Proteomics

About the Proteomics Shared Resource

The Proteomics Shared Resource (PSR) provides mass spectrometry-based analysis services that span the identification, characterization and quantification of proteins. Consultations are offered to assist investigators with experimental designs to meet their project goals. Services are available to VCU Massey members, the VCU community and researchers outside of VCU. Services are available for protein identification (e.g., gel bands, protein binding partners), molecular weight determination for peptides and proteins, protein post-translational modifications (e.g., methylation, acetylation, phosphorylation), and relative quantification (e.g., label free quantification, TMT). 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 below so that we can provide you with a formal quote.

PSR submission form

Services
Services
- In-gel protein identification
  - Low sample complexity¹ (fast gradient): $165
- In-solution protein identification²
  - Low sample complexity (fast gradient): $255
  - Medium (Standard Gradient): $285
  - High(Extended Gradient): $315
- Label Free Quantification³: $1,065
- PTM Analysis⁴: Please inquire
- Additional Sample Preparation: $85/hour
- Additional Data Analysis⁵: $85/hour
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.

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
Instrumentation
LC-MS/MS Instrumentation

Thermo Exploris 480 w/Vanquish Neo UHPLC & UV-vis

Exploris 480 Orbitrap MS
Mass Range: 40-6000 m/z
Mass Accuracy: <3 ppm
Resolving Power: 480,000 @ 195 m/z
Scan Rate: ≤40 Hz @ RP 7500 and 200 m/z
MS/MS: HCD

Vanquish Neo UHPLC
Flow Rate: 1 nl/min – 100𝛍l/min
Max Pressure: 1500 bar
Column Compartment: 15ºC - 80ºC
Variable Wavelength Detector (190-900 nm)

The Exploris 480 system coupled with a Vanquish Neo UHPLC was obtained in 2023 with funds from HEETF and Massey Cancer Center. The instrument is the most advanced Q Exactive Orbitrap platform available with analytical figures of merit that provide outstanding proteome coverage. The high pressure UHPLC system supports extended length nanoflow analytical columns that enable the identification of >5000 proteins from a standard cell lysate sample in a single run. Additional capabilities include relative protein quantification (label free, SILAC, and TMT), post-translational modification analysis (phospho, methyl, etc.), and targeted absolution quantification (parallel reaction monitoring).

Thermo Q Exactive HF-X w/Easy nLC 1200

Q Exactive HF-X Orbitrap MS
Mass Range: 50-6000 m/z
Mass Accuracy: <3 ppm
Resolving Power: 240,000 @ 200 m/z
Scan Rate: ≤40 Hz @ RP 7500 and 200 m/z
MS/MS: HCD

Easy nLC 1200 UHPLC
Flow Rate: 20 nl/min – 2000nl/min
Max Pressure: 1200 bar

The Q Exactive system coupled with an Easy nLC 1200 UHPLC was obtained in 2017 with funds from HEETF and Massey Cancer Center. The instrument is a 3rd generation Q Exactive Orbitrap platform available with analytical figures of merit that provide excellent proteome coverage. The high pressure UHPLC system supports heated nanoflow analytical columns that enable the identification of >4000 proteins from a standard cell lysate sample in a single run. Additional capabilities include relative protein quantification (label free, SILAC, and TMT), post-translational modification analysis (phospho, methyl, etc.), and targeted absolution quantification (parallel reaction monitoring).

Thermo Fusion Lumos ETD w/ Easy nLC 1200

Fusion Lumos ETD Orbitrap MS
Mass Range: 200-6000 m/z
Mass Accuracy: <3 ppm
Resolving Power: 480,000 @ 200 m/z
Scan Rate: ≤45 Hz @ RP 7500 and 200 m/z
MS/MS: CID, HCD, ETD, and EThCD
MS Scan Power: MSn (n = 1-10)

Easy nLC 1200 UHPLC
Flow Rate: 20 nl/min – 2000nl/min
Max Pressure: 1200 bar

The Fusion Lumos with ETD coupled with an Easy nLC 1200 UHPLC was obtained in 2017 with funds from HEETF and the Institute for Structural Biology and is housed in Biotech One. The instrument is a hybrid Orbitrap platform that includes CID, HCD, ETD, and EThCD dissociation techniques and MSn capabilities. These unique technical features are complementary to the QE HFX and 480 Exploris in that they enable a higher degree of peptide/protein structural characterization. This becomes particularly important for site localization of amino acid modifications (e.g. PTMs), complex PTM characterization (e.g., glycosylation), and chemical cross-linked peptides.

