Methods for quantification of glycopeptides by liquid separation and mass spectrometry.

Publisher: Wiley Country of Publication: United States NLM ID: 8219702 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1098-2787 (Electronic) Linking ISSN: 02777037 NLM ISO Abbreviation: Mass Spectrom Rev Subsets: MEDLINE

Original Publication: New York : Wiley, [c1982-

Glycopeptides*/analysis ; Glycoproteins*/analysis; Mass Spectrometry/methods ; Glycosylation ; Chromatography, Liquid/methods

Recent advances in analytical techniques provide the opportunity to quantify even low-abundance glycopeptides derived from complex biological mixtures, allowing for the identification of glycosylation differences between healthy samples and those derived from disease states. Herein, we discuss the sample preparation procedures and the mass spectrometry (MS) strategies that have facilitated glycopeptide quantification, as well as the standards used for glycopeptide quantification. For sample preparation, various glycopeptide enrichment methods are summarized including the columns used for glycopeptide separation in liquid chromatography separation. For MS analysis strategies, MS1 level-based quantification and MS2 level-based quantification are described, either with or without labeling, where we have covered isotope labeling, TMT/iTRAQ labeling, data dependent acquisition, data independent acquisition, multiple reaction monitoring, and parallel reaction monitoring. The strengths and weaknesses of these methods are compared, particularly those associated with the figures of merit that are important for clinical biomarker studies and the pathological and functional studies of glycoproteins in various diseases. Possible future developments for glycopeptide quantification are discussed.
(© 2022 John Wiley & Sons Ltd.)

