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Mass Spectrometry Facility


The Mass Spectrometry Shared Resource provides services to elucidate the primary structure of novel proteins and to analyze protein/protein interactions, post-translational modifications and protein levels. The Resource also offers the ability to detect lipids, metabolites, and other small molecules. The equipment in the facility has been upgraded to provide state-of-the-art analysis using microcapillary LC-MS/MS on linear ion traps and Orbitraps, hybrid quadrupole-TOF mass spectrometers and MALDI-TOF.

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Shared Resource Staff

Resource Head

Darryl Pappin, Ph.D.
pappin@cshl.edu

Research Associate

Keith Rivera
516-367-8452
krivera@cshl.edu

Research Investigator

Sofia Costa, Ph.D.
Metabolomics
516-367-6804
henriqu@cshl.edu

Staff

Krisann Marquart
516-367-8452
marquar@cshl.edu

Facility staff is available to discuss project design and progress. Contact Keith Rivera to schedule an appointment. Services include:

  • Quantitative global proteomic profiling using iTRAQ and SILAC, including data analysis, merging of separate datasets and statistical treatment of results.
  • Quantitative cysteine profiling for global redox proteomics.
  • GSH/GSSG measurement (MRM) for redox assessment.
  • Multiple reaction monitoring (MRM) assays for:
    • Phosphatidylinositols (PIs) including head group, chain length, degree of saturation and phosphorylation state for 20 different PI lipid species.
    • Small molecule/drug measurement & clearance in serum & tissues (e.g. Clozapine and Clozapine N-Oxide, Vitamin C, Vitamin K).
  • Lipid Analysis, including sample preparation and extractions, MRM assay development, LC-MS/MS and data analysis.
  • Quantitative iTRAQ for protein complex IP.
  • Quantitative metabolite profiling of ~250 core metabolites.
  • Intact protein mass measurement for drug binding and to support crystallographic studies.
  • Training in LCMS and MS/MS, both for instrument operation and data analysis.
  • Consultation in experimental planning and customized experimental design.

The Shared Resource currently has three mass spectrometers in operation:

  • Thermo Scientific Orbitrap Fusion Lumos Tribrid Mass Spectrometer.
  • Thermo Scientific Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer.
  • Thermo Scientific Vantage Triple Quadrupole Mass Spectrometer.

Sample preparation for the instruments is supported by a number of capillary liquid chromatography systems, including ultra-high pressure LCs (Thermo 1200 nLCs) and Vanquish H UHPLC.

Proteomics data is analyzed with the following data analysis packages:

  • Mascot and Mascot Integra
  • InSpecT
  • PVIEW
  • Scaffold

Selected publications that resulted from use of this shared resource

Engle DD, Tiriac H, Rivera KD, Pommier A, Whalen S, Oni TE, Alagesan B, Lee EJ, Yao MA, Lucito MS, Spielman B, Da Silva B, Schoepfer C, Wright K, Creighton B, Afinowicz L, Yu KH, Grützmann R, Aust D, Gimotty PA, Pollard KS, Hruban RH, Goggins MG, Pilarsky C, Park Y, Pappin DJ, Hollingsworth MA, Tuveson DA. The glycan CA19-9 promotes pancreatitis and pancreatic cancer in mice. Science. 2019 Jun 21;364(6446):1156-1162. doi: 10.1126/science.aaw3145. PubMed PMID: 31221853.

Melnikov SV, Rivera KD, Ostapenko D, Makarenko A, Sanscrainte ND, Becnel JJ, Solomon MJ, Texier C, Pappin DJ, Söll D. Error-prone protein synthesis in parasites with the smallest eukaryotic genome. Proc Natl Acad Sci U S A. 2018 Jul 3;115(27):E6245-E6253. doi: 10.1073/pnas.1803208115. Epub 2018 Jun 18. PubMed PMID: 29915081; PubMed Central PMCID: PMC6142209.

