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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.

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Shared Resource Staff

Resource Head

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

Director

Paolo Cifani, Ph.D.
Proteomics
cifani@cshl.edu

Research Assistant

Ece Kilic, M.Sc.
kilic@cshl.edu

Research Technician

Francesca Minicozzi, B.S.
fminicoz@cshl.edu

Facility staff is available to discuss project design and progress. Services include:

  • Protein identification using LCMS (in-gel digest, Co-IP, proteomic screens)
  • Characterization of post-translational modifications
  • Quantitative global proteomic & phosphoproteomic profiling using iTRAQ/TMT, SILAC, or label-free methods
  • Quantitative cysteine profiling for global redox proteomics.
  • Quantitative (iTRAQ or label-free) profiling of protein complexes for BioID and dTAG screens
  • Intact protein mass measurement for drug binding and to support crystallographic studies
  • Multiple and parallel reaction monitoring (M/PRM) for peptide, protein, and small molecule quantitation
  • Data analysis, merging of separate datasets and statistical treatment of results
  • Training in LCMS and MS/MS, both for instrument operation and data analysis
  • Consultation in experimental planning and customized experimental design.

We’ve implemented targeted and untargeted LC-MS-based workflows to identify and quantify key primary metabolites and intermediates in a variety of biological matrices (tissues, biofluids, cells, cell culture medium, RNA and DNA). The following classes of compounds are currently covered in our analyses:

  • carboxylic acids
  • amino acids
  • polyamines
  • nucleotides and nucleosides
  • thiols
  • coenzymes and vitamins
  • mono- and disaccharides
  • fatty acids
  • steroids and hormones

We are able to perform stable isotope (13C, 15N, 2H) tracing analyses, which can be used to measure the activity of specific metabolic pathways, directionality of particular reactions, and potentially reveal their sub-cellular localization.

It is also possible to monitor the uptake and metabolism of drug compounds using customized LC-MS methods.

Please contact Ece Kilic (kilic@cshl.edu) to discuss any projects or pilot experiments under consideration. It is strongly advised that experimental design and sample collection are agreed upon prior to carrying out the experiments, as these determine the quality of the data we are able to provide. We are happy to discuss collaborating on the application of current methods, or the implementation of novel ones.

Proteomics data is analyzed with the following data analysis packages:

  • Mascot and Mascot Distiller
  • SEQUEST
  • Proteome Discoverer
  • Skyline
  • PEAKS
  • Scaffold
  • Freestyle

Metabolomics data is processed and analyzed using the following software, databases and informatics tools:

  • XCalibur
  • Compound Discoverer
  • MetaboAnalyst
  • El-MAVEN
  • XCMS
  • R
  • LipidFinder
  • Human Metabolome Database
  • Metlin

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.

Yun J, Mullarky E, Lu C, Bosch KN, Kavalier A, Rivera K, Roper J, Chio, II, Giannopoulou EG, Rago C, Muley A, Asara JM, Paik J, Elemento O, Chen Z, Pappin DJCCC, Dow LE, Papadopoulos N, Gross SS, and Cantley LC (2015). Vitamin C selectively kills KRAS and BRAF mutant colorectal cancer cells by targeting GAPDH. Science 350(6266): p. 1391-6. PMID:26541605. PMCID:PMC4778961.

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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