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

Publikováno v: 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

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 HU

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6fd1540e30b1ed9db633b6604fd71731
https://doi.org/10.1038/s41592-021-01309-x

Community Evaluation of Glycoproteomics Informatics Solutions Reveals High-Performance Search Strategies of SerumN- andO-Glycopeptide Data

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

Glycoproteome profiling (glycoproteomics) is a powerful yet analytically challenging research tool. The complex tandem mass spectra generated from glycopeptide mixtures require sophisticated analysis pipelines for structural determination. Diverse so

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::8808389608862c33bf84f95e426a6ea3
https://doi.org/10.1101/2021.03.14.435332

Assessing the reproducibility of an O ‐glycopeptide enrichment method with a novel software, Pinnacle

Autor: Zsuzsanna Darula, Katalin F. Medzihradszky, Amol Prakash, Adam Pap

Publikováno v: ELECTROPHORESIS. 39:3142-3147

A novel software, Pinnacle was used to reassess the reproducibility of a 2-step lectin-based O-glycopeptide enrichment method. A publicly available dataset consisting of 12 data files representing 3 technical replicates of enriched glycopeptides from

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cd95b947451c2934d825d3a8b8ffbd6a
https://doi.org/10.1002/elps.201800223

Using 'spectral families' to assess the reproducibility of glycopeptide enrichment: human serum O-glycosylation revisited

Autor: Katalin F. Medzihradszky, Zsuzsanna Darula, Adam Pap

Publikováno v: Analytical and Bioanalytical Chemistry. 409:539-550

Growing evidence on the diverse biological roles of extracellular glycosylation as well as the need for quality control of protein pharmaceuticals make glycopeptide analysis both exciting and important again after a long hiatus. High-throughput O-gly

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::29009f0ef06598f99a361b386dfc1238
https://doi.org/10.1007/s00216-016-9960-7

Status Report on the High-Throughput Characterization of Complex Intact O-Glycopeptide Mixtures

Autor: Katalin F. Medzihradszky, Zsuzsanna Darula, Éva Hunyadi-Gulyás, Éva Klement, Adam Pap

Publikováno v: Journal of the American Society for Mass Spectrometry. 29(6)

A very complex mixture of intact, human N- and O-glycopeptides, enriched from the tryptic digest of urinary proteins of three healthy donors using a two-step lectin affinity enrichment, was analyzed by LC-MS/MS, leading to approximately 45,000 glycop

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f150719deacd960732cb6c005f12989d
https://pubmed.ncbi.nlm.nih.gov/29730764