Analysis of maldi-tof mass spectrometry data for detection of glycan biomarkers

Habtom W. Ressom, Rency S. Varghese, Lenka Goldman, Christopher A. Loffredo, Mohamed Abdel-Hamid, Zuzana Kyselova, Yehia Mechref, Milos Novotny, Radoslav Goldman

Research output: Chapter in Book/Report/Conference proceedingConference contribution

14 Scopus citations

Abstract

We present a computational framework for analysis of MALDI-TOF mass spectrometry data to enable quantitative comparison of glycans in serum. The proposed framework enables a systematic selection of glycan structures that have good generalization capability in distinguishing subjects from two pre-labeled groups. We applied the proposed method for a biomarker discovery study that involves 203 participants from Cairo, Egypt; 73 hepatocellular carcinoma (HCC) cases, 52 patients with chronic liver disease (CLD), and 78 healthy individuals. Glycans were enzymatically released from proteins in serum and permethylated prior to mass spectrometric quantification. A subset of the participants (35 HCC and 35 CLD cases) was used as a training set to select global and subgroup-specific peaks. The peak selection step is preceded by peak screening, where we eliminate peaks that seem to have association with covariates such as age, gender, and viral infection based on the 78 spectra from healthy individuals. To ensure that the global peaks have good generalization capability, we subjected the entire spectral preprocessing and peak selection step to a cross-validation; a randomly selected subset of the training set was used for spectral preprocessing and peak selection in multiple runs with resubstitution. In addition to global peak identification method, we describe a new approach that allows the selection of subgroup-specific glycans by searching for glycans that display differential abundance in a subgroup of patients only. The performance of the global and subgroup-specific peaks is evaluated via a blinded independent set that comprises of 38 HCC and 17 CLD cases. Further evaluation of the potential clinical utility of the selected global and subgroup-specific candidate markers is needed.

Original languageEnglish
Title of host publicationPacific Symposium on Biocomputing 2008, PSB 2008
Pages216-227
Number of pages12
StatePublished - 2008
Event13th Pacific Symposium on Biocomputing, PSB 2008 - Kohala Coast, HI, United States
Duration: Jan 4 2008Jan 8 2008

Publication series

NamePacific Symposium on Biocomputing 2008, PSB 2008

Conference

Conference13th Pacific Symposium on Biocomputing, PSB 2008
CountryUnited States
CityKohala Coast, HI
Period01/4/0801/8/08

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    Ressom, H. W., Varghese, R. S., Goldman, L., Loffredo, C. A., Abdel-Hamid, M., Kyselova, Z., Mechref, Y., Novotny, M., & Goldman, R. (2008). Analysis of maldi-tof mass spectrometry data for detection of glycan biomarkers. In Pacific Symposium on Biocomputing 2008, PSB 2008 (pp. 216-227). (Pacific Symposium on Biocomputing 2008, PSB 2008).