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FHS Proteomics Core Facility


Proteomics is the analysis of the entire protein content in biological and clinical samples. As proteins are the de facto functional building blocks in living organisms, it is essential to measure gene expression profiles at the protein level to study biological systems. Besides protein expression profiles, proteomics can also provide information regarding protein post-translational modifications such as phosphorylation and glycosylation, protein interaction with other molecules including proteins, DNA, RNA, lipids, and metabolites.

At the McMaster FHS proteomics core facility, we are equipped with a high-sensitivity LC-MS system featuring Thermo Q Exacitve HF orbitrap mass spectrometer coupled with Thermo RSLCNano 3000 Ultimate nanoflow LC. The proteomics core offers competitive user fees to McMaster users. Please refer to the following fee structure for typical proteomics experiments. And please feel free if you have novel proteomics experiments for which cost is not listed here. In addition, we are happy to discuss about proteomics applications from external academic and private sectors as well.

Typical Proteomics Experiment Costs (McMaster Internal Users)

Application Total Cost
Direct 1D LC-MS run for protein/peptide analysis, 1 sample $100
Simple In-solution Protein Identification, 1 sample $160
SDS-PAGE In-Gel Digestion, 1 gel band $190
Protein interaction analysis using Co-IP, 1 sample $280
Protein interaction analaysis using BioID, 1 sample $280
Global quantitative proteomics analysis, 4 samples $5,510
Global quantitative proteomics analysis, 6 samples $5,850
Global quantitative proteomics analysis, 8 samples $6,190
Global quantitative proteomics analysis, 10 samples $6,530
Global quantitative proteomics analysis, 16 samples $7,550
Global quantative phosphoproteomics analysis, 4 samples $8,200
Global quantative phosphoproteomics analysis, 6 samples $8,540
Global quantative phosphoproteomics analysis, 8 samples $8,880
Global quantative phosphoproteomics analysis, 10 samples $9,220
Global quantative phosphoproteomics analysis, 16 samples $10,240
Bulk samples & specific applications (DIA, nanoproteomics, etc) Contact Us

Detailed Proteomics Step Costs (McMaster Internal Users)

Proteomics Steps Cost
Gel band digestion $60
In-solution digestion $30
CoIP (FLAG or biotin) $100
iTRAQ labeling (per sample) $100
TMT labeling (per sample) $100
Sample desalting $40
Sample drying and reconstitution $10
Phosphoenrichment $100
Sample fractionation $150
LC-MS/MS (1.5hr gradient) $80
LC-MS/MS (2hr gradient) $100
LC-MS/MS (3hr gradient) $120
Data analysis (per hour computer time) $10


  1. Ruilin Wu, Sansi Xing, Maryam Badv, Tohid Didar*, Yu Lu*. Step-wise assessment and optimization of sample handling recovery yield for nanoproteomic analysis of 1,000 mammalian cells. Analytical Chemistry, 91, 10395-10400, 2019 (*. co-corresponding authors).
  2. Ruilin Wu, Akshat Pai, Lina Liu, Sansi Xing, Yu Lu. NanoTPOT: Enhanced Sample Preparation for Quantitative Nanoproteomic Analysis. Analytical Chemistry, 92, 6235-6240, 2020.
  3. Vickie Kwan, Elyse Rosa, Sansi Xing, Nadeem Murtaza, Nicholas T. Holzapfel, Yu Lu*, Karun K. Singh*. Proteomic analysis reveals autism-associated gene DIXDC1 regulates proteins associated with mitochondrial organization and function. Journal of Proteome Research, 20, 1052-1062, 2021. (*. co-corresponding authors).
  4. Sophie M. Poznanski, Kanwaldeep Singh, Tyrah M. Ritchie, Jennifer A. Aguiar, Isabella Y. Fan, Ana L. Portillo, Eduardo A. Rojas, Fatemeh Vahedi, Abdullah El-Sayes, Sansi Xing, Martin Butcher, Yu Lu, Andrew Doxey, Jonathan D. Schertzer, Hal W. Hirte, Ali A. Ashkar. Metabolic flexibility determines human NK cell functional fate in the tumor microenvironment. Cell Metabolism, 33, 1205-1220, 2021.
  5. Sansi Xing, Akshat Pai, Ruilin Wu, Yu Lu. NHS-ester tandem labeling in one pot enables 48-plex proteomics. Analytical Chemistry, accepted, DOI: 10.1021/acs.analchem.1c01314.

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