Keck Mass Spectrometry & Proteomics Resource
About the core
The Keck Mass Spectrometry (MS) & Proteomics Resource at the Yale School of Medicine provides efficient and cost-effective proteomics and small molecule mass spectrometry-based services. Aside from our developed standard operating procedures (SOPs) offered for many of our MS workflows, we also strive to continue to bring state-of-the-art mass spectrometry-based biotechnologies and methodologies to the Resource through input and requests from our users and collaborators. These technologies are developed and implemented with a broad spectrum of mass spectrometry-based techniques and protein/peptide/small molecule chemistries to separate, characterize, profile, and quantify analytes from complex biological samples. Our fee-for-service workflows include:
- Protein ID from the following:
- Gel bands
- IP/co-IP proteins
- Cells: FACs sorted/enriched cell-type/subcellular/pellet/lysate
- Tissue: whole/specific regions (PFC, DS, cerebellum, etc. of brain) / laser capture microdissection / proximity labeling
- Protein posttranslational modification (PTM) identification
- Protein profiling and quantitation. Approaches:
- Label-free quantitation (DDA/DIA)
- TMT multi-plex
- SILAC
- Labeled
- Intact protein determination (<40 kDa)
- High-resolution (HR) MS for small molecule and structural elucidation
- Targeted quantitation of small molecules
- Targeted proteomics (parallel reaction monitoring [PRM])
Instruments
- ACQUITY M-Class UPLC coupled to Q-Exactive HFX mass spectrometer
- NanoACQUITY UPLC coupled to Q-Exactive Plus mass spectrometer
- NanoACQUITY UPLC coupled to Orbitrap Fusion Tribrid mass spectrometer
- Agilent 1200 HPLC coupled to 4000 QTRAP Triple quadrupole mass spectrometer
- ACQUITY H-Class UPLC with fraction collector
Services in detail
Protein/peptide fractionation
- Reverse-phase HPLC (high or low pH)
- Strong cation exchange HPLC
Post-translational modifications (PTMs)
- Phosphorylation & phosphoproteomics
- Phosphopeptides enrichment
- Phosphorylation site identification
- Global phosphor protein identification
- Palmitoylation
- Ubiquitination/SUMOylation
- Acetylation, methylation, and dimethylation
- Other chemical modifications (e.g., covalently bound irreversible molecule)
Protein identification
- Bottom-up LC MS/MS
- Multi-dimensional protein identification technology (MudPIT)
- IP and Co-IP protein identification
- Cross-linked protein identification
- Identification of proximity-labeled proteins (e.g., BioID)
- Contamination protein ID
Protein profiling
- Offline protein/peptide fractionation
- Stable isotopic labeling by amino acids in cell culture (SILAC)
- Label-free quantitation (LFQ)
- Multi-dimensional protein identification technology (MudPIT)
- TMT
- Data-independent acquisition (DIA)
Small-molecules quantitation
- MRM (multiple reaction monitoring)
- Biocrates p180 assay
- PK study
- Drug metabolite quantitation
Targeted proteomics
- PRM (parallel reaction monitoring)
- Data-independent acquisition (DIA) for cerebrospinal fluid (CSF)
Available to Yale researchers & external researchers
Core websiteFrequently asked questions
Learn about the decoy score, expectation measures, protein abundances, enzyme options, and more.
Note to users
This website is under construction.
Have a question or require a quote? Please email the director.
Survey: Let us know your thoughts and recommendations on how we can do a better job to help you. Use this anonymous feedback survey link or the below QR code.
Disclaimer
Due to their high complexity and variability, we cannot guarantee that our SOP for sample preparation will be applicable to all proteomics samples that we receive. ALL CLAIMS, REGARDLESS OF THEIR NATURE, MUST BE BROUGHT TO OUR ATTENTION WITHIN 30 DAYS OF RESULTS DISSEMINATION. However, we will do our very best to ensure (by looking through literature and other sources) that the highest quality services are provided for every sample submitted to us.
