iLab Organizer :: Vermont Biomedical Research Network (VBRN) Proteomics Facility

Overview of Services

The VBRN Proteomics Facility (https://vbrn.org/proteomics/) is located in the Marsh Life Science Building (Room 333 - 337). It enables investigators to use an array of state-of-the-art mass spectrometry-based techniques for proteomics experiments, ranging from routine protein identification, post-translational modification characterization and finding protein interacting partners, to large-scale quantitative proteomics analyses using stable isotopes. Since its inception in 2006, the facility has analyzed over 20,000 samples and facilitated data acquisition to support close to 180 publications (https://vbrn.org/proteomics-publications/). The facility personnel train investigators in experimental design and proteomics methods, as well as assist with data interpretation, manuscript preparation, and grant submission. Our user base includes investigators from UVM and from institutions in 15 states. A summary of the facility’s impact on the development of the network can be found at https://vbrn.org/proteomics-impact/.

The Proteomics Facility (Room 335) is equipped with standard laboratory equipment (freezers, centrifuges, incubators, microscopes, and analytical balances, etc.), a Shimadzu analytical HPLC system with UV detection for offline fractionation, electrophoresis systems, a Sutter P-2000 laser puller, a Savant SpeedVac concentrator, a Labconco lyophilizer, five mass spectrometers from Thermo Fisher Scientific, as well as a hydrogen deuterium exchange (HDX) workflow station:

Orbitrap Fusion Tribrid mass spectrometer (MS) coupled to an EASY-nLC ULTRA UPLC system
Q-Exactive Hybrid Quadrupole-Orbitrap MS Plus coupled to an EASY-nLC 1200 UPLC system
LTQ Orbitrap Discovery MS coupled to a Surveyor HPLC system
LTQ XL Linear Ion Trap MS equipped with electron transfer dissociation (ETD) coupled to a Surveyor HPLC system
LTQ Linear Ion Trap MS coupled to a Prominence (Shimadzu) HPLC system
HDX workflow station, HDx-3 PAL (Leap Technologies), which can be coupled to the LTQ or LTQ-Orbitrap Discovery MS with a Workplace Modular systems cart for conducting HDX MS experiments

The Data Processing unit (Room 333) maintains five computers (4 Dell Optiplex 7060 Workstations, i7 Processor, 32GB RAM, 2 displays for each, and 1 Dell Precision Tower 5810 with 1 display), and offers a suite of software including three copies of Proteome Discoverer embedded with SEQUEST, MASCOT and Byonic, SCAFFOLD Q+S, SIEVE, PEAKS, Skyline, SimGlycan, and HD Examiner to evaluate the datasets generated from various types of proteomics experiments.

The Proteomics Facility is located in the Marsh Life Science Building and occupies 1,408 ft² of lab, data processing unit, office, and consultation space. There are bench spaces for accommodating up to six persons working simultaneously for sample preparation. The facility is supported by INBRE funding (P20GM103449).

Contacts

Name	Role	Phone	Email	Location
Dr. Bin Deng	Manager	(802) 656-5099	Bin.Deng@uvm.edu	337 Marsh Life Science Building
Dr. Ying Wai Lam	Core Director	(802) 656-4709	Ying-Wai.Lam@uvm.edu	337 Marsh Life Science Building

