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!

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.

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.”

-Jeremy

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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

July 1, 2022 marks the beginning of Fiscal Year (FY) 2023 at UConn.  We’ve recently performed extensive budget analysis using past and anticipated instrument usage numbers plus current service and reagent costs to determine the new rates for sample preparation, LC-MS/MS analysis, training, and data analysis.  All FY2023 rates have now been posted on our Rates page and are officially active as of today.  Please note that rates subject to change.

UConn PMF will be closed for the holidays from Friday, Dec 24th through Sunday, Jan 2.  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 3.  Happy holidays to all!

UConn PMF is excited to announce the second iteration of our hands-on proteomics workshop!  This 3-day course will include both lectures and hands-on experience with sample preparation, instrumentation, and software designed to educate UConn scientists in current methodologies and analysis options for quantitative proteomics using state-of-the-art mass spectrometry (MS).  The course will be held January 12-14, 2022 and will be co-taught by UConn PMF Director, Jeremy Balsbaugh, Ph.D. and Facility Scientist Jen Liddle, Ph.D.  For more information and to register, visit our Workshops page.

FY22 Facility Rates now active: After an initial delay, our FY22 rates are now fully approved and are retroactively taking effect beginning Oct 1, 2021.  All new rates are posted HERE.  This is the first rate increase PMF has experienced since July 2019 (start of FY20) and represents updated reagent and instrument service costs over the last 2 years.  Some rates increased while others decreased slightly due to ever changing reagent costs.  New rates include those for our newly installed Orbitrap Eclipse Tribrid proteomics instrument (soon to be available for PMF users – we are now in the initial benchmarking phase) and the introduction of PMF-assisted rates for the Synapt G2Si and Xevo G2-XS instruments.  Previously, these two mass spectrometers were available for user-operation only, but we are now offering full-service or assisted usage for those that would prefer this option.

New Policy for User-Operation Instrument Reservations:  As of November 18, 2021 all instrument reservations for the Synapt G2Si and Xevo G2-XS instruments must be requested using the new “Reservation Request Form” located on the PMF website HERE.  The new online form will provide me and Jen with all of the information necessary so that we can finalize reservation schedules and accurately prepare the instrumentation prior to each new appointment.  This will cut down substantially on the number of emails we need to respond to daily by providing all required details in one simple form.  You should be aware that the form requires the inclusion of KFS (Storrs) or Banner Account (UConn Health/TIP) information which will be used to process all instrument usage.  This will help us save time tracking down these accounts well after the experiments are finished and allow us to process billing events much faster.  Our policy on billable usage time has not changed: you will only be charged for the time used for acquired experiments, not for the requested reservation time.

Please direct any questions to Jeremy or Jen (contact information can be found HERE).

The UConn Proteomics and Metabolomics Facility (PMF) is excited to announce our first joint data analysis workshop with UConn Statistical Consulting Services (SCS)!  This in-person, 2-day course will include a mixture of in-depth lectures and hands-on data analysis exercises in R using complex proteomics datasets.  Due to the limited time available for room reservations and the need to cover complex details of bioinformatic analysis in a short period of time, this workshop is specifically designed for UConn scientists that already have an introductory understanding of current mass spectrometry-based methodologies and data analysis options for quantitative proteomics.  As a result, users with previous experience with proteomics analysis in PMF (or elsewhere) will be given priority.  Because the course will involve hands-on analysis exercises, all participants must supply their own laptop for the workshop.  The course will be presented by UConn PMF Director Jeremy Balsbaugh, Ph.D., PMF Facility Scientist Jen Liddle, Ph.D., and UConn SCS Director, Tim Moore, Ph.D.  To register, click HERE!

UConn Proteomics Users: As of early April 2021, PMF has upgraded to Scaffold Q+S v 5.0.0.  From this point forward, all new proteomics results will be uploaded into this version and will not be accessible using older versions of Scaffold Q+S Viewer that you may currently have installed.  Please visit this website to get the newest version.  The newest upgrade features a new logo and new graphics throughout, but keeps the same base functionalities to help you make the most of your quantitative proteomics data.  Proteome Software specified that backward compatibility should be maintained (e.g. all previously generated files can be opened with Scaffold Q+S Viewer v5).  Contact us with any questions.

UConn PMF will be operating with limited hours during the period beginning Thursday, Dec 24th through Friday, Jan 1.  Instrument reservations can be made with enough lead time and are subject to PMF faculty work schedules.  Full facility operations will resume Monday, Jan 4.  Happy holidays to all!