Nat Methods. 2018 Jun;15(6):440-448. (PMID: 29735998)
Proteomics Clin Appl. 2018 Nov;12(6):e1800062. (PMID: 29888876)
Anal Chem. 2009 May 15;81(10):3776-83. (PMID: 19366252)
Anal Chem. 2020 Sep 15;92(18):12588-12595. (PMID: 32786443)
Rapid Commun Mass Spectrom. 2009 Feb;23(4):495-505. (PMID: 19145579)
J Virol. 2020 Feb 14;94(5):. (PMID: 31826991)
Mol Cell Proteomics. 2020 Apr;19(4):672-689. (PMID: 32102970)
Nat Biotechnol. 2014 Mar;32(3):219-23. (PMID: 24727770)
Nat Rev Mol Cell Biol. 2020 Dec;21(12):729-749. (PMID: 33087899)
J Proteome Res. 2020 Aug 7;19(8):3452-3466. (PMID: 32412768)
Mass Spectrom Rev. 2020 Jul;39(4):371-409. (PMID: 32350911)
J Proteomics. 2012 Feb 2;75(4):1318-29. (PMID: 22120122)
Anal Chem. 1997 Nov 15;69(22):4530-5. (PMID: 9375514)
Mass Spectrom Rev. 2023 Mar;42(2):577-616. (PMID: 34159615)
Molecules. 2014 Jul 09;19(7):9944-61. (PMID: 25010467)
Mol Cell Proteomics. 2021;20:100060. (PMID: 33556625)
Curr Protoc Protein Sci. 2012 Apr;Chapter 12:12.11.1-12.11.11. (PMID: 22470127)
J Proteome Res. 2015 Nov 6;14(11):4876-84. (PMID: 26403951)
Analyst. 2006 Dec;131(12):1316-21. (PMID: 17124539)
Anal Chem. 2020 Jan 21;92(2):1680-1686. (PMID: 31859482)
Anal Chim Acta. 2020 Mar 15;1102:130-139. (PMID: 32043992)
Nat Biotechnol. 2003 Jun;21(6):660-6. (PMID: 12754519)
Anal Bioanal Chem. 2019 May;411(14):3009-3019. (PMID: 31076819)
J Proteome Res. 2020 Aug 7;19(8):3286-3301. (PMID: 32500713)
Curr Opin Chem Biol. 2009 Oct;13(4):421-6. (PMID: 19700364)
Anal Chem. 2019 Apr 16;91(8):5433-5445. (PMID: 30882205)
J Proteome Res. 2016 Aug 5;15(8):2826-40. (PMID: 27399812)
Methods Mol Biol. 2017;1503:109-119. (PMID: 27743362)
Front Chem. 2020 Apr 17;8:240. (PMID: 32363175)
Metabolites. 2021 Aug 23;11(8):. (PMID: 34436504)
ACS Med Chem Lett. 2018 Aug 10;9(9):889-894. (PMID: 30258536)
Talanta. 2010 Feb 15;80(4):1476-86. (PMID: 20082805)
Sci Adv. 2020 Oct 2;6(40):. (PMID: 33008897)
J Proteome Res. 2016 Jul 1;15(7):2198-210. (PMID: 27267458)
Anal Chem. 2015 Oct 20;87(20):10222-9. (PMID: 26398777)
Mol Aspects Med. 2021 Jun;79:100964. (PMID: 33775405)
Sci Rep. 2019 Apr 2;9(1):5522. (PMID: 30940835)
Mol Cell Proteomics. 2016 Jan;15(1):141-53. (PMID: 26537798)
Chem Rev. 2018 Sep 12;118(17):7886-7930. (PMID: 29553244)
Anal Chem. 2020 Jan 7;92(1):690-698. (PMID: 31859485)
Anal Biochem. 2009 Dec 15;395(2):178-88. (PMID: 19699707)
Mass Spectrom Rev. 2022 Nov;41(6):922-937. (PMID: 33764573)
Nat Methods. 2015 Mar;12(3):258-64, 7 p following 264. (PMID: 25599550)
J Proteome Res. 2007 Mar;6(3):1126-38. (PMID: 17249709)
Analyst. 2018 May 29;143(11):2508-2519. (PMID: 29687791)
J Chromatogr B Analyt Technol Biomed Life Sci. 2019 Mar 15;1110-1111:101-107. (PMID: 30798070)
Anal Bioanal Chem. 2017 Jan;409(2):589-606. (PMID: 27796459)
Nat Methods. 2015 Jun;12(6):561-7. (PMID: 25894945)
Biochemistry. 2020 Sep 1;59(34):3089-3097. (PMID: 31833756)
Mol Cell Proteomics. 2020 Jul;19(7):1088-1103. (PMID: 32312845)
Anal Chem. 2015 Nov 3;87(21):10830-8. (PMID: 26451657)
J Proteome Res. 2015 Dec 4;14(12):5179-92. (PMID: 26510530)
Anal Biochem. 2020 May 15;597:113667. (PMID: 32119847)
Nat Protoc. 2009;4(4):484-94. (PMID: 19300442)
J Proteome Res. 2013 May 3;12(5):2225-32. (PMID: 23581850)
J Proteome Res. 2017 Apr 7;16(4):1706-1718. (PMID: 28244757)
Cancer Cell. 2017 Jun 12;31(6):733-735. (PMID: 28609653)
Mol Omics. 2020 Apr 1;16(2):100-112. (PMID: 32104808)
Mol Cell Proteomics. 2021;20:100081. (PMID: 33862227)
Electrophoresis. 2018 Sep;39(18):2351-2361. (PMID: 29405331)
