The MMS core provides investigators with access to state-of-the-art mass spectrometry technology to support a broad range of molecular-level studies within basic, translational, and clinical research programs.
The technologies available in the MMS core support research requiring targeted and untargeted analyses of biological molecules and support identification, characterization, and quantification of peptides, proteins, metabolites, glycans, lipids, and small molecules. We accomplish this by using advanced sample preparation robotics, high performance mass spectrometry instrumentation, and cutting-edge bioinformatics tools.
Collectively, these technologies enable reproducible and quantitative measurements from low sample inputs.
Sample Preparation Equipment
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Opentrons OT-2Description: The OT-2 is a liquid handling workstation capable of semi- and fully-automated sample preparation workflows. It is fully customizable and can perform magnetic-bead based separations and multi-channel pipette liquid transfers. Services: The OT-2 is used to perform preparation of biological samples for proteomics including interactome studies, peptide desalting, and derivatization and extraction workflows for metabolomics and lipidomics. This equipment is operated by MMS core staff only. |
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Tecan Resolvex A200Description: The Tecan is a positive-pressure liquid handling workstation capable of semi-automated filter plate-based sample preparation workflows. Services: The Tecan is used for customized solid-phase extraction workflows for qualitative and quantitative label-free proteomics, metabolomics, lipidomics, glycomics, and glycoproteomics. For most workflows, the Tecan is used in combination with the OT-2 for liquid delivery. This equipment is operated by MMS core staff only. |
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Thermo Scientific AccelerOmeDescription: The Thermo Scientific AccelerOme automated sample preparation platform includes an automated liquid handler and UV detector to prepare samples for quantitative proteomics. Services: The AccelerOme uses reagent kits and pre-configured methods to prepare samples for quantitative proteomics, most commonly those using tandem mass tag (TMT-labeled workflows). This equipment is operated by MMS core staff only. |
Mass Spectrometry Instrumentation
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Thermo Orbitrap Exploris 480 LC-MS systemDescription: High resolution, high mass accuracy MS in-line with a Dionex UltiMate 3000 Binary RSLCnano System (proteomics) and Thermo Vanquish Neo UHPLC (metabolomics). This MS is equipped with HCD fragmentation that support identification and quantification of peptides (data independent acquisition, TMT), post-translationally modified peptides, and metabolites.
Services: The Exploris is used for discovery and targeted proteomics and metabolomics. This instrument is operated by MMS core staff only. |
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Thermo Orbitrap Fusion Lumos LC-MS systemDescription: High resolution, high mass accuracy MS in-line with a Dionex UltiMate 3000 Binary RSLCnano System. This MS is equipped with electrospray and nanospray sources and four modes of fragmentation (CID, HCD, ETD, EThcD) that support the identification and quantification of a wide range of molecules, including glycopeptides, glycans, lipids, and post-translationally modified peptides.
Services: The Lumos is used for discovery proteomics and determination of protein post-translational modifications. This instrument is operated by MMS core staff only. |
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Sciex QTRAP 6500+ LC-MS systemDescription: Sensitive quadrupole MS in-line with a Waters Acquity HPLC. Designed for ultra-low-level targeted quantification of small and large molecules.
Services: Targeted analysis of metabolites and lipids using custom and established assays. This instrument is operated by MMS core staff only. |
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Bruker autoflex maX MALDI-TOF/TOFDescription: MALDI MS with MS/MS capabilities for high and low resolution mass spectrometry of small molecules, peptides, proteins, metabolites, and polymers. Resolving power = 26,000. Mass accuracy 2ppm. Smartbeam-II laser with repetition rate of 2kHz and lateral resolution of 100 µm. Services: Intact mass analysis of peptides, small molecules, lipids, glycans. This instrument can by operated by MMS core staff and trained investigators. |
Bioinformatic Tools
Our established data analysis workflows include software for processing raw data files and performing statistical analyses.
Major software includes:
- ProteomeDiscoverer (including Sequest HT, MS Fragger, SAINT, Percolator, and ptmRS algorithms)
- Byonic
- Spectronaut
- SpectroDive
- QuiC
- GlycoWorkbench
- Skyline
- MSstats
- MetaboAnalyst
- CompoundDiscoverer
- TraceFinder
- LipidSearch
- GraphPad Prism
- R studio
- Python