Analysis of MALDI-TOF mass spectrometry data for discovery of peptide and glycan biomarkers of hepatocellular carcinoma

Journal of Proteome Research
Habtom W RessomRadoslav Goldman

Abstract

This paper presents computational methods to analyze MALDI-TOF mass spectrometry data for quantitative comparison of peptides and glycans in serum. The methods are applied to identify candidate biomarkers in serum samples of 203 participants from Egypt; 73 hepatocellular carcinoma (HCC) cases, 52 patients with chronic liver disease (CLD) consisting of cirrhosis and fibrosis cases, and 78 population controls. Two complementary sample preparation methods were applied prior to generating mass spectra: (1) low molecular weight (LMW) enrichment of each serum sample was carried out for MALDI-TOF quantification of peptides, and (2) glycans were enzymatically released from proteins in each serum sample and permethylated for MALDI-TOF quantification of glycans. A peak selection algorithm was applied to identify the most useful peptide and glycan peaks for accurate detection of HCC cases from high-risk population of patients with CLD. In addition to global peaks selected by the whole population based approach, where identically labeled patients are treated as a single group, subgroup-specific peaks were identified by searching for peaks that are differentially abundant in a subgroup of patients only. The peak selection process was preced...Continue Reading

References

Jun 30, 1992·Clinica Chimica Acta; International Journal of Clinical Chemistry·G A Turner
Sep 1, 1995·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·K ShirakiT Nakano
Mar 9, 2002·Science·Sena J LeeMichel C Nussenzweig
Feb 24, 2005·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·E Ellen SchweglerRichard R Drake
Apr 16, 2005·Clinics in Liver Disease·Jorge A Marrero
Sep 3, 2005·Journal of Hepatology·Jorge A MarreroTimothy M Block
Sep 15, 2005·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·Ola NadaChristopher A Loffredo
Sep 15, 2005·Bioinformatics·Habtom W RessomRadoslav Goldman
Oct 13, 2005·International Journal of Hygiene and Environmental Health·Sameera EzzatChristopher A Loffredo
Oct 22, 2005·Nature Reviews. Cancer·Joseph A Ludwig, John N Weinstein
Oct 28, 2005·Rapid Communications in Mass Spectrometry : RCM·Pilsoo KangMilos V Novotny
Jan 24, 2007·Bioinformatics·H W RessomR Goldman
Apr 17, 2007·Journal of Proteome Research·Zuzana KyselovaMilos V Novotny

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Citations

Jun 27, 2012·Analytical and Bioanalytical Chemistry·John E Schiel
Sep 5, 2009·ACS Chemical Biology·Lakshmi Krishnamoorthy, Lara K Mahal
Dec 14, 2011·Journal of Proteome Research·Dragan IsailovicDavid E Clemmer
Dec 17, 2008·Journal of Proteome Research·Chen LiDavid M Lubman
Mar 30, 2010·Journal of Proteome Research·William R Alley, Milos V Novotny
May 7, 2010·Omics : a Journal of Integrative Biology·Joseph Zaia
Mar 25, 2011·Clinical Chemistry and Laboratory Medicine : CCLM·Tomomi Masuda, Eiji Miyoshi
Oct 9, 2009·Expert Review of Proteomics·Xin-Qing PengWei-Ming Zhang
Feb 14, 2012·Journal of Proteomics·S BekesovaR Goldman
Jan 31, 2012·Thrombosis Research·Domenico RotilioMaria Benedetta Donati
Aug 2, 2013·Liver International : Official Journal of the International Association for the Study of the Liver·Jian ZhuYunsen Li
Apr 9, 2014·Journal of Biopharmaceutical Statistics·Kristopher AttwoodChengjie Xiong
Dec 5, 2012·Journal of Proteome Research·Helle MalerodSonja Hess
Sep 4, 2016·Analytical and Bioanalytical Chemistry·Muchena J KailemiaCarlito B Lebrilla
Nov 26, 2018·Mass Spectrometry Reviews·Jianhui ZhuDavid M Lubman
Dec 19, 2020·Comprehensive Reviews in Food Science and Food Safety·Meisam BaratiAmin Mousavi Khaneghah
May 20, 2008·Analytical Chemistry·Masaaki ToyodaAkihiko Kameyama

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