Mass Spectrometry

Johns Hopkins University, Baltimore MD

Investigators

Linked publications, trials & patents

Abstract

ABSTRACT The Sidney Kimmel Comprehensive Cancer Center (SKCCC) Mass Spectrometry Core is a part of the larger institutional Johns Hopkins University School of Medicine (JHUSOM) Mass Spectrometry and Proteomics Facility. It provides SKCCC investigators access at a reduced cost to advanced proteomic services, a designated Core Mass Spectrometrist and a Proteomics Specialist, a specific biostatistician/bioinformatician for post-identification/quantification data analysis. The Mass Spectrometry Core couples multidimensional separations by column chromatography or gel electrophoresis to mass spectrometry analysis. It is used to identify, quantify and characterize proteins and their post-translational modifications expressed in well- characterized protein fractions from cancerous cells, tissues or body fluids. Techniques such as isobaric mass tag labeling (TMT, tandem mass tags, or iTRAQ, isobaric tag for relative and absolute quantitation), stable isotope labeling of amino acids in cell culture (SILAC) and nonlabeling methods (MuDPIT, multidimensional protein identification technology) are available for quantifying relative differences in protein expression and post-translational modifications, such as acetylation, AMPylation, citrullination, glycosylation, phosphorylation, nitrosation, proline hydroxylation, ubiquitination and novel cleavage sites. The Core offers recently established targeted proteomic methods, such as absolute quantification (AQUA) and protein standard absolute quantification (PSAQ) methods, to determine the amount of specific proteins. In addition, the Core offers high-resolution mass and fragmentation analysis of intact proteins?a top down approach to characterize proteins and their modifications. Core services include pre- and post-analysis consultation on sample preparation, data analysis and interpretation; proteolytic digestion, peptide extraction, labeling and fractionation; nanoliquid chromatography separation coupled with tandem mass spectrometry analysis; database searching; compiled results reports; and educational programs through core presentations and technical workshops. A biostatistician/bioinformatician is available when more in-depth statistical and ontological analyses of the proteomic results are needed. When SKCCC investigators wish to perform their own analysis, the Core provides access to proprietary software and equipment. Core workshops on operating the Core MALDI mass spectrometer are offered several times a year. During this funding period, 57 SKCCC investigators have used the Mass Spectrometry Core, and more than 50 manuscripts are attributed to this Core. Jointly SKCCC and Department of Biological Chemistry Managed Core Reporting Period: Jan. 1, 2015, to Dec. 31, 2015