The National Bio-Organic, Biomedical Mass Spectrometry Resource Center, supported by the NIH National Institute of General Medical Sciences and the Adelson Medical Research Foundation, provides both scientific and technical expertise and state-of-the-art high-performance, tandem mass spectrometric instrumentation. The facility is a world leader in proteomic analysis although it also analyzes other biomolecules. Significant instrumentation in the facility includes a Q-Exactive Plus for complex sample and low-level analyses; an LTQ-Orbitrap Velos with electron transfer dissociation (ETD), which is effective at analyzing peptides with labile post-translational modifications; an Exactive EMR for native protein-protein interaction analysis; and a QTRAP 5500 hybrid triple quadrupole linear ion trap instrument, used for high-throughput targeted quantification analysis. The resource also has an LTQ-Orbitrap XL with ETD capability, and a QSTAR Elite instrument.

Major research focuses within the Center are the analysis of post-translational modifications, including phosphorylation and O-GlcNAcylation and development of methods for quantitative comparative analysis of protein and post-translational modification levels. The program also continues to develop one of the leading suites of tools for analysis of mass spectrometry proteomics data, Protein Prospector. The current web-based release allows unrestricted searching of MS and MSMS data, as well as the ability to perform comparative quantitative analysis of samples using isotopic-labeling reagents. It is the only freely-available web-based resource that allows this type of analysis.

Bekshe Lokappa S, Balakrishna Chandrababu K, Dutta K, Perovic I, Spencer Evans J, Moradian-Oldak J. Interactions of amelogenin with phospholipids. Biopolymers. 2015 Feb;103(2),96-108 (2015). [Pubmed] Doll S, Burlingame AL. Mass spectrometry-based detection and assignment of protein posttranslational modifications. ACS Chem Biol. 2015 Jan 16;10(1),63-71 (2015). [Pubmed] Duong BH, Onizawa M, Oses-Prieto JA, Advincula R, Burlingame A, Malynn BA, Ma A. A20 Restricts Ubiquitination of Pro-Interleukin-1β Protein Complexes and Suppresses NLRP3 Inflammasome Activity. Immunity. 2015 Jan 20;42(1),55-67 (2015). [Pubmed] Abernathy E, Clyde K, Yeasmin R, Krug LT, Burlingame A, Coscoy L, Glaunsinger B. Gammaherpesviral gene expression and virion composition are broadly controlled by accelerated mRNA degradation. PLoS Pathog. 2014 Jan;10(1), e1003882 (2014). [Pubmed] Asmussen J, Lasater EA, Tajon C, Oses-Prieto J, Jun YW, Taylor BS, Burlingame A, Craik CS, Shah NP. MEK-Dependent Negative Feedback Underlies BCR-ABL-Mediated Oncogene Addiction. Cancer Discov. 4(2),200-15 (2014). [Pubmed] Baker PR, Chalkley RJ. MS-viewer: a web-based spectral viewer for proteomics results. Mol Cell Proteomics. 2014 May;13(5), 1392-6 (2014). [Pubmed] Bradshaw RA, Pundavela J, Biarc J, Chalkley RJ, Burlingame AL, Hondermarck H. NGF and ProNGF: Regulation of neuronal and neoplastic responses through receptor signaling. Adv Biol Regul. 2014 Nov 20. pii, S2212-4926(14)00062-1 (2014). [Pubmed] Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, Hüttenhain R, Koomen JM, Liebler DC, Liu T, MacLean B, Mani DR, Mansfield E, Neubert H, Paulovich AG, Reiter L, Vitek O, Aebersold R, Anderson L, Bethem R, Blonder J, Boja E, Botelho J, Boyne M, Bradshaw RA, Burlingame AL, Chan D, Keshishian H, Kuhn E, Kinsinger C, Lee JS, Lee SW, Moritz R, Oses-Prieto J, Rifai N, Ritchie J, Rodriguez H, Srinivas PR, Townsend RR, Van Eyk J, Whiteley G, Wiita A, Weintraub S. