Biological Mass Spectrometry Shared Resource
The Biological Mass Spectrometry (BMS) facility was developed based on exceptional strengths in lipidomics, proteomics, and metabolomics. The facility provides SBU investigators with a wide range of analytical capabilities to support their research programs. The facility has instrumentation and expertise in three broad areas of molecular analysis: proteomics, lipidomics, and metabolite/small molecule. Advances in the sampling rate and sensitivity of mass spectrometry have enhanced global and targeted analyte measurements as well as structural analysis. Moreover, the ability of mass spectrometry to identify and precisely quantify thousands of analytes from complex samples augments molecular analysis in both basic cancer biology and clinical translation. Intra- and inter-programmatic interaction among Stony Brook Cancer Center (SBCC) investigators is enhanced by utilization of this facility for all mass spectrometry, which is further augmented by specific expertise of SBCC Research Program members. BMS services are critical to multiple funded R01s and NCI grant applications. 
Current services include protein/peptide quantitation, small molecule/pharmacokinetic (PK) analysis, polar metabolite studies, bioactive lipid profiling and quantitation, lipid flux, and the quantitation of DNA adducts and repair intermediates. We have established routine use of qualitative and quantitative proteomics (using both label free and stable isotope approaches), with experience in the analysis of protein complexes and in post-translational modifications important in cancer cell signaling and drug action (e.g., Canals et al, JASEB J. 2020; Bogenhagen and Haley, JBC 2020). Proteomic, phosphoproteomic and small molecule services support 56 users, 19 from the SBCC.
The lipidomics portion of the BMS offers targeted analysis of multiple lipid classes, notably sphingolipids and ceramides by liquid chromatography (LC)-MS/MS. This service has transformed the field of lipids in cancer biology, and the BMS facility and SBCC investigators have played a pivotal role in advancing this field. The BMS continues to develop cutting-edge methodology utilizing a pulse of unnatural sphingolipid to accurately monitor metabolic flux in this pathway. For example, studies enabled by the BMS resulted in identification of the novel acyl-ceramides with important roles in regulating apoptosis and cancer therapy (Can et al, Cell Metabolism 2017). Lipidomic services support 28 users, 14 from the SBCC supporting their publications and grant applications. The SBCC recently acquired two state-of-the-art Bruker scanning matrix-assisted laser desorption/electrospray (MALDI/ESI) instruments, timsTOFfleX and rapifleX, for the BMS. These two instruments allow investigators to measure lipids, metabolites, drug levels and proteins in tissue scanning mode, thus, providing marked synergy between digital pathology and immunohistochemistry (IHC) data from the same tissue blocks. This is revolutionizing the translational activities of research at the SBCC. Our metabolite analysis suite offers an array of targeted assays covering a broad spectrum of inflammatory and biosynthetic pathways (e.g., Ruiz et al, FASEB J. 2020). We have developed considerable experience in absolute quantitation of polar metabolites and drug metabolites in mouse and human tissue and plasma samples, most frequently for drug development projects. Furthermore, this facility also acts as the Proteomics and Lipidomics facility for the Mount Sinai Medical Center in New York City. The facility Director, John Haley is NCI funded and has active collaborations resulting in 15 publications in the past two years. The facility supports >20 grant applications per year, and supports undergraduate, graduate and medical resident studies, functioning as an important grant development and educational component.
The aims of the BMS are to:
- Offer expertise in experimental design and sample preparation for protein, peptide, lipid, small molecule, and metabolite identification and quantitation. Provide expertise in tissue preparation for scanning MALDI and MALDI/ESI lipid, metabolite and drug studies.
- Provide instructional sessions to SBCC investigators, students and laboratory personnel on methodological, bioinformatics, and statistical approaches to biological mass spectrometry.
- Provide services for the measurement of proteins, post-translational modifications of proteins (PTMs), lipid, and metabolic intermediates by both global/shotgun and/or targeted mass spectrometry approaches.
- Analyze and quantify mass spectrometry data, in addition to analysis of integration and linear scaling of protein/peptide, lipid, and metabolite data with RNA abundance, DNA mutation, and copy number datasets.
- Enhance the clinical translation of molecular results through proteomic, lipidomic, and metabolomic workflows. Enable clinical translation of tissue scanning MALDI/ESI technologies.