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- Kawahara, R. (author)
Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis
- Article/chapterEnglish2021
Publisher, publication year, extent ...
- 2021-11-01
- Springer Science and Business Media LLC,2021
Numbers
- LIBRIS-ID:oai:gup.ub.gu.se/311196
- https://gup.ub.gu.se/publication/311196URI
- https://doi.org/10.1038/s41592-021-01309-xDOI
Supplementary language notes
- Language:English
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- SwePubSwePub
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Notes
- 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.
Subject headings and genre
- MEDICIN OCH HÄLSOVETENSKAP Klinisk medicin hsv//swe
- MEDICAL AND HEALTH SCIENCES Clinical Medicine hsv//eng
- mass-spectrometry
- glycosylation analysis
- liquid-chromatography
- o-glycopeptides
- identification
- glycomics
- proteins
- cell
- sialylglycopeptide
- algorithm
- Biochemistry & Molecular Biology
Added entries (persons, corporate bodies, meetings, titles ...)
- Chernykh, A. (author)
- Alagesan, K. (author)
- Bern, M. (author)
- Cao, W. Q. (author)
- Chalkley, R. J. (author)
- Cheng, K. (author)
- Choo, M. S. (author)
- Edwards, N. (author)
- Goldman, R. (author)
- Hoffmann, M. (author)
- Hu, Y. W. (author)
- Huang, Y. F. (author)
- Kim, J. Y. (author)
- Kletter, D. (author)
- Liquet, B. (author)
- Liu, M. Q. (author)
- Mechref, Y. (author)
- Meng, B. (author)
- Neelamegham, S. (author)
- Nguyen-Khuong, T. (author)
- Nilsson, Jonas,1970Gothenburg University,Göteborgs universitet,Institutionen för biomedicin, avdelningen för laboratoriemedicin,Department of Laboratory Medicine(Swepub:gu)xnjoni (author)
- Pap, A. (author)
- Park, G. W. (author)
- Parker, B. L. (author)
- Pegg, C. L. (author)
- Penninger, J. M. (author)
- Phung, T. K. (author)
- Pioch, M. (author)
- Rapp, E. (author)
- Sakalli, E. (author)
- Sanda, M. (author)
- Schulz, B. L. (author)
- Scott, N. E. (author)
- Sofronov, G. (author)
- Stadlmann, J. (author)
- Vakhrushev, S. Y. (author)
- Woo, C. M. (author)
- Wu, H. Y. (author)
- Yang, P. Y. (author)
- Ying, W. T. (author)
- Zhang, H. (author)
- Zhang, Y. (author)
- Zhao, J. F. (author)
- Zaia, J. (author)
- Haslam, S. M. (author)
- Palmisano, G. (author)
- Yoo, J. S. (author)
- Larson, Göran,1953Gothenburg University,Göteborgs universitet,Institutionen för biomedicin, avdelningen för laboratoriemedicin,Department of Laboratory Medicine(Swepub:gu)xlarsg (author)
- Khoo, K. H. (author)
- Medzihradszky, K. F. (author)
- Kolarich, D. (author)
- Packer, N. H. (author)
- Thaysen-Andersen, M. (author)
- Göteborgs universitetInstitutionen för biomedicin, avdelningen för laboratoriemedicin (creator_code:org_t)
Related titles
- In:Nature Methods: Springer Science and Business Media LLC18, s. 1304-13161548-70911548-7105
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- Cheng, K.
- Choo, M. S.
- Edwards, N.
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- Hu, Y. W.
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- 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. Y.
- Ying, W. T.
- Zhang, H.
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- Haslam, S. M.
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