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

John Moses, Ph.D.


Paolo Cifani, Ph.D.

Research Associate

Maria Antonelli, Ph.D.

Juliana Magalhaes de Oliveira, Ph.D.

Research Technician

Francesca Minicozzi, B.S.

Ava Sann, B.S.

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.

Proteomics data is analyzed with the following data analysis packages:

  • Mascot and Mascot Distiller
  • Proteome Discoverer
  • Skyline
  • 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

Klingbeil, Olaf, Skopelitis, Damianos, Tonelli, Claudia, Alpsoy, Aktan, Minicozzi, Francesca, Aggarwal, Disha, Russo, Suzanne, Ha, Taehoon, Demerdash, Osama E, Spector, David L, Tuveson, David A, Cifani, Paolo , Vakoc, Christopher R (2024) MARK2/MARK3 kinases are catalytic co-dependencies of YAP/TAZ in human cancer. bioRxiv,

Perlee, Sarah, Kikuchi, Sota, Nakadai, Tomoyoshi, Masuda, Takeshi, Ohtsuki, Sumio, Matsumoto, Makoto, Rahmutulla, Bahityar, Fukuyo, Masaki, Cifani, Paolo, Kentsis, Alex, Roeder, Robert G, Kaneda, Atsushi , Hoshii, Takayuki (2023) SETD1A function in leukemia is mediated through interaction with mitotic regulators BuGZ/BUB3. EMBO Reports, 24(10) pp. e57108.

Yao, Min, Preall, Jonathan, Yeh, Johannes, Pappin, Darryl J, Cifani, Paolo, Zhao, Yixin, Shen, Sophia, Moresco, Philip, He, Brian, Patel, Hardik, Habowski, Amber N, King, Daniel A, Raphael, Kara L, Rishi, Arvind, Sejpal, Divyesh V, Weiss, Matthew, Tuveson, David , Fearon, Douglas T (2023) Plasma cells in human pancreatic ductal adenocarcinoma secrete antibodies to self-antigens. JCI Insight, pp. e172449.

Herrejon Chavez, Florisela, Luo, Hanzhi, Cifani, Paolo, Pine, Alli, Chu, Karen L, Joshi, Suhasini, Barin, Ersilia, Schurer, Alexandra, Chan, Mandy, Chang, Kathryn, Han, Grace YQ, Pierson, Aspen J, Xiao, Michael, Yang, Xuejing, Kuehm, Lindsey M, Hong, Yuning, Nguyen, Diu TT, Chiosis, Gabriela, Kentsis, Alex, Leslie, Christina, Vu, Ly P , Kharas, Michael G (2023) RNA binding protein SYNCRIP maintains proteostasis and self-renewal of hematopoietic stem and progenitor cells. Nature Communications, 14(1) pp. 2290.

Zhang, Lifang, Braynen, Janeen, Fahey, Audrey, Chopra, Kriti, Cifani, Paolo, Tadesse, Dimiru, Regulski, Michael, Hu, Fangle, van Dam, Hubertus JJ, Xie, Meng, Ware, Doreen , Blaby-Haas, Crysten E (2023) Two related families of metal transferases, ZNG1 and ZNG2, are involved in acclimation to poor Zn nutrition in Arabidopsis. Frontiers in Plant Science, 14 pp. 1237722.

Cifani, Paolo , Kentsis, Alex (2022) Quantitative Cell Proteomic Atlas: Pathway-Scale Targeted Mass Spectrometry for High-Resolution Functional Profiling of Cell Signaling. Journal of Proteome Research, 21(10) pp. 2535-2544.

Paul, Shilpi, Cifani, Paolo, Pappin, Darryl , Spratt, Thomas (2022) Unique DNA Polymerase kappa Interactome Suggests Novel Cellular Functions. The FASEB Journal, 36 Sup(S1)

Paul, Shilpi, Rebok, Abbey, Cifani, Paolo, Paul, Anirban, Pappin, Darryl, Huang, Tony , Spratt, Thomas (2022) Translesion DNA synthesis polymerase κ is essential to a carcinogen-induced nucleolar stress response. bioRxiv,

Cifani, Paolo, Li, Zhi, Luo, Danmeng, Grivainis, Mark, Intlekofer, Andrew M, Fenyö, David , Kentsis, Alex (2021) Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics. Journal of Proteome Research, 20(4) pp. 1835-1848.

Antao, Noelle V, Marcet-Ortega, Marina, Cifani, Paolo, Kentsis, Alex , Foley, Emily A (2019) A Cancer-Associated Missense Mutation in PP2A-Aα Increases Centrosome Clustering during Mitosis. iScience, 19 pp. 74-82.

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