Name

Role

Phone

Location

Dr. Bin Deng

Manager

(802) 656-5099

Bin.Deng@uvm.edu

337 Marsh Life Science Building

Dr. Ying Wai Lam

Core Director

(802) 656-4709

Ying-Wai.Lam@uvm.edu

337 Marsh Life Science Building

Name	Description	Price
Absolute quantification of proteins using stable isotopically labeled standards	A consultation is required prior to sample submission	Inquire
Consultation	Please consult with the facility personnel to: 1) select what sample preparation method(s) you would like to perform on your digests (e.g, Ziptip, TMT labeling, etc.) 2) select from the LC/MS category which instrument to use and the associated run time. A consultation is required prior to sample submission For gel samples, please provide an image of the gel and mark the bands or spots that are to be analyzed. We need to be sure your samples and sample preparation methods are compatible with mass spectrometry and your sample has an adequate amount of the target proteins to be measured by mass spectrometry. For protein samples in solution, you must provide us the expected protein concentration and the composition of the solution Turnaround time: 2-3 weeks	Inquire
De novo sequencing	A consultation is required prior to sample submission	Inquire
Desalting (for removing TMT labels)	Performed by facility personnel Desalting columns and reagents provided.	UVM Internal $57.15 each External $62.86 each COM $46.45 each BPI $57.15 each
Exploris 240 (0.5 h) - simple mixture	Performed by user	UVM Internal $66.17 each External $72.79 each COM $53.79 each BPI $66.17 each
Exploris 240 (0.5 h) - simple mixture	Performed by facility personnel	UVM Internal $83.98 each External $92.38 each COM $68.26 each BPI $83.98 each
Exploris 240 (1 h) - complex mixture	Performed by user	UVM Internal $99.56 each External $109.52 each COM $80.93 each BPI $99.56 each
Exploris 240 (1 h) - complex mixture	Performed by facility personnel	UVM Internal $103.94 each External $106.87 each COM $84.49 each BPI $103.94 each
Exploris 240 (3 h) - highly complex mixture	Performed by user	UVM Internal $233.13 each External $256.44 each COM $189.49 each BPI $233.13 each
Exploris 240 (3 h) - highly complex mixture	Performed by facility personnel	UVM Internal $251.35 each External $276.49 each COM $204.31 each BPI $251.35 each
Exploris 240 (0.25 h) - single protein	Performed by user	UVM Internal $49.47 each External $54.42 each COM $40.21 each BPI $49.47 each
Exploris 240 (0.25 h) - single protein	Performed by facility personnel	UVM Internal $67.70 each External $74.47 each COM $55.03 each BPI $67.70 each
Fusion (0.25 h) - single protein	Performed by user	UVM Internal $47.80 each External $52.59 each COM $38.86 each BPI $47.80 each
Fusion (0.25 h) - single protein	Performed by facility personnel	UVM Internal $66.03 each External $72.63 each COM $53.67 each BPI $66.03 each
Fusion (0.5 h) - simple mixture	Performed by user	UVM Internal $62.83 each External $69.11 each COM $51.07 each BPI $62.83 each
Fusion (0.5 h) - simple mixture	Performed by facility personnel	UVM Internal $80.64 each External $88.70 each COM $65.55 each BPI $80.64 each
Fusion (1 h) - complex mixture	Performed by user	UVM Internal $92.88 each External $102.17 each COM $75.50 each BPI $92.88 each
Fusion (1 h) -complex mixture	Performed by facility personnel	UVM Internal $97.26 each External $106.99 each COM $79.06 each BPI $97.26 each
Fusion (3 h) - highly complex mixture	Performed by user	UVM Internal $213.09 each External $234.40 each COM $173.21 each BPI $213.09 each
Fusion (3 h) - highly complex mixture	Performed by facility personnel	UVM Internal $221.14 each External $243.25 each COM $179.75 each BPI $221.14 each
High-pH fractionation	Performed by users in the facility Kit and reagents provided. 1 set (8 fractions)	UVM Internal $35.48 each External $39.03 each COM $28.84 each BPI $35.48 each
High-pH fractionation	Performed by facility personnel 1 set (8 fractions)	UVM Internal $179.02 each External $196.92 each COM $145.51 each BPI $179.02 each
Identification of post-translational modifications (PTMs)	A consultation is required prior to sample submission	Inquire
Identification of protein-protein interacting partners (Interactomes)	A consultation is required prior to sample submission	Inquire
In-gel digestion	Performed by users in the facility Enzyme and reagents provided.	UVM Internal $11.80 each External $12.98 each COM $9.59 each BPI $11.80 each