Computers and Data Analysis Software Resources

HP Z8G4 8 Core @ 3.2GHz
32 GB Memory
Windows 10
- Thermo Proteome Discoverer 3.0
- XlinkX Node
- Protein Metrics Byonic
HP Z8G4T 8 Core @ 3.5GHz
32 GB Memory
Windows 10
- Thermo Proteome Discoverer 3.0
- XlinkX Node
Ancillary Instrumentation

Thermo Vanquish Horizon UHPLC

Variable Wavelength UV-vis: 190-900 nm, ≤ 4 channels
Fluorescence Detector F: ≤ 4 channels
Integrated Fraction Collector: 0.05 - 10 ml/min
Column Compartment H: 5°C - 120°C

Agilent BioTek Synergy H1 Plate Reader

UV-vis: 200-999 nm
Fluorescence: 300-700 nm
Linear Shaking
Incubator ≤ 50ºC
6-384-well plates
Education
Courses Offered

PSCI 692/PCEU 675 (3 credits)

Course Description: This is an introductory course in Proteomics with an emphasis on contemporary mass spectrometry-based measurements including protein identification, protein quantification and mapping post-translational modifications. The course will cover essential aspects of mass spectrometry-based proteomics including sample preparation, mass spectrometry instrumentation, separation science fundamentals, protein identification, protein quantification, post-translational modification analysis strategies and data analysis.
- Adam Hawkridge (Course Coordinator and Primary Contact)
- Charles (Chuck) Lyons (Instructor and Member of the Proteomics Shared Resource)
- Arjun Rijal (Instructor and Member of the Proteomics Shared Resource)
Data consultation

Consultations are available to assist investigators with experimental designs to meet their project goals. Services are available toVCU Massey members, the VCU community and researchers outside of VCU. Services are currently available for protein identification (e.g., gel bands, protein binding partners), molecular weight determination for peptides and proteins, protein post-translational modifications (e.g., methylation, acetylation, phosphorylation), and relative quantification (e.g., label free quantification, TMT).

To initiate your project, please complete this submission form so that we can provide you with a formal quote.
Contact

The Proteomics Shared Resource is ready to assist you with your analysis needs. The facility is located in the Molecular Medicine Research Building lab, number 2001/2003 or office number 2038.

Contact information

Investigators are strongly encouraged to discuss their projects with the PSR staff before submitting samples for analyses. For assistance with grant applications, letters of support, or other related needs, please contact a member of the PSR team.

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

Chuck Lyons
Lab/Resource Manager
celyons@vcu.edu

Arjun Rijal, M.S.
Senior Biological Mass Spectrometrist
rijala2@vcu.edu

Proteomics Laboratory

Molecular Medicine Research Building
Lab: 2001 and 2003A/B
1220 E. Broad St.

Download building map to building

Consultation Office

Molecular Medicine Research Building
Office: 2038
1220 E. Broad St.

Download map to building to find office and lab

Selected Recent Publications Supported by the PSR

Wu P, Van Scoyk M, McHale S, Chou CF, Riddick G, Farouq K, Hu B, Kraskauskiene V, Koblinski J, Lyons CE, Rijal A, Vudatha V, Zhang D, Trevino J, Shah R, Nana-Sinkam P, Huang Y, Ma S-F, Noth I Hughes-Halvert C, Seewaldt V, Chen C-Y and Winn R. Cooperation Between PRMT1 and PRMT6 Drives Lung Cancer Health Disparities Among Black/African American Men. iScience 2024 January 7.

Shang S, Li X, Azzo A, Truong T, Dozmorov M, Lyons CE, Manna A, Williams, Jr. D and Ginder G. MBD2a-NuRD binds to the methylated gamma-globin gen promoter and uniquely forms a complex required for silencing of HbF expression. PNAS 2023 June 12.