J Biomol Tech. 2016 Sep;27(3):98-104. (PMID: 27582638)
Anal Chem. 2018 Nov 6;90(21):12714-12722. (PMID: 30350625)
Anal Chem. 2012 Oct 16;84(20):8452-6. (PMID: 23009578)
Clin Proteomics. 2017 Aug 15;14:31. (PMID: 28814946)
Anal Chem. 2019 May 7;91(9):6064-6071. (PMID: 30983324)
Mass Spectrom Rev. 2022 Nov;41(6):901-921. (PMID: 33565652)
J Am Soc Mass Spectrom. 2003 May;14(5):492-500. (PMID: 12745218)
Sci Rep. 2017 Jun 16;7(1):3733. (PMID: 28623326)
Mol Cell Proteomics. 2018 Jan;17(1):18-30. (PMID: 28993419)
ACS Chem Biol. 2018 Aug 17;13(8):1983-1989. (PMID: 30059200)
J Proteomics. 2017 Feb 5;153:44-52. (PMID: 27646713)
Anal Chem. 2021 Mar 30;93(12):5061-5070. (PMID: 33720700)
Anal Chem. 2015;87(10):5181-8. (PMID: 25945896)
J Am Soc Mass Spectrom. 2018 Jun;29(6):1210-1220. (PMID: 29730764)
Anal Chem. 2017 Jun 20;89(12):6590-6597. (PMID: 28475308)
J Proteome Res. 2012 Apr 6;11(4):2272-81. (PMID: 22335271)
Anal Chem. 2020 Jun 16;92(12):8201-8208. (PMID: 32426967)
Mol Cell Proteomics. 2012 Jun;11(6):O111.016717. (PMID: 22261725)
J Proteome Res. 2015 Apr 3;14(4):1968-78. (PMID: 25732060)
Mol Cell Proteomics. 2021;20:100029. (PMID: 33583771)
Anal Chem. 2013 Sep 17;85(18):8585-93. (PMID: 23944609)
Anal Chem. 2021 May 25;93(20):7473-7480. (PMID: 33973768)
Hepatol Commun. 2019 Aug 09;3(10):1400-1414. (PMID: 31592495)
Proteomics. 2013 Apr;13(8):1247-56. (PMID: 23322582)
J Chromatogr A. 2007 Apr 13;1147(1):30-6. (PMID: 17320886)
Nat Methods. 2019 Sep;16(9):902-910. (PMID: 31384044)
Analyst. 2020 Aug 7;145(15):5353-5362. (PMID: 32568312)
Anal Chem. 2016 Oct 18;88(20):10118-10125. (PMID: 27649061)
Proc Natl Acad Sci U S A. 2010 Mar 2;107(9):3988-93. (PMID: 20142501)
Curr Protoc Bioinformatics. 2012 Dec;Chapter 13:13.20.1-13.20.14. (PMID: 23255153)
Mass Spectrom Rev. 2010 Sep-Oct;29(5):830-44. (PMID: 20077480)
Protein J. 2018 Apr;37(2):164-179. (PMID: 29411222)
Front Physiol. 2017 Jul 07;8:472. (PMID: 28736531)
Anal Bioanal Chem. 2018 Aug;410(20):5001-5008. (PMID: 29806066)
Mass Spectrom Rev. 2022 May;41(3):488-507. (PMID: 33393161)
Analyst. 2009 Oct;134(10):2158-64. (PMID: 19768230)
Nat Protoc. 2020 Aug;15(8):2668-2704. (PMID: 32681150)
Anal Chem. 2019 Jul 16;91(14):9206-9212. (PMID: 31268672)
J Proteome Res. 2016 Dec 2;15(12):4146-4164. (PMID: 27760464)
Mol Cell Proteomics. 2014 Jun;13(6):1563-72. (PMID: 24692641)
Electrophoresis. 2014 Aug;35(15):2091-107. (PMID: 24729282)
J Proteome Res. 2012 Sep 7;11(9):4517-25. (PMID: 22800195)
Cancer Cell. 2017 Jun 12;31(6):804-819.e7. (PMID: 28609658)
Int J Mol Sci. 2013 Oct 17;14(10):20890-912. (PMID: 24141187)
Anal Bioanal Chem. 2013 May;405(14):4953-8. (PMID: 23525540)
Nat Methods. 2020 Nov;17(11):1125-1132. (PMID: 33020657)
Mol Cell Proteomics. 2011 Feb;10(2):M110.002931. (PMID: 20664071)
Talanta. 2016;146:225-30. (PMID: 26695256)
Talanta. 2021 Feb 1;223(Pt 1):121676. (PMID: 33303137)
Anal Biochem. 2016 Oct 1;510:106-113. (PMID: 27318240)
J Proteome Res. 2016 Sep 2;15(9):3358-76. (PMID: 27500424)
Anal Chem. 2013 Jun 4;85(11):5353-7. (PMID: 23638883)
Mol Cell Proteomics. 2015 Jun;14(6):1630-44. (PMID: 25755295)
Anal Chem. 1996 Jan 1;68(1):1-8. (PMID: 8779426)
J Proteome Res. 2015 Sep 4;14(9):3957-69. (PMID: 26202417)
Anal Bioanal Chem. 2020 Apr;412(11):2423-2432. (PMID: 32030495)
Sci Rep. 2016 Feb 17;6:21175. (PMID: 26883985)
Front Oncol. 2021 Apr 06;11:651421. (PMID: 33889548)
J Am Soc Mass Spectrom. 2009 Jun;20(6):1048-59. (PMID: 19278867)
Mol Cell Proteomics. 2012 Dec;11(12):1709-23. (PMID: 22962056)