In-gel digestion (> 15 gel bands)	Performed by facility personnel	UVM Internal $49.12 each External $54.03 each COM $39.93 each BPI $49.12 each
In-gel digestion (< 15 gel bands)	Performed by facility personnel	UVM Internal $80.97 each External $89.07 each COM $65.82 each BPI $80.97 each
In-solution digestion (User provides enzyme)	Performed by facility personnel	UVM Internal $119.57 each External $131.53 each COM $97.19 each BPI $119.57 each
Label-Free quantification (Spectral counting)	A consultation is required prior to sample submission	Inquire
Lyophilizer	Operated by users (assisted by facility personnel, if necessary)	UVM Internal $53.43 each External $58.77 each COM $43.43 each BPI $53.43 each
Peptide fractionation of complex mixtures	Off-line peptide separation (e.g., SCX) Strong cation exchange fractionation High-pH reverse phase fractionation A consultation is required prior to sample submission	Inquire
Phosphopeptide-enrichment	Performed by users in the facility Kit and reagents provided.	UVM Internal $22.26 each External $24.48 each COM $18.09 each BPI $22.26 each
Phosphopeptide-enrichment	Performed by facility personnel	UVM Internal $51.44 each External $56.58 each COM $41.81 each BPI $51.44 each
Prepare Figures (fee for service)	fee / figure	UVM Internal $589.29 each External $648.22 each COM $487.99 each BPI $589.29 each
Protein identification, isoform characterization (In-gel/In-solution digestion)	A consultation is required prior to sample submission	Inquire
Proteome Discoverer	Performed by user	UVM Internal $0.00 each External $0.00 each COM $0.00 each BPI $0.00 each
Proteome Discoverer	Performed by facility personnel Fee for all samples submitted in 1 batch	UVM Internal $66.19 each External $72.81 each COM $53.80 each BPI $66.19 each
Q-Exactive Plus (0.25 h) - single protein	Performed by user	UVM Internal $41.13 each External $45.24 each COM $33.43 each BPI $41.13 each
Q-Exactive Plus (0.25 h) - single protein	Performed by facility personnel	UVM Internal $59.21 each External $65.13 each COM $48.13 each BPI $59.21 each
Q-Exactive Plus (0.5 h) - simple mixture	Performed by user	UVM Internal $49.47 each External $54.42 each COM $40.21 each BPI $49.47 each
Q-Exactive Plus (0.5 h)- simple mixture	Performed by facility personnel	UVM Internal $60.00 each External $66.00 each COM $48.77 each BPI $60.00 each
Q-Exactive Plus (1 h) - complex mixture	Performed by user	UVM Internal $66.17 each External $72.79 each COM $53.79 each BPI $66.17 each
Q-Exactive Plus (1 h) - complex mixture	Performed by facility personnel	UVM Internal $77.33 each External $85.07 each COM $62.86 each BPI $77.33 each
Q-Exactive Plus (3 h) - highly complex mixture	Performed by user	UVM Internal $132.95 each External $146.25 each COM $108.07 each BPI $132.95 each
Q-Exactive Plus (3 h) - highly complex mixture	Performed by facility personnel	UVM Internal $144.10 each External $158.51 each COM $117.13 each BPI $144.10 each
Quantification of target peptides using Parallel Reaction Monitoring and Skyline	A consultation is required prior to sample submission	Inquire
Quantitative Proteomics (with peptide fractionation/enrichment)	Mass spectrometry-based global quantification of protein expression and PTMs in biological samples using stable isotopes. Stable Isotope Labeling by Amino acids in Cell culture (SILAC) Dimethyl Labeling Tandem Mass Tags	Inquire
Scaffold	Performed by user	UVM Internal $0.00 each External $0.00 each COM $0.00 each BPI $0.00 each
Scaffold	Performed by facility personnel All samples submitted at 1 time	UVM Internal $74.64 each External $82.10 each COM $60.67 each BPI $74.64 each
TMT labeling	Performed by users in the facility TMT reagents NOT provided.	UVM Internal $12.07 each External $13.27 each COM $9.81 each BPI $12.07 each
TMT labeling	Performed by facility personnel. 1 set (e.g., 10-plex)	UVM Internal $91.89 each External $101.08 each COM $74.69 each BPI $91.89 each
TMT labeling	Performed by facility personnel Additional 1 set	UVM Internal $26.66 each External $29.32 each COM $21.67 each BPI $26.66 each
Zip tip	Performed by users in the facility Kit and reagents provided.	UVM Internal $9.97 each External $10.97 each COM $8.10 each BPI $9.97 each
Zip tip	Performed by facility personnel	UVM Internal $32.36 each External $35.60 each COM $26.30 each BPI $32.36 each