Li H, Zhu H, Sarbeng EB, Liu Q, Tian X, Yang Y, Lyons CE, Zhou L, Liu Q. An unexpected second binding site for polypeptide substrates is essential for Hsp70 chaperone activity.J Biol Chem. 2020 Jan 10;295(2):584-596. doi: 10.1074/jbc.RA119.009686. Epub 2019 Dec 5.PMID: 31806707

Services

In-gel protein identification
- Low sample complexity¹ (fast gradient): $165
In-solution protein identification²
- Low sample complexity (fast gradient): $255
- Medium (Standard Gradient): $285
- High(Extended Gradient): $315
Label Free Quantification³: $1,065
PTM Analysis⁴: Please inquire
Additional Sample Preparation: $85/hour
Additional Data Analysis⁵: $85/hour

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.

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

LC-MS/MS Instrumentation

Thermo Exploris 480 w/Vanquish Neo UHPLC & UV-vis

Proteomics Equipment - Thermo Exploris 480 w/Vanquish Neo UHPLC & UV-vis

Exploris 480 Orbitrap MS
Mass Range: 40-6000 m/z
Mass Accuracy: <3 ppm
Resolving Power: 480,000 @ 195 m/z
Scan Rate: ≤40 Hz @ RP 7500 and 200 m/z
MS/MS: HCD

Vanquish Neo UHPLC
Flow Rate: 1 nl/min – 100𝛍l/min
Max Pressure: 1500 bar
Column Compartment: 15ºC - 80ºC
Variable Wavelength Detector (190-900 nm)

The Exploris 480 system coupled with a Vanquish Neo UHPLC was obtained in 2023 with funds from HEETF and Massey Cancer Center. The instrument is the most advanced Q Exactive Orbitrap platform available with analytical figures of merit that provide outstanding proteome coverage. The high pressure UHPLC system supports extended length nanoflow analytical columns that enable the identification of >5000 proteins from a standard cell lysate sample in a single run. Additional capabilities include relative protein quantification (label free, SILAC, and TMT), post-translational modification analysis (phospho, methyl, etc.), and targeted absolution quantification (parallel reaction monitoring).

Thermo Q Exactive HF-X w/Easy nLC 1200

Q Exactive HF-X Orbitrap MS
Mass Range: 50-6000 m/z
Mass Accuracy: <3 ppm
Resolving Power: 240,000 @ 200 m/z
Scan Rate: ≤40 Hz @ RP 7500 and 200 m/z
MS/MS: HCD

Easy nLC 1200 UHPLC
Flow Rate: 20 nl/min – 2000nl/min
Max Pressure: 1200 bar

The Q Exactive system coupled with an Easy nLC 1200 UHPLC was obtained in 2017 with funds from HEETF and Massey Cancer Center. The instrument is a 3rd generation Q Exactive Orbitrap platform available with analytical figures of merit that provide excellent proteome coverage. The high pressure UHPLC system supports heated nanoflow analytical columns that enable the identification of >4000 proteins from a standard cell lysate sample in a single run. Additional capabilities include relative protein quantification (label free, SILAC, and TMT), post-translational modification analysis (phospho, methyl, etc.), and targeted absolution quantification (parallel reaction monitoring).

Thermo Fusion Lumos ETD w/ Easy nLC 1200

Fusion Lumos ETD Orbitrap MS
Mass Range: 200-6000 m/z
Mass Accuracy: <3 ppm
Resolving Power: 480,000 @ 200 m/z
Scan Rate: ≤45 Hz @ RP 7500 and 200 m/z
MS/MS: CID, HCD, ETD, and EThCD
MS Scan Power: MSn (n = 1-10)

Easy nLC 1200 UHPLC
Flow Rate: 20 nl/min – 2000nl/min
Max Pressure: 1200 bar

The Fusion Lumos with ETD coupled with an Easy nLC 1200 UHPLC was obtained in 2017 with funds from HEETF and the Institute for Structural Biology and is housed in Biotech One. The instrument is a hybrid Orbitrap platform that includes CID, HCD, ETD, and EThCD dissociation techniques and MSn capabilities. These unique technical features are complementary to the QE HFX and 480 Exploris in that they enable a higher degree of peptide/protein structural characterization. This becomes particularly important for site localization of amino acid modifications (e.g. PTMs), complex PTM characterization (e.g., glycosylation), and chemical cross-linked peptides.