ACS Chem Neurosci. 2018 Jan 17;9(1):51-72. (PMID: 28982002)
Nat Rev Cancer. 2015 Sep;15(9):540-55. (PMID: 26289314)
J Proteome Res. 2014 May 2;13(5):2328-38. (PMID: 24628331)
Bioinformatics. 2010 Apr 1;26(7):966-8. (PMID: 20147306)
Anal Chem. 2020 Jul 21;92(14):9556-9565. (PMID: 32544320)
Proteomics. 2015 Jul;15(13):2177-86. (PMID: 25737293)
J Proteome Res. 2016 Sep 2;15(9):2935-44. (PMID: 27354006)
Anal Chem. 2017 Apr 18;89(8):4532-4539. (PMID: 28353332)
Nat Commun. 2020 Oct 19;11(1):5268. (PMID: 33077710)
J Proteome Res. 2018 Jan 5;17(1):222-233. (PMID: 29207246)
Anal Chem. 2013 Jun 18;85(12):5666-75. (PMID: 23662732)
Mol Omics. 2020 Aug 1;16(4):355-363. (PMID: 32281997)
J Proteomics. 2018 Oct 30;189:67-74. (PMID: 29427759)
Rapid Commun Mass Spectrom. 2012 Sep 15;26(17):1941-54. (PMID: 22847692)
Nat Commun. 2017 Sep 5;8(1):438. (PMID: 28874712)
Anal Chem. 2017 Nov 7;89(21):11193-11197. (PMID: 29016103)
Anal Chem. 2020 Jan 7;92(1):267-291. (PMID: 31626732)
J Proteome Res. 2016 Oct 7;15(10):3624-3634. (PMID: 27533485)
Anal Chem. 2020 Jul 7;92(13):9230-9238. (PMID: 32510927)
Nat Protoc. 2020 Aug;15(8):2589-2610. (PMID: 32681153)
Mol Cell Proteomics. 2013 Jan;12(1):158-71. (PMID: 23090970)
J Proteome Res. 2018 Aug 3;17(8):2755-2766. (PMID: 29972295)
J Mass Spectrom. 2021 Jan;56(1):e4693. (PMID: 33277714)
J Proteome Res. 2021 Jun 4;20(6):3278-3289. (PMID: 33929864)
J Proteome Res. 2010 Feb 5;9(2):798-805. (PMID: 19961239)
ACS Chem Biol. 2019 Jan 18;14(1):4-10. (PMID: 30620550)
Mass Spectrom Rev. 2019 May;38(3):265-290. (PMID: 30472795)
Nat Commun. 2019 Mar 21;10(1):1311. (PMID: 30899004)
J Proteome Res. 2014 Apr 4;13(4):1873-84. (PMID: 24571389)
Molecules. 2020 Oct 13;25(20):. (PMID: 33065988)
Anal Bioanal Chem. 2020 Jul;412(18):4423-4432. (PMID: 32377867)
J Proteome Res. 2013 Jun 7;12(6):2630-40. (PMID: 23586699)
Mol Cell Proteomics. 2012 Nov;11(11):1475-88. (PMID: 22865924)
Mol Cell Proteomics. 2021;20:100054. (PMID: 32576592)
J Chromatogr A. 2017 Oct 13;1519:152-155. (PMID: 28888681)
Mol Cell Proteomics. 2019 Nov;18(11):2262-2272. (PMID: 31501225)
Nat Commun. 2018 Apr 27;9(1):1692. (PMID: 29703890)
Analyst. 2019 Jun 7;144(11):3601-3612. (PMID: 31065629)
Nat Biotechnol. 2010 Jul;28(7):710-21. (PMID: 20622845)
Anal Chem. 2011 Nov 15;83(22):8802-9. (PMID: 21970473)
Anal Chem. 2021 Mar 16;93(10):4449-4455. (PMID: 33630567)
Urolithiasis. 2015 Aug;43(4):303-12. (PMID: 25935139)
Biomed Chromatogr. 2017 Nov;31(11):. (PMID: 28409865)
Mass Spectrom Rev. 2019 Aug;38(4-5):356-379. (PMID: 30605224)
J Proteome Res. 2006 Jul;5(7):1792-802. (PMID: 16823988)
Mol Cell Proteomics. 2013 May;12(5):1294-305. (PMID: 23389048)
J Proteomics. 2018 Feb 10;172:68-75. (PMID: 29069609)
Glycoconj J. 2019 Feb;36(1):13-26. (PMID: 30612270)
Front Chem. 2021 Jul 14;9:705341. (PMID: 34336790)
Nat Commun. 2018 Dec 3;9(1):5128. (PMID: 30510204)
Chem Biol. 2014 Jan 16;21(1):1-15. (PMID: 24439204)
J Am Soc Mass Spectrom. 2017 Sep;28(9):1751-1764. (PMID: 28695533)
J Proteome Res. 2019 Jul 5;18(7):2885-2895. (PMID: 31117584)
J Mass Spectrom. 2013 Jun;48(6):i. (PMID: 23776102)
Electrophoresis. 2018 Dec;39(24):3104-3122. (PMID: 30203847)
Mol Cell Proteomics. 2010 Nov;9(11):2354-68. (PMID: 20571061)
J Proteome Res. 2019 Jan 4;18(1):359-371. (PMID: 30370771)

R50 CA221808 United States CA NCI NIH HHS

0 (Glycopeptides)
0 (Glycoproteins)

Date Created: 20220131 Date Completed: 20230201 Latest Revision: 20230328

20230328

PMC9339036

10.1002/mas.21771

35099083