Welcome to PMF, Dr. Sonam Tamrakar!

I’m happy to announce that PMF has hired a new Research Assistant to expand our analytical offerings.  Sonam Tamrakar, Ph.D. has over 8 years of experience incorporating liquid chromatography and mass spectrometry for the identification and quantification of biologically relevant small molecules present in a wide range of organisms – including wild mushrooms from Nepal (Sonam’s home country)!  Sonam’s sample preparation experience for metabolite extraction and LCMS analysis from various types of tissues and biofluids will be extremely helpful as we begin to roll-out metabolomic analysis as a full service in the coming months.  We are very excited to welcome her to our team.  Her expertise and previous research experience will help substantially expand our metabolomics capabilities.  She will be integrated into small molecule projects and user training exercises moving forward.  Feel free to stop by PBB 511 and say “hi!”

Register NOW for our Hands-On Proteomics Workshop in Jan 2024!

We have opened registration for our 4th Annual Mass Spectrometry-Based Proteomics Workshop to be held in PMF on the Storrs campus from January 10-12, 2024.  Come join us and learn the basics of mass spectrometry with respect to proteome analysis, participate in proteomic sample preparation, learn about the advanced instrumentation housed in PMF, and get an introduction to bioinformatics processing of UPLC-MS/MS data!  You can find more information about topics to be covered and register on our Workshops page.

PMF is hiring a metabolomics scientist!

UConn PMF has an immediate opening for a full-time scientist with demonstrated experience in small molecule analysis using quantitative mass spectrometry.  Check out the full job listing below and apply soon.  Applications will be accepted through August 18, 2023.



The UConn Proteomics and Metabolomics Facility (PMF) (https://proteomics.uconn.edu) has an opening for a full-time Research Assistant 3 (RA). The Research Assistant will assist the Facility Director with quantitative metabolomics analysis using advanced mass spectrometry instrumentation and leading bioinformatics software.

UConn PMF opened in 2017 as the University of Connecticut’s first fully dedicated proteomics and metabolomics core facility and is housed administratively within the Center for Open Research Resources and Equipment. The laboratory exists to provide fully customized analysis, user training, and educational opportunities in analytical techniques to more than 150 faculty across multiple UConn campuses and external academic and industry research institutions. The position will provide a unique opportunity to work in a rapidly growing and highly productive core facility at a large research university currently ranked in the top 25 of all public universities in the U.S. The diverse research community at UConn participates in both basic science and clinical research that provides opportunities for a wide variety of innovative proteomics and metabolomics analysis.

For more information regarding the Center for Open Research Resources and Equipment (COR²E) please visit https://core.uconn.edu.


  1. Master’s or doctoral degree in chemistry, biochemistry, analytical chemistry, or a related field
  2. At least two years of experience implementing sample preparation techniques and tandem mass spectrometry for metabolite identification and quantification.
  3. Extensive familiarity with operation, maintenance, and troubleshooting of ultra-high performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS) instrumentation.
  4. Publication history that demonstrates the successful application of UPLC-MS/MS methods for targeted and/or untargeted quantitative metabolomics.
  5. Proficiency with commonly used metabolomics software platforms for compound identification and quantification such as Progenesis QI, Metaboscape, XCMS, or MetaboAnalyst.
  6. Clear communication skills and the ability to effectively inform researchers with varied scientific backgrounds about analytical techniques and informatics methods.
  7. Desire to work and train scientists in a highly collaborative environment that emphasizes comprehensive analysis and one-on-one consultations with researchers.
  8. Competency in lab management including product and consumable ordering, meticulous record keeping, and outstanding organizational skills.


  1. Previous experience with highly collaborative projects and/or work experience in a core facility setting.
  2. Operation, maintenance, and troubleshooting experience using Bruker timsTOF, Waters Synapt G2Si HDMS, and/or Xevo G2-XS mass spectrometers with Waters or Thermo Scientific UPLC instrumentation.
  3. Experience with UPLC-MS/MS-based lipidomic analysis.
  4. Familiarity with common techniques used in modern day proteomics analysis including sample preparation, UPLC-MS/MS methods for peptide sequencing, and current bioinformatics tools.


This is a 1 year, full-time position with an anticipated start date of August 13, 2023. Salary will be commensurate with qualifications and experience.


