Subscriber access provided by Northern Illinois University
Technical Note
Towards Automated N-Glycopeptide Identification in Glycoproteomics Ling Y. Lee, Edward S.X. Moh, Benjamin L. Parker, Marshall Bern, Nicolle H. Packer, and Morten Thaysen-Andersen J. Proteome Res., Just Accepted Manuscript • DOI: 10.1021/acs.jproteome.6b00438 • Publication Date (Web): 12 Aug 2016 Downloaded from http://pubs.acs.org on August 16, 2016
Just Accepted “Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society provides “Just Accepted” as a free service to the research community to expedite the dissemination of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully peer reviewed, but should not be considered the official version of record. They are accessible to all readers and citable by the Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore, the “Just Accepted” Web site may not include all articles that will be published in the journal. After a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web site and published as an ASAP article. Note that technical editing may introduce minor changes to the manuscript text and/or graphics which could affect content, and all legal disclaimers and ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or consequences arising from the use of information contained in these “Just Accepted” manuscripts.
Journal of Proteome Research is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the course of their duties.
Page 1 of 35
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
Journal of Proteome Research
Towards Automated N-glycopeptide Identification in Glycoproteomics Ling Y. Lee1, Edward S. X. Moh1, Benjamin L. Parker2, Marshall Bern3, Nicolle H. Packer1, and Morten Thaysen-Andersen*1 1
Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109,
Australia. 2
Charles Perkins Centre, School of Molecular Bioscience, The University of Sydney, Sydney, Australia.
3
Protein Metrics Inc., San Carlos, California 94070, United States.
Running title: Towards automated N-glycopeptide identification in glycoproteomics
Keywords: N-glycosylation, LC-MS/MS, glycopeptide, glycoproteomics, basigin, glycoprofiling, glycomics, automated glycopeptide identification, Byonic.
*Corresponding author: Dr. Morten Thaysen-Andersen Department of Chemistry and Biomolecular Sciences Macquarie University Sydney, NSW-2109 Australia Phone / Fax: (+61) 2 9850 7487 / (+61) 2 9850 6192 E-mail:
[email protected] 1 ACS Paragon Plus Environment
Journal of Proteome Research
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
Page 2 of 35
ABSTRACT Advances in software-driven glycopeptide identification have facilitated N-glycoproteomics studies reporting thousands of intact N-glycopeptides, i.e. N-glycan-conjugated peptides, but the automated identification process remains to be scrutinised. Herein, we compare the site-specific glycoprofiling efficiency of the PTM-centric search engine Byonic relative to manual expert annotation utilising typical glycoproteomics acquisition and data analysis strategies, but of a single glycoprotein, the uncharacterised multiple N-glycosylated human basigin. Detailed site-specific reference glycoprofiles of purified basigin were manually established using ion trap CID-MS/MS and high-resolution QExactive Orbitrap HCD-MS/MS of tryptic N-glycopeptides and released N-glycans. The micro- and macro-heterogeneous basigin N-glycosylation was site-specifically glycoprofiled using Byonic with or without a background of complex peptides using Q-Exactive Orbitrap HCD-MS/MS. The automated glycoprofiling efficiencies were assessed against the site-specific reference glycoprofiles and target/decoy proteome databases. Within the limits of this single glycoprotein analysis, the search criteria and confidence thresholds (Byonic scores) recommended by the vendor provided high glycoprofiling accuracy and coverage (both >80%) and low peptide FDRs (