Krishnan N, Felice C, Rivera K, Pappin DJ, Tonks NK. DPM-1001 decreased copper levels and ameliorated deficits in a mouse model of Wilson’s disease. Genes Dev. 2018 Jul 1;32(13-14):944-952. doi: 10.1101/gad.314658.118. PubMed PMID: 29945887; PubMed Central PMCID: PMC6075031.

Chio IIC, Jafarnejad SM, Ponz-Sarvise M, Park Y, Rivera K, Palm W, Wilson J, Sangar V, Hao Y, Öhlund D, Wright K, Filippini D, Lee EJ, Da Silva B, Schoepfer C, Wilkinson JE, Buscaglia JM, DeNicola GM, Tiriac H, Hammell M, Crawford HC, Schmidt EE, Thompson CB, Pappin DJ, Sonenberg N, Tuveson DA. NRF2 Promotes Tumor Maintenance by Modulating mRNA Translation in Pancreatic Cancer. Cell. 2016 Aug 11;166(4):963-976. doi: 10.1016/j.cell.2016.06.056. Epub 2016 Jul 28. PubMed PMID: 27477511; PubMed Central PMCID: PMC5234705.

Roe JS, Mercan F, Rivera K, Pappin DJ, Vakoc CR. BET Bromodomain Inhibition Suppresses the Function of Hematopoietic Transcription Factors in Acute Myeloid Leukemia. Mol Cell. 2015 Jun 18;58(6):1028-39. doi: 10.1016/j.molcel.2015.04.011. Epub 2015 May 14. PubMed PMID: 25982114; PubMed Central PMCID: PMC4475489.

Naguib A, Bencze G, Cho H, Zheng W, Tocilj A, Elkayam E, Faehnle CR, Jaber N, Pratt CP, Chen M, Zong WX, Marks MS, Joshua-Tor L, Pappin DJ, Trotman LC. PTEN functions by recruitment to cytoplasmic vesicles. Mol Cell. 2015 Apr 16;58(2):255-68. doi: 10.1016/j.molcel.2015.03.011. Epub 2015 Apr 9. PubMed PMID: 25866245; PubMed Central PMCID: PMC4423730.

Boj SF, Hwang CI, Baker LA, Chio II, Engle DD, Corbo V, Jager M, Ponz-Sarvise M, Tiriac H, Spector MS, Gracanin A, Oni T, Yu KH, van Boxtel R, Huch M, Rivera KD, Wilson JP, Feigin ME, Öhlund D, Handly-Santana A, Ardito-Abraham CM, Ludwig M, Elyada E, Alagesan B, Biffi G, Yordanov GN, Delcuze B, Creighton B, Wright K, Park Y, Morsink FH, Molenaar IQ, Borel Rinkes IH, Cuppen E, Hao Y, Jin Y, Nijman IJ, Iacobuzio-Donahue C, Leach SD, Pappin DJ, Hammell M, Klimstra DS, Basturk O, Hruban RH, Offerhaus GJ, Vries RG, Clevers H, Tuveson DA. Organoid models of human and mouse ductal pancreatic cancer. Cell. 2015 Jan 15;160(1-2):324-38. doi:10.1016/j.cell.2014.12.021. Epub 2014 Dec 31. PubMed PMID: 25557080; PubMed Central PMCID: PMC4334572

Krishnan N, Fu C, Pappin DJ, Tonks NK. H2S-Induced sulfhydration of the phosphatase PTP1B and its role in the endoplasmic reticulum stress response. Sci Signal. 2011 Dec 13;4(203):ra86. doi:10.1126/scisignal.2002329. PubMed PMID: 22169477; PubMed Central PMCID: PMC3328411.

Obad S, dos Santos CO, Petri A, Heidenblad M, Broom O, Ruse C, Fu C, Lindow M, Stenvang J, Straarup EM, Hansen HF, Koch T, Pappin D, Hannon GJ, Kauppinen S. Silencing of microRNA families by seed-targeting tiny LNAs. Nat Genet. 2011 Mar 20;43(4):371-8. doi: 10.1038/ng.786. PubMed PMID: 21423181; PubMed Central PMCID: PMC3541685.


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