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Proteomics

About the Proteomics Shared Resource (PSR)

The PSR provides mass spectrometry-based analysis services that span the identification, characterization and quantification of proteins. We routinely provide consultations to assist investigators with experimental designs to meet their project goals. Services are available to the Massey Cancer Center members, VCU community and interested collaborators outside VCU. We currently offer services for protein identification (e.g., gel bands, protein binding partners), molecular weight determination for purified peptides and proteins, protein post-translational modifications (e.g., methylation, acetylation, phosphorylation), and relative quantification (e.g., label free quantification). Additional services are currently under development (e.g., SILAC, TMT, PRM).

Investigators are strongly encouraged to discuss their projects with the PSR staff before submitting samples for analyses. To initiate your project, please complete the submission form so that we can provide you a formal quote.   

Services

Service Sample Complexity1 PTM Analysis4 Additional Sample Preparation Additional Data Analysis5
Low
(Fast Gradient)
Medium
(Standard Gradient)
High
(Extended Gradient)
In-gel protein identification $155     Please Inquire $65/hr $65/hr
Protein molecular weight analysis $70    
In-solution protein identification2 $225 $245 $265
Label Free Quantification3 $825 $945 $1065

1Sample complexity refers to the expected size of the proteome being analyzed. A “Low” complexity sample might include a gel band or purified recombinant protein in which case we recommend a fast UHPLC gradient (1 hour). A “Medium” complexity sample might include an enriched sample (e.g., pull-down, sub-cellular fraction, PTM) in which case we recommend a standard UHPLC gradient (2 hours). A “High” complexity sample might include a total cellular or tissue lysate in which case we recommend an extended UHPLC gradient (3 hours). A longer UHPLC gradient (i.e., greater separation and MS/MS data acquisition time) generally translates to higher numbers of protein identifications but this becomes less of a factor for simpler samples where shorter separation and MS/MS acquisition time is sufficient. Please speak with lab personnel if you have questions about which analysis type best suits your project goals.

2Rates include BCA and fluorescence assays to determine total protein and peptide, respectively.

3Rates assume a binary comparison (e.g., Control vs. Treatment, WT vs. KO) with 3 replicates each (i.e., 6 LC-MS/MS runs total). Rates for larger numbers of conditions and replicates will be quoted accordingly, please inquire. Rates also include BCA and fluorescence assays to determine total protein and peptide, respectively. Report includes spreadsheet with identified proteins, filter levels used, log2 expression levels, and basic statistical analysis (adjusted p-values). Note: more advanced data analysis and figure types such as protein enrichment, signaling pathways, Venn diagrams, volcano plots, and heatmaps require additional fees listed as ‘Additional Data Analysis’.

4Post-translational modification (PTM) analysis is priced based on sample, type of PTM(s), and experimental goals. In some cases, there may not be an additional charge added but in others there could be charges related to additional reagents (e.g., multiple enzymes), sample preparation time (e.g., enrichment, clean-up), and data analysis (e.g., manual spectral analysis). Please speak with lab personnel to determine which analysis type best suits your project goals.

5Additional data analysis includes re-analyzing a proteomics dataset generated in the PSR, manual data analysis, advanced statistical analysis, protein enrichment, pathway analysis, or advanced plotting (e.g., volcano plots, Venn diagrams, heatmaps). Note, some of these additional services will be carried out in the Bioinformatics Core.

Contact

The Proteomics Shared Resource is ready to assist you with your analysis needs. We are located in MCC 1-132 and office G-129.

Adam Hawkridge, Ph.D.
Director
Associate professor, Department of Pharmaceutics
amhawkridge@vcu.edu

Chuck Lyons
Resource Manager
celyons@vcu.edu

Arjun Rijal
Biological Mass Spectrometrist

Massey member subsidy benefit

Massey subsidizes 25 percent of the cost of members’ core laboratory usage for the following Massey-supported, fee-for-service shared resources:

  • Flow Cytometry Shared Resource
  • Lipidomics & Metabolomics Shared Resource
  • Microscopy Shared Resource
  • Tissue and Data Acquisition and Analysis Core
  • Transgenic/Knockout Mouse Shared Resource
  • Cancer Mouse Models Core
  • Proteomics Shared Resource

To receive this member benefit, please initiate core lab services using a VCU index code associated with your name. When you are billed for core laboratory usage, the Rams FORCE system will automatically split the invoice between your index code and a Massey account established for this purpose. You will be charged 75 percent of the published rate and Massey will provide a 25 percent co-pay to cover the balance. Please direct any questions or concerns about the member subsidy benefit to Paul Fawcett, Ph.D. at paul.fawcett@vcuhealth.org or (804) 827-0975.

Acknowledge the Proteomics Shared Resource

All publications that include results, services or products generated by the VCU Massey Cancer Center Shared Resources must include the following acknowledgement in the manuscript:

"Services and products in support of the research project were generated by the VCU Massey Cancer Center Proteomics Shared Resource, supported, in part, with funding from NIH-NCI Cancer Center Support Grant P30 CA016059."

PubMed Central (PMC) ID numbers are required for those publications that use CCSG-supported shared resources. All of Massey Cancer Center's Shared Resources are supported by the CCSG.