▼ ► Current Proteomics Facility Capabilities (10)
Name	Description	Price
Consultation	Please consult with the facility personnel to: 1) select what sample preparation method(s) you would like to perform on your digests (e.g, Ziptip, TMT labeling, etc.) 2) select from the LC/MS category which instrument to use and the associated run time. A consultation is required prior to sample submission For gel samples, please provide an image of the gel and mark the bands or spots that are to be analyzed. We need to be sure your samples and sample preparation methods are compatible with mass spectrometry and your sample has an adequate amount of the target proteins to be measured by mass spectrometry. For protein samples in solution, you must provide us the expected protein concentration and the composition of the solution Turnaround time: 2-3 weeks	Inquire
Quantification of target peptides using Parallel Reaction Monitoring and Skyline	A consultation is required prior to sample submission	Inquire
Protein identification, isoform characterization (In-gel/In-solution digestion)	A consultation is required prior to sample submission	Inquire
Identification of protein-protein interacting partners (Interactomes)	A consultation is required prior to sample submission	Inquire
Identification of post-translational modifications (PTMs)	A consultation is required prior to sample submission	Inquire
De novo sequencing	A consultation is required prior to sample submission	Inquire
Peptide fractionation of complex mixtures	Off-line peptide separation (e.g., SCX) Strong cation exchange fractionation High-pH reverse phase fractionation A consultation is required prior to sample submission	Inquire
Quantitative Proteomics (with peptide fractionation/enrichment)	Mass spectrometry-based global quantification of protein expression and PTMs in biological samples using stable isotopes. Stable Isotope Labeling by Amino acids in Cell culture (SILAC) Dimethyl Labeling Tandem Mass Tags	Inquire
Absolute quantification of proteins using stable isotopically labeled standards	A consultation is required prior to sample submission	Inquire
Label-Free quantification (Spectral counting)	A consultation is required prior to sample submission	Inquire
▼ ► Data visualization and Figures preparation for publication (heat maps or volcano plots, etc.) (1)
Name	Description	Price
Prepare Figures (fee for service)	fee / figure	UVM Internal $589.29 each External $648.22 each COM $487.99 each BPI $589.29 each
▼ ► Database searches / Software Analysis (with statistics) (4)
Name	Description	Price
Proteome Discoverer	Performed by user	UVM Internal $0.00 each External $0.00 each COM $0.00 each BPI $0.00 each
Proteome Discoverer	Performed by facility personnel Fee for all samples submitted in 1 batch	UVM Internal $66.19 each External $72.81 each COM $53.80 each BPI $66.19 each
Scaffold	Performed by user	UVM Internal $0.00 each External $0.00 each COM $0.00 each BPI $0.00 each
Scaffold	Performed by facility personnel All samples submitted at 1 time	UVM Internal $74.64 each External $82.10 each COM $60.67 each BPI $74.64 each
▼ ► LC-MS (24)
Name	Description	Price
Exploris 240 (0.5 h) - simple mixture	Performed by user	UVM Internal $66.17 each External $72.79 each COM $53.79 each BPI $66.17 each
Exploris 240 (0.5 h) - simple mixture	Performed by facility personnel	UVM Internal $83.98 each External $92.38 each COM $68.26 each BPI $83.98 each
Exploris 240 (1 h) - complex mixture	Performed by user	UVM Internal $99.56 each External $109.52 each COM $80.93 each BPI $99.56 each
Exploris 240 (1 h) - complex mixture	Performed by facility personnel	UVM Internal $103.94 each External $106.87 each COM $84.49 each BPI $103.94 each
Exploris 240 (3 h) - highly complex mixture	Performed by user	UVM Internal $233.13 each External $256.44 each COM $189.49 each BPI $233.13 each
Exploris 240 (3 h) - highly complex mixture	Performed by facility personnel	UVM Internal $251.35 each External $276.49 each COM $204.31 each BPI $251.35 each
Exploris 240 (0.25 h) - single protein	Performed by user	UVM Internal $49.47 each External $54.42 each COM $40.21 each BPI $49.47 each
Exploris 240 (0.25 h) - single protein	Performed by facility personnel	UVM Internal $67.70 each External $74.47 each COM $55.03 each BPI $67.70 each
Fusion (0.25 h) - single protein	Performed by user	UVM Internal $47.80 each External $52.59 each COM $38.86 each BPI $47.80 each
