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(Glyco-AMP): a Simple Method for Detailed and Quantitative Glycoproteomic Characterization Serenus Hua, Chloe Y Hu, Bum Jin Kim, Sarah M

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(Glyco-AMP): a Simple Method for Detailed and Quantitative Glycoproteomic Characterization Serenus Hua, Chloe Y Hu, Bum Jin Kim, Sarah M Subscriber access provided by - Access paid by the | UC Davis Libraries Article Glyco-analytical multispecific proteolysis (Glyco-AMP): A simple method for detailed and quantitative glycoproteomic characterization Serenus Hua, Chloe Y Hu, Bum Jin Kim, Sarah M. Totten, Myung Jin Oh, Nayoung Yun, Charles Chuks Nwosu, Jong Shin Yoo, Carlito B. Lebrilla, and Hyun Joo An J. Proteome Res., Just Accepted Manuscript • DOI: 10.1021/pr400442y • Publication Date (Web): 09 Sep 2013 Downloaded from http://pubs.acs.org on September 13, 2013 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 41 Journal of Proteome Research 1 2 3 4 Glyco-analytical multispecific proteolysis (Glyco-AMP): A 5 6 7 8 simple method for detailed and quantitative glycoproteomic 9 10 11 characterization 12 13 14 15 16 1,2 3 1 3 1 17 Serenus Hua, Chloe Y. Hu, Bum Jin Kim, Sarah M. Totten, Myung Jin Oh, 18 19 Nayoung Yun,1 Charles C. Nwosu,3 Jong Shin Yoo,1,4 Carlito B. Lebrilla,3*† and 20 21 22 Hyun Joo An1,2*† 23 24 25 26 27 28 1. Graduate School of Analytical Science and Technology, Chungnam National University, 29 30 Daejeon, Korea 31 32 33 2. Cancer Research Institute, Chungnam National University, Daejeon, Korea 34 35 3. Department of Chemistry, University of California, Davis, CA 36 37 4. Division of Mass Spectrometry Research, Korea Basic Science Institute, Ochang, Korea 38 39 40 41 42 * 43 To whom correspondence should be addressed: 44 45 Hyun Joo An, email: [email protected], Tel: 82 42-821-8547, Fax: 82 42-821-8551 46 47 48 Carlito B. Lebrilla, email: [email protected], Tel: 1 530-752-0504, Fax: 1 530-752-8995 49 50 51 52 53 † Hyun Joo An and Carlito B. Lebrilla contributed equally to this paper as co-corresponding 54 55 authors. 56 57 58 59 60 ACS Paragon Plus Environment Journal of Proteome Research Page 2 of 41 1 2 3 4 5 6 7 KEYWORDS: multispecific proteases, non-specific proteases, site-specific glycosylation, 8 9 glycoproteomics, biopharmaceutical glycoproteins, glycan isomers 10 11 12 13 14 ABBREVIATIONS: Glyco-AMP, glyco-analytical multispecific proteolysis; Hex, hexose; 15 16 HexNAc, N-acetylhexosamine; Man, mannose; GlcNAc, N-acetylglucosamine; Fuc, fucose; G1F, 17 18 Hex HexNAc Fuc; NeuAc, N-acetylneuraminic acid; OAc, O-acetylation 19 4 4 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 ACS Paragon Plus Environment Page 3 of 41 Journal of Proteome Research 1 2 3 4 ABSTRACT 5 6 7 8 9 Despite recent advances, site-specific profiling of protein glycosylation remains a significant 10 11 analytical challenge for conventional proteomic methodology. To alleviate the issue, we propose 12 13 glyco-analytical multispecific proteolysis (Glyco-AMP) as a strategy for glycoproteomic 14 15 16 characterization. Glyco-AMP consists of rapid, in-solution digestion of an analyte glycoprotein 17 18 (or glycoprotein mixture) by a multispecific protease (or protease cocktail). Resulting 19 20 glycopeptides are chromatographically separated by isomer-specific porous graphitized carbon 21 22 23 nano-LC, quantified by high-resolution MS, and structurally elucidated by MS/MS. To 24 25 demonstrate the consistency and customizability of Glyco-AMP methodology, the glyco- 26 27 analytical performances of multispecific proteases subtilisin, pronase, and proteinase K were 28 29 30 characterized in terms of quantitative accuracy, sensitivity, and digestion kinetics. Glyco-AMP 31 32 was shown be effective on glycoprotein mixtures as well as glycoproteins with multiple 33 34 35 glycosylation sites, providing detailed, quantitative, site- and structure-specific information about 36 37 protein glycosylation. 