Proteomics & Metabolomics Shared Resource

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Publications

2006

Orvisky E, Drake SK, Martin BM, Abdel-Hamid M, Ressom HW, Varghese RS, An Y, Saha D, Hortin GL, Loffredo CA, Goldman R. Enrichment of low molecular weight fraction of serum for MS analysis of peptides associated with hepatocellular carcinoma. Proteomics 2006;6:2895-2902.

Ressom HW, Varghese RS, Orvisky E, Drake SK, Hortin GL, Abdel-Hamid M, Loffredo CA, Goldman R. Ant colony optimization for biomarker identification from MALDI-TOF mass spectra. Conf Proc IEEE Eng Med Biol Soc 2006;1:4560-4563.

2007

Emami A, Dyba M. Cheema AK, Pan J, Nath RG, Chung FL. Detection of the acrolein-derived cyclic DNA adduct by a quantitative 32P-postlabeling/solid-phase extraction/HPLC method: blocking its artifact formation with glutathione. Anal Biochem 2008 Mar 1;374(1):163-72. Epub 2007 Oct 24.

Goldman R, Ressom HW, Abdel-Hamid M, Goldman L, Wang A, Varghese RS, An Y, Loffredo CA, Drake SK, Eissa SA, Gouda S, Moisewitsch FS. Candidate markers for the detection of hepatocellular carcinoma in low-molecular weight fraction of serum. Carcinogenesis 2007;28:2149-2153.

Li HH, Aubrecht J, Fornace AJ, Jr. Toxicogenomics: overview and potential applications for the study of non-covalent DNA interacting chemicals. Mutat Res 2007;623:98-108.

Mi L, Wang X, Govind S, Hood BL, Veenstra TD, Conrads TP, Saha DT, Goldman R, Chung FL. The role of protein binding in induction of apoptosis by phenethyl isothiocynate and sulforaphane in human nonsmall lung cancer cells. Cancer Res. 2007;67(13):6409-16.

Ressom HW, Varghese RS, Drake SK, Hortin GL, Abdel-Hamid M, Loffredo CA, Goldman R. Peak selection from MALDI-TOF mass spectra using ant colony optimization. Bioinformatics 2007;23:619-626.

Wong CM, Cheema AK, Zhang L, Suzuki YJ. Protein carbonylation as a novel mechanism in redox signaling. Circ Res. 2008 Feb 15;102(3):310-8. Epub 2007 Dec 13.

2008

Isailovic D, Kurulugama RT, Plasencia MD, Stokes ST, Kyselova Z, Goldman R, Mechref Y, Novotny MV, Clemmer DE. Profiling of human serum glycans associated with liver cancer and cirrhosis by IMS-MS. J Proteome Res. 2008 Mar;7(3):1109-17.

Patterson AD, Li H, Eichler GS, Krausz KW, Weinstein JN, Fornace AJ, Jr. Gonzalez FJ, Idle JR. UPLC-ESI-TOFMS-based metabolomics and gene expression dynamics inspector self-organizing metabolomic maps as tools for understanding the cellular response to ionizing radiation. Anal Chem 2008;80:665-674.

Ressom HW, Varghese RS, Goldman L, An Y, Loffredo CA, Abdel-Hamid M, Kyselova Z, Mechref Y, Novotny M, Drake SK, Goldman R. Analysis of MALDI-TOF mass spectrometry data for discovery of peptide and glycan biomarkers of hepatocellular carcinoma. J Proteome Res 2008;7:603-610.

Ressom HW, Varghese RS, Goldman L, An Y, Loffredo CA, Abdel-Hamid M, Kyselova Z, Mechref Y, Novotny M, Goldman R. Analysis of MALDI-TOF mass spectometry data for detection of glycan biomarkers. Pac Symp Biocomput. 2008:216-27.

Tan D, Goerlitz DS, Dumitrescu RG, Han D, Seillier-Moiseiwitsch F, Spernak SM, Orden RA, Chen J, Goldman R, Shields PG. Associations between cigarette smoking and mitochondrial DNA abnormalities in buccal cells.Carcinogenesis. 2008 Jun;29(6):1170-7. Epub 2008 Feb 14.

Tyburski JB, Patterson AD, Krausz KW, Slavik J, Fornace AJ, Jr. Gonzalez FJ, Idle JR. Radiation metabolomics. 1. Identification of minimally invasive urine biomarkers for gamma-radiation exposure in mice. Radiat Res 2008;170:1-14.

Zhang-Zhi Hu, Hongzhan Huang, Amrita Cheema, Mira Jung, Anatoly Dritschilo, Cathy H. Wu Integrated Bioinformatics for Radiation-Induced Pathway Analysis from Proteomics and Microarray Data. J Proteomics & Bioinformatics 2008

2009

An Y, Ressom HW, Goldman R. Analysis of Enriched Peptides by MALDI-TOF Mass Spectometry. The Proteins Protocol Handbook, 3rd edition. Humana Press, USA; 1163-1170.

Balal R, Cheema A, Saha T. Fluorescent Oligonucleotides Can Serve As Suitable Alternative to Hazardous Radioactivity. J.Biomol.Tech. 2009. (in press)

Cheema A, Catania J, Dakshanamurthy S, Shen W, Simons B, Knights C, Albanese C, Avantaggiati ML. A SUMO-1 Acetylated Motif, SAM, Regulates SUMO-1 Ubiquitination, Stability, and DNA-Damage. Tolerance J.Biol. Chem. 2009. (under revision)

Goldman R, Ressom HW, Varghese RS, Goldman L, Bascug G, Loffredo CA, Abdel-Hamid M, Gouda I, Ezzat S, Kyselova Z, Mechref Y, Novotny MV. Detection of hepatocellular carcinoma using glycomic analysis.Clin Cancer Res. 2009 Mar 1;15(5):1808-13. Epub 2009 Feb 17

Lattova E, McKenzie EJ, Gruwel MLH, Spicer V, Goldman R, Perrault H. Mass Spectrometric Profile of N-glycans in Woodchuck Sera with Liver Cancer. Rapid Com. Mass Spec; 2983-2995.

Lixin Mi, Nanqin Gan, Amrita Cheema, Sivanesan Dakshanamurthy, David C. H. Yang, Fung-Lung Chung. Cancer preventive isothiocyanates induce selective degradation of cellular alpha- and beta-tubulins by proteasomes J.Biol. Chem. 2009. (accepted, in press)

Pan J, Keffer J, Emami A, Ma X, Lan R, Goldman R, Chung FL. Acrolein-derived DNA adduct formation in human colon cancer cells: its role in apoptosis induction by docosahexaenoic acid. Chem Res Toxicol. 2009 May;22(5):798-806.

2010

An Y, Bekesova S, Edwards N, Goldman R. Peptides in low molecular weight fraction of serum associated with hepatocellular carcinoma. Disease Markers. (In Press)

Tang Z, Varghese RS, Bekesova S, Loffredo CA, Hamid MA, Kyselova Z, Mechref Y, Novotny MV, Goldman R, Ressom HW. Identification of N-glycan serum markers associated with hepatocellular carcinoma from mass spectrometry data. J Proteome Res. 2010 Jan;9(1):104-12.