Employment of the successful candidate is contingent upon the successful completion of a pre-employment criminal background check.


Please apply online at https://hr.uconn.edu/jobs, Staff Positions, Search #497693 to upload a resume, cover letter, and contact information for three (3) professional references.

This job posting is scheduled to be removed at 11:55 p.m. Eastern time on August 18, 2023.

All employees are subject to adherence to the State Code of Ethics which may be found at http://www.ct.gov/ethics/site/default.asp.

All members of the University of Connecticut are expected to exhibit appreciation of, and contribute to, an inclusive, respectful, and diverse environment for the University community.

The University of Connecticut aspires to create a community built on collaboration and belonging and has actively sought to create an inclusive culture within the workforce.  The success of the University is dependent on the willingness of our diverse employee and student populations to share their rich perspectives and backgrounds in a respectful manner.  This makes it essential for each member of our community to feel secure and welcomed and to thoroughly understand and believe that their ideas are respected by all.  We strongly respect each individual employee’s unique experiences and perspectives and encourage all members of the community to do the same.  All applicants will receive consideration for employment without regard to race, color, religion, gender, gender identity or expression, sexual orientation, national origin, genetics, disability, age, or veteran status.

 The University of Connecticut is an AA/EEO Employer.

Waters Seminar Day Hosted by UConn PMF – Wed, July 19, 2023

Are you interested in the analysis of peptides and/or oligonucleotides?  Want to meet our local Waters mass spec and LC sales representatives?  Join us in Pharmacy/Biology Building room 131 on Wed, July 19th from 9.30 to 2pm!  Waters will provide several seminars on LC and MS applications for biomolecule separation and identification.  Free food too!  Register here to save your spot ASAP: www.waters.com/UCONNJuly2023

June 2023 UConn PMF New Instrumentation Update

We’ve recently added to our fleet of advanced analytical instrumentation housed in UConn PMF!  Installation updates on several new technologies can be found listed below.

Bruker timsTOF HT & Thermo Scientific Vanquish Flex & Neo UPLCs: In early 2022, UConn PMF was granted funds from the UConn OVPR to acquire a brand new state-of-the-art mass spectrometer that will provide substantially improved analytical capabilities for both proteomics and metabolomics applications!  These funds allowed us to purchase a brand new Bruker timsTOF HT plus 2 new UPLCs (nanoflow + analytical flow).  We’ve completed installation of this new instrumentation in Spring 2023 and are currently in the midst of method optimization studies prior to opening the instrument up for new user experiments.  Stay tuned for announcements about new functionalities, a summary of instrument performance, and user access details!

Biognosys Spectronaut v17 DIA analysis software: We’ve recently purchased a perpetual license for the Spectronaut software program, which allows us to expand our acquisition method options to include Data-Independent Acquisition (DIA) MS for deeper proteome coverage and greater quantitative reproducibility across proteomic experiments.  We are also working on a post-Spectronaut statistical analysis platform for UConn PMF users in partnership with UConn Statistical Consulting Services (https://statsconsulting.uconn.edu/).  We will provide more information on this new tool very soon!

Waters Corporation Hydrogen-Deuterium Exchange (HDX) capabilities featuring Trajan Scientific Automation: In late 2022 we were awarded a College of Liberal Arts (CLAS) Shared Equipment Award to purchase HDX hardware to install on our existing Waters Synapt G2Si TOF mass spectrometer.  We have recently installed the Waters UPLC pumps and are awaiting delivery of the Trajan robotics system to allow fully automated HDX-MS analysis for the first time at UConn!  We anticipate that this new technology will be available for users beginning in late Summer 2023.

Stay tuned for more information and announcements regarding upcoming seminars, during which we will formally introduce our new analysis options!

UConn PMF Upcoming Holiday Closure

UConn PMF will be closed for the holidays from Saturday, Dec 24th through Sunday, Jan 1.  No instruments will be available for user-operation during this time.  Instrument reservation requests for the week following the closure can be submitted at any time using the online form, but responses will be delayed and eventually granted on a first-come, first-served basis.  Please do not send any proteomics or metabolomics samples during this time, as we will not be available to receive them or guarantee proper storage conditions.  Full facility operations will resume Monday, Jan 2.  Happy holidays to all!

