, KH, Medzihradszky, KF, Kolarich, D, Packer, NH & Thaysen-Andersen, M 2021, 'Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis', Nature Methods, bind 18, nr. 11, s. 1304-1316. https://doi.org/10.1038/s41592-021-01309-x

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abstract = "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 {\textquoteleft}high-coverage{\textquoteright} and {\textquoteleft}high-accuracy{\textquoteright} 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.",

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AU - Kawahara, Rebeca

AU - Chernykh, Anastasia

AU - Alagesan, Kathirvel

AU - Bern, Marshall

AU - Cao, Weiqian

AU - Chalkley, Robert J.

AU - Cheng, Kai

AU - Choo, Matthew S.

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AU - Goldman, Radoslav

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AU - Nguyen-Khuong, Terry

AU - Nilsson, Jonas

AU - Pap, Adam

AU - Park, Gun Wook

AU - Parker, Benjamin L.

AU - Pegg, Cassandra L.

AU - Penninger, Josef M.

AU - Phung, Toan K.

AU - Pioch, Markus

AU - Rapp, Erdmann

AU - Sakalli, Enes

AU - Sanda, Miloslav

AU - Schulz, Benjamin L.

AU - Scott, Nichollas E.

AU - Sofronov, Georgy

AU - Stadlmann, Johannes

AU - Vakhrushev, Sergey Y.

AU - Woo, Christina M.

AU - Wu, Hung Yi

AU - Yang, Pengyuan

AU - Ying, Wantao

AU - Zhang, Hui

AU - Zhang, Yong

AU - Zhao, Jingfu

AU - Zaia, Joseph

AU - Haslam, Stuart M.

AU - Palmisano, Giuseppe

AU - Yoo, Jong Shin

AU - Larson, Göran

AU - Khoo, Kai Hooi

AU - Medzihradszky, Katalin F.

AU - Kolarich, Daniel

AU - Packer, Nicolle H.

AU - Thaysen-Andersen, Morten

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AB - 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.

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