Improved identification of O-linked glycopeptides from ETD data with optimized scoring for different charge states and cleavage specificities.

Amino Acids
Zsuzsa DarulaKatalin F Medzihradszky

Abstract

This article describes the effect of re-interrogation of electron-transfer dissociation (ETD) data with newly developed analytical tools. MS/MS-based characterization of O-linked glycopeptides is discussed using data acquired from a complex mixture of O-linked glycopeptides, featuring mucin core 1-type carbohydrates with and without sialic acid, as well as after partial deglycosylation to leave only the core GalNAc units (Darula and Medzihradszky in Mol Cell Proteomics 8:2515, 2009). Information content of collision-induced dissociation spectra generated in collision cell (in QqTOF instruments) and in ion traps is compared. Interpretation of the corresponding ETD data using Protein Prospector is also presented. Search results using scoring based on the frequency of different fragment ions occurring in ETD spectra of tryptic peptides are compared with results obtained after ion weightings were adjusted to accommodate differential ion frequencies in spectra of differing charge states or cleavage specificities. We show that the improved scoring is more than doubled the glycopeptide assignments under very strict acceptance criteria. This study illustrates that "old" proteomic data may yield significant new information when re-inter...Continue Reading

References

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May 5, 1999·Journal of Mass Spectrometry : JMS·K AlvingJ Peter-Katalinic
Jun 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·John E P SykaDonald F Hunt
Jan 18, 2006·Methods in Enzymology·Jasna Peter-Katalinić
Aug 14, 2009·Molecular & Cellular Proteomics : MCP·Zsuzsanna Darula, Katalin F Medzihradszky
Apr 1, 1996·Journal of the American Society for Mass Spectrometry·K F MedzihradszkyaffM R Hardyaff

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Citations

May 20, 2011·Amino Acids·Hartmut Schlüter, Peter R Jungblut
Aug 14, 2012·Glycoconjugate Journal·Jonas NilssonGöran Larson
Mar 7, 2012·Molecular & Cellular Proteomics : MCP·Z DarulaK F Medzihradszky
Mar 26, 2014·Journal of the American Society for Mass Spectrometry·Zsuzsanna Darula, Katalin F Medzihradszky
May 2, 2013·Journal of the American Society for Mass Spectrometry·Irina PerdivaraKenneth B Tomer
Jun 14, 2015·Annual Review of Analytical Chemistry·Zhikai Zhu, Heather Desaire
May 16, 2015·Analytical Chemistry·Zsuzsanna Darula, Katalin F Medzihradszky
Nov 28, 2013·Analytical Chemistry·Anoop MayampurathHaixu Tang
Nov 3, 2016·Molecular & Cellular Proteomics : MCP·Jason C MaynardKatalin F Medzihradszky
Dec 22, 2011·Circulation. Cardiovascular Genetics·Venkata D P Paruchuri, Natasha E Zachara
Jan 6, 2016·Glycoconjugate Journal·Zsuzsanna DarulaKatalin F Medzihradszky
May 24, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Laure ToniniMichel Rivière
May 8, 2018·Journal of the American Society for Mass Spectrometry·Adam PapKatalin F Medzihradszky
Jul 29, 2021·ACS Chemical Biology·Valentina Rangel-Angarita, Stacy A Malaker
Dec 31, 2016·Analytical Chemistry·Hongqiang QinHanfa Zou
Jun 6, 2020·Journal of Proteome Research·Nicholas M RileyCarolyn R Bertozzi
Dec 15, 2016·Chemical Reviews·Krishnan K Palaniappan, Carolyn R Bertozzi

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Methods Mentioned

BETA
glycosylation
acetylation

Software Mentioned

Protein Prospector Batch - Tag
Prospector
PAVA
Protein Prospector
Bioworks

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