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 ACS Paragon Plus Environment Journal of Proteome Research Page 4 of 41 1 2 3 4 INTRODUCTION 5 6 7 8 9 Proteins are commonly decorated with long carbohydrate chains, known as glycans, during 10 11 normal biosynthesis. Over 60% of the known proteome is believed to be glycosylated.1 As the 12 13 importance of glycosylation towards protein structure and function becomes ever more apparent, 14 15 16 glycomic methods for profiling the detached glycan component of a glycoprotein have 17 18 undergone extensive innovation and development.2-4 However, glycoproteomic methods that 19 20 characterize both glycosylation site and glycan structure are still in their infancy. Until now, the 21 22 5-7 23 most commonly-used methods have been adapted from traditional proteomics and often do not 24 25 sufficiently address the complexities of characterizing a post-translational modification as 26 27 intricate as glycosylation. 28 29 30 Whereas peptides can be identified and characterized simply by their linear sequence, 31 32 glycans are branched, with different linkage possibilities between each monosaccharide residue. 33 34 35 When peptide and glycan moieties both exist on a single molecule, as with glycopeptides, 36 37 peptide sequence isomers and glycosylation site isomers further increase the already significant 38 39 structural complexity.8 The abundance of isomeric glycopeptides encountered during 40 41 42 glycoproteomic analysis is problematic for mass spectrometry, which cannot distinguish between 43 44 isomers without the assistance of additional analytical technologies. Consequently, 45 46 glycoproteomic methods incorporating isomer-specific chromatographic separation and/or 47 48 9 49 tandem MS are crucial for effective glycoprotein characterization. 50 51 When analyzing peptides with post-translational modifications such as glycosylation, peptide 52 53 54 length must be considered. Large glycopeptides are not only harder to detect by mass 55 56 spectrometry (due to decreased ionization efficiency as well as instrumental mass limitations) but 57 58 59 60 ACS Paragon Plus Environment Page 5 of 41 Journal of Proteome Research 1 2 3 can also incorporate multiple glycosylation sites, severely complicating or obfuscating site- 4 5 10-12 6 specific analysis. Proteases with high substrate specificity, such as trypsin, are especially 7 8 prone to creating these large glycopeptides, since their specificity severely limits potential 9 10 13 11 cleavage sites. This is exacerbated by the well-known phenomenon of glycoprotein trypsin 12 13 resistance, wherein large glycosyl modifications sterically hinder protease access to a 14 15 glycoprotein cleavage site, resulting in a missed cleavage.14, 15 16 17 18 While the amino acid sequences of some glycoproteins may be fortuitously rich in tryptic 19 20 cleavage sites, many are not so easily dissected.16, 17 The glycoproteomics community is 21 22 therefore in great need of alternative proteases and proteolytic digestion strategies that can be 23 24 25 broadly applied to enhance and/or replace conventional trypsin-based methodology. One such 26 27 strategy is multispecific (or non-specific) proteolysis, which utilizes proteases or protease 28 29 cocktails with multiple substrate specificities to hydrolyze peptide bonds at a number of different 30 31 32 sites on a glycoprotein. The resulting digest contains glycopeptides of a roughly consistent size, 33 34 irrespective of the glycoprotein's amino acid sequence or steric hindrance by the glycan moiety.18, 35 36 19 37 38 39 Early forays into glycoprotein characterization via multispecific proteolysis involved MS- 40 41 only analysis of single glycoprotein digests.20 Sensitivity and specificity were relatively low, due 42 43 44 to interference from ion-suppressing unglycosylated peptides. Later iterations of the strategy 45 46 used various chemical methods to immobilize the multispecific proteases on solid supports, 47 48 removing a significant amount of the peptide interference originating from protease autolysis.21, 49 50 22 51 However, the most dramatic improvements in glycoproteomics have come just recently, with 52 53 the incorporation of nano-LC separation into established mass spectrometric methods.8, 9, 23 Use 54 55 of nano-LC/MS not only boosts sensitivity by vastly reducing interference from ion-suppressing 56 57 58 59 60 ACS Paragon Plus Environment Journal of Proteome Research Page 6 of 41 1 2 3 peptides, but also enables differentiation of isobaric or even isomeric molecules.
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