Computers and Data Analysis Software Resources

Thermo Fusion Lumos ETD w/ Easy nLC 1200

HP Z8G4 8 Core @ 3.2GHz
32 GB Memory
Windows 10

Thermo Proteome Discoverer 3.0
XlinkX Node
Protein Metrics Byonic

HP Z8G4T 8 Core @ 3.5GHz
32 GB Memory
Windows 10

Thermo Proteome Discoverer 3.0
XlinkX Node

Ancillary Instrumentation

Thermo Vanquish Horizon UHPLC

Variable Wavelength UV-vis: 190-900 nm, ≤ 4 channels
Fluorescence Detector F: ≤ 4 channels
Integrated Fraction Collector: 0.05 - 10 ml/min
Column Compartment H: 5°C - 120°C

Agilent BioTek Synergy H1 Plate Reader

UV-vis: 200-999 nm
Fluorescence: 300-700 nm
Linear Shaking
Incubator ≤ 50ºC
6-384-well plates

Courses Offered

PSCI 692/PCEU 675 (3 credits)

Course Description: This is an introductory course in Proteomics with an emphasis on contemporary mass spectrometry-based measurements including protein identification, protein quantification and mapping post-translational modifications. The course will cover essential aspects of mass spectrometry-based proteomics including sample preparation, mass spectrometry instrumentation, separation science fundamentals, protein identification, protein quantification, post-translational modification analysis strategies and data analysis.

Adam Hawkridge (Course Coordinator and Primary Contact)
Charles (Chuck) Lyons (Instructor and Member of the Proteomics Shared Resource)
Arjun Rijal (Instructor and Member of the Proteomics Shared Resource)

Data consultation

Consultations are available to assist investigators with experimental designs to meet their project goals. Services are available toVCU Massey members, the VCU community and researchers outside of VCU. Services are currently available for protein identification (e.g., gel bands, protein binding partners), molecular weight determination for peptides and proteins, protein post-translational modifications (e.g., methylation, acetylation, phosphorylation), and relative quantification (e.g., label free quantification, TMT).

To initiate your project, please complete this submission form so that we can provide you with a formal quote.

The Proteomics Shared Resource is ready to assist you with your analysis needs. The facility is located in the Molecular Medicine Research Building lab, number 2001/2003 or office number 2038.

Contact information

Investigators are strongly encouraged to discuss their projects with the PSR staff before submitting samples for analyses. For assistance with grant applications, letters of support, or other related needs, please contact a member of the PSR team.

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

Chuck Lyons
Lab/Resource Manager
celyons@vcu.edu

Arjun Rijal, M.S.
Senior Biological Mass Spectrometrist
rijala2@vcu.edu

Proteomics Laboratory

Molecular Medicine Research Building
Lab: 2001 and 2003A/B
1220 E. Broad St.

Download building map to building

Consultation Office

Proteomics Office Consultation

Molecular Medicine Research Building
Office: 2038
1220 E. Broad St.

Download map to building to find office and lab

Selected Recent Publications Supported by the PSR

Wu P, Van Scoyk M, McHale S, Chou CF, Riddick G, Farouq K, Hu B, Kraskauskiene V, Koblinski J, Lyons CE, Rijal A, Vudatha V, Zhang D, Trevino J, Shah R, Nana-Sinkam P, Huang Y, Ma S-F, Noth I Hughes-Halvert C, Seewaldt V, Chen C-Y and Winn R. Cooperation Between PRMT1 and PRMT6 Drives Lung Cancer Health Disparities Among Black/African American Men. iScience 2024 January 7.

Shang S, Li X, Azzo A, Truong T, Dozmorov M, Lyons CE, Manna A, Williams, Jr. D and Ginder G. MBD2a-NuRD binds to the methylated gamma-globin gen promoter and uniquely forms a complex required for silencing of HbF expression. PNAS 2023 June 12.

Li H, Zhu H, Sarbeng EB, Liu Q, Tian X, Yang Y, Lyons CE, Zhou L, Liu Q. An unexpected second binding site for polypeptide substrates is essential for Hsp70 chaperone activity.J Biol Chem. 2020 Jan 10;295(2):584-596. doi: 10.1074/jbc.RA119.009686. Epub 2019 Dec 5.PMID: 31806707

Acknowledge the Proteomics Shared Resource

All publications that include results, services or products generated by the VCU Massey Comprehensive 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 Comprehensive 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.

Office of the Vice President for Research and Innovation

This Shared Resource is jointly supported by VCU Massey Comprehensive Cancer Center and the Office of the Vice President for Research and Innovation.