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol Cell Proteomics. 2014 Mar;13(3), 907-17(2014). [Pubmed] Chalkley RJ, Bandeira N, Chambers MC, Clauser KR, Cottrell JS, Deutsch EW, Kapp EA, Lam HH, McDonald WH, Neubert TA, Sun RX. Proteome Informatics Research Group (iPRG)_2012: A Study on Detecting Modified Peptides in a Complex Mixture. Mol Cell Proteomics. 13(1),360-71 (2014). [Pubmed] Cho Y, Di Liberto V, Carlin D, Abe N, Li KH, Burlingame AL, Guan S, Michaelevski I, Cavalli V. Syntaxin13 expression is regulated by mammalian target of rapamycin (mTOR) in injured neurons to promote axon regeneration. J Biol Chem. 2014 May 30; 289(22),15820-32 (2014). [Pubmed] Darula Z, Medzihradszky KF. Glycan side reaction may compromise ETD-based glycopeptide identification. J Am Soc Mass Spectrom. 2014 Jun;25(6), 977-87 (2014). [Pubmed] Deng Z, Oses-Prieto JA, Kutschera U, Tseng TS, Hao L, Burlingame AL, Wang ZY, Briggs WR. Blue light-induced proteomic changes in etiolated Arabidopsis seedlings. J Proteome Res. 2014 May 2;13(5), 2524-33 (2014). [Pubmed] Hirsch J, Chalkley RJ, Bentley T, Burlingame AL, Frank JA. Double impact of cigarette smoke and mechanical ventilation on the alveolar epithelial type II cell. Crit Care. 2014 Mar 25;18(2), R50 (2014). [Pubmed] Julien O, Kampmann M, Bassik MC, Zorn JA, Venditto VJ, Shimbo K, Agard NJ, Shimada K, Rheingold AL, Stockwell BR, Weissman JS, Wells JA. Unraveling the mechanism of cell death induced by chemical fibrils. Nat Chem Biol. 2014 Nov;10(11),969-76 (2014). [Pubmed] Kido-Nakahara M, Buddenkotte J, Kempkes C, Ikoma A, Cevikbas F, Akiyama T, Nunes F, Seeliger S, Hasdemir B, Mess C, Buhl T, Sulk M, Müller FU, Metze D, Bunnett NW, Bhargava A, Carstens E, Furue M, Steinhoff M. Neural peptidase endothelin-converting enzyme 1 regulates endothelin 1-induced pruritus. J Clin Invest. 2014 Jun 2;124(6),2683-95 (2014). [Pubmed] Krishnan S, Miller RM, Tian B, Mullins RD, Jacobson MP, Taunton J. Design of reversible, cysteine-targeted Michael acceptors guided by kinetic and computational analysis. J Am Chem Soc. 2014 Sep 10;136(36), 12624-30 (2014). [Pubmed] Martins MM, Zhou AY, Corella A, Horiuchi D, Yau C, Rakshandehroo T, Gordan JD, Levin RS, Johnson J, Jascur J, Shales M, Sorrentino A, Cheah J, Clemons PA, Shamji AF, Schreiber SL, Krogan NJ, Shokat KM, McCormick F, Goga A, Bandyopadhyay S. Linking Tumor Mutations to Drug Responses via a Quantitative Chemical-Genetic Interaction Map. Cancer Discov. 2014 Dec 12. [Epub ahead of print] [Pubmed] Medzihradszky KF. Noncovalent dimer formation in liquid chromatography-mass spectrometry analysis. Anal Chem. 2014 Sep 16;86(18), 8906-9 (2014). [Pubmed] Morris JH, Knudsen GM, Verschueren E, Johnson JR, Cimermancic P, Greninger AL, Pico AR. Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc. 2014 Nov;9(11), 2539-54 (2014). [Pubmed] Pando-Robles V, Oses-Prieto JA, Rodríguez-Gandarilla M, Meneses-Romero E, Burlingame AL, Batista CV. Quantitative proteomic analysis of Huh-7 cells infected with Dengue virus by label-free LC-MS. J Proteomics. 2014 Dec 5;111, 16-29 (2014). [Pubmed]