Fusion (0.25 h) - single protein	Performed by facility personnel	UVM Internal $66.03 each External $72.63 each COM $53.67 each BPI $66.03 each
Fusion (0.5 h) - simple mixture	Performed by user	UVM Internal $62.83 each External $69.11 each COM $51.07 each BPI $62.83 each
Fusion (0.5 h) - simple mixture	Performed by facility personnel	UVM Internal $80.64 each External $88.70 each COM $65.55 each BPI $80.64 each
Fusion (1 h) - complex mixture	Performed by user	UVM Internal $92.88 each External $102.17 each COM $75.50 each BPI $92.88 each
Fusion (1 h) -complex mixture	Performed by facility personnel	UVM Internal $97.26 each External $106.99 each COM $79.06 each BPI $97.26 each
Fusion (3 h) - highly complex mixture	Performed by user	UVM Internal $213.09 each External $234.40 each COM $173.21 each BPI $213.09 each
Fusion (3 h) - highly complex mixture	Performed by facility personnel	UVM Internal $221.14 each External $243.25 each COM $179.75 each BPI $221.14 each
Q-Exactive Plus (0.25 h) - single protein	Performed by user	UVM Internal $41.13 each External $45.24 each COM $33.43 each BPI $41.13 each
Q-Exactive Plus (0.25 h) - single protein	Performed by facility personnel	UVM Internal $59.21 each External $65.13 each COM $48.13 each BPI $59.21 each
Q-Exactive Plus (0.5 h) - simple mixture	Performed by user	UVM Internal $49.47 each External $54.42 each COM $40.21 each BPI $49.47 each
Q-Exactive Plus (0.5 h)- simple mixture	Performed by facility personnel	UVM Internal $60.00 each External $66.00 each COM $48.77 each BPI $60.00 each
Q-Exactive Plus (1 h) - complex mixture	Performed by user	UVM Internal $66.17 each External $72.79 each COM $53.79 each BPI $66.17 each
Q-Exactive Plus (1 h) - complex mixture	Performed by facility personnel	UVM Internal $77.33 each External $85.07 each COM $62.86 each BPI $77.33 each
Q-Exactive Plus (3 h) - highly complex mixture	Performed by user	UVM Internal $132.95 each External $146.25 each COM $108.07 each BPI $132.95 each
Q-Exactive Plus (3 h) - highly complex mixture	Performed by facility personnel	UVM Internal $144.10 each External $158.51 each COM $117.13 each BPI $144.10 each
▼ ► Sample Preparation (10)
Name	Description	Price
Desalting (for removing TMT labels)	Performed by facility personnel Desalting columns and reagents provided.	UVM Internal $57.15 each External $62.86 each COM $46.45 each BPI $57.15 each
In-gel digestion	Performed by users in the facility Enzyme and reagents provided.	UVM Internal $11.80 each External $12.98 each COM $9.59 each BPI $11.80 each
In-gel digestion (> 15 gel bands)	Performed by facility personnel	UVM Internal $49.12 each External $54.03 each COM $39.93 each BPI $49.12 each
In-gel digestion (< 15 gel bands)	Performed by facility personnel	UVM Internal $80.97 each External $89.07 each COM $65.82 each BPI $80.97 each
In-solution digestion (User provides enzyme)	Performed by facility personnel	UVM Internal $119.57 each External $131.53 each COM $97.19 each BPI $119.57 each
Lyophilizer	Operated by users (assisted by facility personnel, if necessary)	UVM Internal $53.43 each External $58.77 each COM $43.43 each BPI $53.43 each
Phosphopeptide-enrichment	Performed by users in the facility Kit and reagents provided.	UVM Internal $22.26 each External $24.48 each COM $18.09 each BPI $22.26 each
Phosphopeptide-enrichment	Performed by facility personnel	UVM Internal $51.44 each External $56.58 each COM $41.81 each BPI $51.44 each
Zip tip	Performed by users in the facility Kit and reagents provided.	UVM Internal $9.97 each External $10.97 each COM $8.10 each BPI $9.97 each
Zip tip	Performed by facility personnel	UVM Internal $32.36 each External $35.60 each COM $26.30 each BPI $32.36 each
▼ ► Tandem Mass Tags (5)
Name	Description	Price
High-pH fractionation	Performed by users in the facility Kit and reagents provided. 1 set (8 fractions)	UVM Internal $35.48 each External $39.03 each COM $28.84 each BPI $35.48 each
High-pH fractionation	Performed by facility personnel 1 set (8 fractions)	UVM Internal $179.02 each External $196.92 each COM $145.51 each BPI $179.02 each
TMT labeling	Performed by users in the facility TMT reagents NOT provided.	UVM Internal $12.07 each External $13.27 each COM $9.81 each BPI $12.07 each
TMT labeling	Performed by facility personnel. 1 set (e.g., 10-plex)	UVM Internal $91.89 each External $101.08 each COM $74.69 each BPI $91.89 each
TMT labeling	Performed by facility personnel Additional 1 set	UVM Internal $26.66 each External $29.32 each COM $21.67 each BPI $26.66 each