THE MS & PROTEOMICS RESOURCE SHALL NOT BE LIABLE FOR INCIDENTAL, CONSEQUENTIAL, OR UNANTICIPATED OUTCOME RESULTING FROM SAMPLE PREPARATION INCOMPATIBILITY TO OUR SOP, NOR SHALL ITS LIABILITY IN ANY CASE EXCEED THE ESTIMATED COST OF THE SERVICES RENDERED.
Acknowledgements
Please acknowledge our funders in your publication!
If any part of the mass spectrometry data/analyses provided by us is to be included in a manuscript, please use the below statement and include it in the acknowledgment section of your manuscript submission. Thank you.
“We also thank the MS & Proteomics Resource at Yale University for providing the necessary mass spectrometers and the accompanying biotechnology tools, funded in part by the Yale School of Medicine and by the Office of the Director, National Institutes of Health (S10OD02365101A1, S10OD019967, and S10OD018034). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.”
Our history
The Mass Spectrometry & Proteomics Resource of the W.M. Keck Biotechnology Resource Laboratory at Yale’s School of Medicine had its beginnings in 1980 in the Department of Molecular Biochemistry and Biophysics.
Dr. Kenneth R. Williams founded the Keck Lab, then called the Protein Chemistry Facility. He is still director of the resulting and evolving Keck Lab, which now encompasses Proteomics, Genomics, Biostatistics, and Bioinformatics.
For more fun facts on the journey of the MS & Proteomics Resource, download our PDF.
Rates
Effective 7/1/2024
| Service | Internal customers | External non-profit customers |
|---|---|---|
| Sample prep, simple | $61.00 | $88.00 |
| Sample prep, complex | $90.00 | $128.00 |
| Sample prep, trypsin | $53.00 | $76.00 |
| Sample prep, custom enzyme | $75.00 | $108.00 |
| Sample prep, TiO2 | $100.00 | $135.00 |
| Sample prep, desalt | $52.00 | $76.00 |
| Sample prep, NanoDrop | $10.00 | $16.00 |
| Sample prep, offline LC | $365.00 | $504.00 |
| Sample prep, isotopic labeling | $1,975.00 | $2,843.00 |
| HRMS, exact mass | $203.00 | $314.00 |
| HRMS, intact protein mass | $402.00 | $594.00 |
| LCMSMS, short gradient | $99.00 | $140.00 |
| LCMSMS, medium gradient | $115.00 | $162.00 |
| LCMSMS, long gradient | $132.00 | $190.00 |
| Targeted SM, sample | $70.00 | $103.00 |
| Targeted SM, stdCurve | $350.00 | $530.00 |
| Targeted SM, optimization | $990.00 | $1,430.00 |
| Targeted SM, data analysis | $278.00 | $388.00 |
| Data analysis, protein quantitation | $870.00 | $1,260.00 |
| Data analysis, protein ID | $51.00 | $75.00 |
| Data analysis, database configuration | $75.00 | $263.00 |
| Consulting | $303.00 | $439.00 |
| Open access, usage | $605.00 | $860.00 |
Contacts
Shipping address:
Keck MS & Proteomics Resource
Yale School of Medicine
300 George Street
Ground floor, room G001
New Haven, CT 06511
Faculty Director
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Core/facility
Yale Center for Genome Analysis (YCGA)
The Yale Center for Genome Analysis is a full-service facility dedicated to providing RNA expression profiling, DNA genotyping, and high-throughput sequencing using state-of-the-art technologies.
Primary contact
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Core/facility
Yale Center for Molecular Discovery
We provide resources for assay development and high-throughput screening with small molecules and arrayed siRNA and sgRNA/CRISPR libraries in biochemical, cell-based and image-based assays (primarily 384-well format).
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Core/facility
Chemical Metabolism Core
Previously called the Islet, Oxygen consumption, Mass Isotopomer flux Core (IOMIC), the Chemical Metabolism Core offers targeted and untargeted metabolomics, stable isotope-based metabolic flux analysis, quantitative metabolic panels of central carbon metabolism and adjacent pathways, measurements of cellular bioenergetics, islet isolation and functional studies. Services include study assistance and data analysis.