Register NOW for our Hands-On Proteomics Workshop in Jan 2023!

We have opened registration for our 3rd Annual Mass Spectrometry-Based Proteomics Workshop to be held in PMF on the Storrs campus from January 11-13, 2023.  Come join us and learn the basics of mass spectrometry with respect to proteome analysis, participate in proteomic sample preparation, learn about the advanced instrumentation housed in PMF, and get an introduction to bioinformatics processing of UPLC-MS/MS data!  You can find more information about topics to be covered and register on our Workshops page.

Summer 2022 Updates from UConn PMF

On Friday July 8, 2022, the email pasted below was sent to the full list of Principal Investigators that have previously completed experiments in PMF with the subject line “Summer 2022 Updates from UConn PMF.”



Good afternoon,

I hope you’ve been having a healthy and safe start to the summer.  I’m writing to provide UConn Proteomics & Metabolomics Facility (PMF) users some important updates from the lab.

First, new PMF rates for FY2023 have been posted here and were active as of July 1, 2022.  Most rates were subject to a small percentage increase due to steady increases in the cost of consumables, reagents, and instrument service contracts.  I’m happy to report that our rates are still heavily subsidized by UConn and as a result, remain much lower than the average UPLC-MS/MS analysis costs at nearby institutions.  In the event you are unaware, we’ve introduced PMF-assisted rates for our small molecule metabolomics instruments in the last year.  This removes the previous requirement that metabolomics users had to analyze their own samples after instrument training by PMF scientists.  If you have any questions about changes to the metabolomics platform, please let me know.

Second, I am happy to announce that the ETD-enabled Orbitrap Eclipse mass spectrometer purchased through the NIH S10 HEI funding mechanism is now fully operational with optimized UPLC-MS/MS methods following installation completion earlier in 2022.  This instrument offers a significant boost in protein/peptide identifications compared to the older Q Exactive HF instrument and features additional gas phase dissociation methods that are useful for intact protein or non-tryptic peptide MS/MS analyses plus site localization of labile PTMs (e.g. phosphorylation and glycosylation).  In addition, we now have Real-Time Search and MS3 options for quantitative Tandem Mass Tag (TMT)-based multiplexed experiments.  Having all of these new features in lab has opened up a large number of new experimental options for PMF users and it’s been exciting to begin incorporating these over the last several months.

Third, over the next few weeks we expect receive our own license for Spectronaut 16 software from Biognosys.  This program will allow us to expand our proteomic platform to include large-scale data-independent analysis (DIA) for a wide range of biological applications.  In the event you are unfamiliar with DIA experiments, the primary benefit is that it provides a substantial increase in the number of proteins and peptides identified and quantified using simultaneous peptide fragmentation MS/MS acquisition methods.  As a result, DIA experiments typically allow shorter UPLC-MS/MS runtimes compared to the 3-5 hr UPLC-MS/MS data-dependent experiments we’ve completed in the past for whole proteome samples.  If you are interested in pursuing DIA analysis in the coming months, please reach out and we can provide you with more information.

Lastly, and the most exciting announcement of all, UConn PMF will very soon be adding another state-of-the-art mass spectrometer to the lab!  Thanks to generous financial support from the UConn OVPR, we have just recently finalized the purchase of a brand new Bruker timsTOF HT instrument that is scheduled to arrive in early Fall 2022.  This instrument will substantially upgrade the analytical capabilities and software analysis options for untargeted metabolomics analysis in PMF.  In addition, we’ve purchased the necessary hardware to make this a dual-platform instrument capable of running nanoflow proteomics analysis with trapped ion mobility and PASEF and DIA-PASEF.  Jen and I are both very excited to bring this new instrument to UConn PMF users and can’t wait to show you the substantial boost in analyte identifications possible on this extremely sensitive and fast-scanning instrument.  Keep an eye out for future seminar/workshop announcements that will feature more information about this new technology.

Thanks for making FY2022 our most productive and successful FY yet.  Jen and I look forward to continue working with you in FY2023!


Jeremy L. Balsbaugh, Ph.D.

Director, UConn Proteomics & Metabolomics Facility

Center for Open Research Resources & Equipment