III-CXT-Small: Analysis of Mass Spectrometry Data for Biomarker Discovery

Funded by : National Science Foundation (NSF) IIS-0812246  

ContactHabtom Ressom

Project Aims

The specific research aims of this project are the following: (1) to investigate normalization and alignment methods for label-free quantification and comparison of peptides using liquid chromatography-mass spectrometry (LC-MS) technologies, and (2) to investigate feature selection algorithms that can isolate subgroup-specific biomarkers.

Related Articles and Papers

Tuli L, Tsai T-H, Varghese R, Xiao JF, Cheema A, and Ressom HW (2012). Using a spike-in experiment to evaluate analysis of LC-MS data. Proteome Science. 10(1):13. PMID:22369182

Zhang Y, Xuan J, Clarke R, Ressom HW (2012). Module-based breast cancer classification. International Journal of Data Mining and Bioinformatics. In Press.

Tsai T-H,Tadesse MG, Wang Y, and Ressom HW (2011). Bayesian alignment model for LC-MS data. Proceeding of the IEEE interantional conference on Bioinformatics & Biomedicine, Altanta, GA, November 12-15, 2011,pp.261-264

Tang Z, Zhang L, Cheema A, Ressom HW (2011). A new method for alignment of LC-MALDI-TOF data. Proteome Science.9 Suppl 1:S10. PMID:22166061

Varghese RS and Ressom HW (2011). LC-MS data analysis for differential protein expression detection. Methods Mol Biol. 2011; 694: 139-50. PMID: 21082433.

Befekadu GK, Tadesse MG, Tsai T-H, Ressom HW (2011). Probabilistic mixture regression models for alignment of LC-MS data. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Vol. 8, No. 7; 1417-1424. PMID: 20837998.

Zhang Y, Xuan J, Clarke R, Ressom HW (2010). Module-based biomarker discovery in breast cancer. Proceedings of the IEEE International Conference on Bioinformatics & Biomedicine, Hong Kong, December 18-21, 2010, pp. 352-356.

Tuli L, Tsai T-H, Varghese R, Cheema A, and Ressom HW (2010). Using a spike-in experiment to evaluate analysis of LC-MS data. Proceedings of the IEEE International Workshop on Computational Proteomics, Hong Kong, December 18-21, 2010, pp. 67-72.

Zhou B, Cheema A, Ressom HW (2010). SVM-based spectral matching for metabolite identification. Conf Proc IEEE Eng Med Biol Soc. 2010;2010:756-9. PMID: 21095903.

Tang Z, Varghese RS, Bekesova S, Loffredo CA, Abdel-Hamid M, Kyselova Z, Mechref Y, Novotny M, Goldman R, Ressom HW (2010). Identification of N-glycan serum markers associated with hepatocellular carcinoma from mass spectrometry data. Journal of Proteome Research 9(1):104-12.PMID:19764807

Varghese RS, Cheema A, Cheema P, Bourbeau M, Tuli L, Zhou B, Jung M, Dritschilo A, Ressom HW (2010). Analysis of LC-MS data for characterizing the metabolic changes in response to radiation. Journal of Proteome Research 9(5):2786-93. PMID: 20329776.

Tuli L, Ressom HW (2009). LC-MS based detection of differential protein expression. Journal of Proteomics and Bioinformatics 2(10):416-438. PMID: 20473349.

Ressom HW, Befekadu GK, Tadesse MG (2009). Analysis of LC-MS data using probabilistic-based mixture regression models. at - Automatisierungstechnik 57(9): 453-465.

Befekadu GK, Tadesse MG, Ressom HW (2009). A bayesian based functional mixed-effects model for analysis of LC-MS data. Conf Proc IEEE Eng Med Biol Soc. 2009; 6743-6746. PMID: 19963938

Ressom HW, Varghese RS, Goldman R (2009). Computational Methods for Analysis of MALDI-TOF Spectra to Discover Peptide Serum Biomarkers. Editor: John M. Walker, The Protein Protocols Handbook (Methods in Molecular Biology. Humana Press. ISBN: 978-1-60327-474-6

Research Team

PI: Habtom Ressom
Co-PI: Radoslav Goldman
Graduate Students:
Bin Zhou , Tsung-Heng Tsai, Mohammad R Nezami Ranjbar ,Yuji Zhang, and Yi Zhao
Postdoctoral fellows:
Getachew Befekadu ,Zhiqun Tang, and Leepike Tuli