▼ ► Current Proteomics Facility Capabilities (10)

Name

Description

Price

Consultation

Please consult with the facility personnel to:

1) select what sample preparation method(s) you would like to perform on your digests (e.g, Ziptip, TMT labeling, etc.)

2) select from the LC/MS category which instrument to use and the associated run time.

A consultation is required prior to sample submission

For gel samples, please provide an image of the gel and mark the bands or spots that are to be analyzed. We need to be sure your samples and sample preparation methods are compatible with mass spectrometry and your sample has an adequate amount of the target proteins to be measured by mass spectrometry.
For protein samples in solution, you must provide us the expected protein concentration and the composition of the solution

Turnaround time: 2-3 weeks

Inquire

Quantification of target peptides using Parallel Reaction Monitoring and Skyline

A consultation is required prior to sample submission

Inquire

Protein identification, isoform characterization (In-gel/In-solution digestion)

A consultation is required prior to sample submission

Inquire

Identification of protein-protein interacting partners (Interactomes)

A consultation is required prior to sample submission

Inquire

Identification of post-translational modifications (PTMs)

A consultation is required prior to sample submission

Inquire

De novo sequencing

A consultation is required prior to sample submission

Inquire

Peptide fractionation of complex mixtures

Off-line peptide separation (e.g., SCX)
Strong cation exchange fractionation
High-pH reverse phase fractionation

A consultation is required prior to sample submission

Inquire

Quantitative Proteomics (with peptide fractionation/enrichment)

Mass spectrometry-based global quantification of protein expression and PTMs in biological samples using stable isotopes.

Stable Isotope Labeling by Amino acids in Cell culture (SILAC)
Dimethyl Labeling
Tandem Mass Tags

Inquire

Absolute quantification of proteins using stable isotopically labeled standards

A consultation is required prior to sample submission

Inquire

Label-Free quantification (Spectral counting)

A consultation is required prior to sample submission

Inquire

▼ ► Data visualization and Figures preparation for publication (heat maps or volcano plots, etc.) (1)

▼ ► Database searches / Software Analysis (with statistics) (4)

▼ ► LC-MS (24)

Name

Description

Price

Exploris 240 (0.5 h) - simple mixture

Performed by user

UVM Internal $66.17 each
External $72.79 each
COM $53.79 each
BPI $66.17 each

Exploris 240 (0.5 h) - simple mixture