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