Proteomics: Policies

Facility Policies

The VGN Proteomics Facility was designed for use by faculty, staff, and students at UVM, VGN Baccalaureate Partners and other Institutions throughout the state of Vermont. The facility also provides services to external users from outside Vermont. We provide comprehensive support from experimental design to downstream data analysis.  The following policies have been established to insure quality control and success of proteomics analysis.

For projects that are technically challenging, involve complicated proteomics procedures (e.g. enrichment and characterization of post-translational modifications), or require a long time commitment by the facility, we often work with investigators (especially users outside the University of Vermont) on a collaborative basis with an expectation of shared authorship in publications.

Projects that have defined goals and would ultimately lead to publications are given high priority; on the other hand, projects/samples from experiments of screening type (e.g., analyzing hundreds of samples) that would take up a big portion of our time are of low priority.

We ask that users perform their own trypsin digestion if at all possible.  We will train lab members to carry out digestions, and the lab should be responsible for sample quality.  Alternative, we will carry out the trypsin digestion for an additional fee. 


We are happy to provide education and training to faculty, staff and students depending upon their needs and skill levels.  Investigators should contact the facility prior to sample submission to ensure a clear understanding of sample requirements for processing through the facility. To arrange a consultation you can contact Drs. Wai Lam / Bin Deng by phone (802-656-4709, 802-656-5099) or email (,

Consultations are usually attended by the investigators, their staff (postdoc, students and research associates) and the facility personnel and usually last for 1-2 h. During consultation, details of the project are discussed, including 1) background and goals of experiments; 2) feasible plans and solutions based on the facility personnel experience on similar projects; 3) advantages and disadvantages of various proteomics technologies and strategies; 4) proteomics solutions the facility can provide, and, depending on projects, what levels of success investigators could expect;  5) technical details of the experiments.  The facility personnel have strong backgrounds in both biology and analytical chemistry. They will provide protocols and relevant literature regarding experimental designs and recommend the best reagents to use for experiments.  An average of 1-2 consultations can be arranged per month for each investigator.  As the projects progress, we will discuss results, assist in paper preparation, and grant submission.  A Facility tour and a brief overview of proteomics technologies via Powerpoint presentations will be given to new users.

Sample Preparation

Sample Preparation is applied to make samples from various sources (e.g. purified proteins, gel band samples, cell culture pellets and complex protein extracts, etc) compatible to mass spectrometry analysis.   The common preparation methodologies include trypsin digestion and subsequent clean-up procedures.  Depending on sample types, in-gel or in-solution digestion will be applied.  The resulting tryptic digests are analyzed by mass spectrometry.  In some cases, fractionation is needed to reduce the complexity for in-depth analysis of the proteome.  Charges are based on the types of sample preparations plus LCMS analysis. 

Sample preparation is critical for a good mass spec analysis.  We have developed sample preparation procedures for various types of sample analyses.

Sample Submission

Investigators are required to submit their samples via our iLab portal.  Each sample must be accompanied by a completed on line form.   In addition, the information investigators provide will help us to ensure proper handling and analysis of your samples.

Data Analysis

Only trained personnel directly operate the mass spectrometers in the facility.  However, users are welcome to learn to use the equipment and participate in data analysis.  We will guide investigators throughout the experiments, discuss the results, provide assistance in manuscript preparations, and plan future experiments.  Facility personnel will spend the time needed to analyze the data manually or with a suite of software.

Delivery of Results

Results will be sent via e-mail or provided as a printed copy.  Raw data will be provided upon request.

It is best to ship the samples via overnight shipping if you are a non-UVM user, otherwise please drop them off in person.  Please note that drop-off hours are Monday through Friday, 9:00 AM to 4:00 PM, and investigators are encouraged to give the facility personnel a call before dropping by.

Data Management and Quality Controls

The facility works closely with the clients and cooperates in a professional and confidential manner. We will archive a copy of mass spectrometry data for you, but we strongly suggest that you also make your own back up for protection.

Sample submission Sample analysis and instrument use will be prioritized by the Facility Director and Manager.

Data format and processing Large amount of unprocessed data in the form of instrument-specific raw files (.RAW) will be produced from the many projects described in the proposal.  The raw files will then be processed using a variety of software for specific purposes (Bioworks, Proteome Discoverer, Scaffold, etc) and converted to software specific file types (e.g. .srf, .msf, .sfd).

Archiving data All the unprocessed raw data and the processed results will be archived in three separate computers housed in the Facility’s Data Processing Center (Room 333 Marsh Life Science), as well as on a designated storage server maintained by the UVM EMS team.

Data Dissemination The research data are disseminated through:

  • Publications (The facility has tracked publications that used facility proteomics data since 2006)
  • Public domains(e.g. PRIDE ,TRANCHE (Site No Longer Maintained) )
  • Facility open houses and seminars (Since 2007, the facility has organized a number of open houses, where a number of investigators shared their proteomics studies that had been assisted by the facility).

The VBRN Proteomics Facility reserves the right to use all data from mass spectrometry in the facility for the purpose of assessing quality of data and for the development of quantitation and analysis tools. All data used in quality control will remain strictly anonymous. We work closely with the VBRN Data Science Core for in-depth analysis of proteomics data.