iiinova — where your digital self keeps evolving

Reposted by Tonya Zeczycki

PastelBio @pastelbio.bsky.social · 19/03/2025

Kingfisher: An open‐sourced web‐based platform for the analysis of hydrogen exchange mass spectrometry data onlinelibrary.wiley.... --- #proteomics #prot-paper

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Reposted by Tonya Zeczycki

Raul Pacheco-Vega @raulpachecovega.bsky.social · 14/03/2025

“You don't start out writing good stuff. You start out writing crap and thinking it's good stuff, and then gradually you get better at it. That's why I say one of the most valuable traits is persistence.” ― Octavia E. Butler #WritingSky #AcademicSky

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Reposted by Tonya Zeczycki

US HUPO @us-hupo.org · 08/03/2025

Celebrate International Women's Day by reading the Special Issue of the Journal of Proteome Research, highlighting the essential contributions women scientists have made—and continue to make—in the fields of Proteomics and Metabolomics. ow.ly/eBcV50TWOpV #InternationalWomensDay 🧪

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Tonya Zeczycki @tnzeczycki.bsky.social · 02/03/2025

Pubmed is up here, but logging in to access the SciEnv gives me a site not found message...

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Reposted by Tonya Zeczycki

Jeremy Koster @jeremykoster.bsky.social · 19/02/2025

Upon learning that yesterday would be my last day as a program officer at the National Science Foundation, I shared this parting message with my colleagues. The next few months will be frenetic and stressful for them. Here are some things that you can do to help them with the mission ahead. (1)

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Tonya Zeczycki @tnzeczycki.bsky.social · 17/02/2025

I have a bad case of FOMO. Again. Next year...next year.

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Tonya Zeczycki @tnzeczycki.bsky.social · 17/02/2025

I have been looking for something like this for AGES!

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Reposted by Tonya Zeczycki

Martin Pacesa @martinpacesa.bsky.social · 01/02/2024

Absolutely captivating article from @fraserlab.bsky.social and Mark Murcko! Very down to earth discussion on what protein "structures" really are www.cell.com/cell/fulltex...

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Reposted by Tonya Zeczycki

Nicholas Fitzkee @fitzkeelab.bsky.social · 22/01/2024

Radha follows up her work with a publication in Langmuir. She used NMR hydrogen exchange and methylation mass spec to probe the structure of a small protein binding to a polystyrene nanoparticle. She finds evidence consistent with the adsorbotope model. doi.org/10.1021/acs....

Scheme indicating the use of hydrogen-deuterium exchange and lysine methylation to probe protein structure on a polystyrene nanoparticle.

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Reposted by Tonya Zeczycki

Natalie Turner @natalieturnerau.bsky.social · 18/01/2024

Here’s a good one for TeamMassSpec (I hope!)- I’m working on a small project which involves enrichment and MRM of circulating neuropeptides (from blood plasma). Most are hydrophilic peptides (< 3 kDa), 1 is amphipathic (~60 kDa).

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Reposted by Tonya Zeczycki

Matt Padula @mattpadula.bsky.social · 08/01/2024

Anyone with experience of converting Waters .raw files into mzML (or something) that can be searched with Fragpipe and other software? MS Convert settings that work would be very helpful. #MassSOS

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Tonya Zeczycki @tnzeczycki.bsky.social · 10/01/2024

I have struggled with this since we have gotten our Synapt XS. Add ion-mobility ontop of it and...yah. This sometimes works for me, but I have not tried it with FragPipe after. github.com/AnP311/Water...

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Reposted by Tonya Zeczycki

Castañeda Lab at SU @castanedalab.bsky.social · 28/12/2023

Pls reskeet: We're accepting PhD apps to Syracuse University Biology! (Priority deadline of 1/4/24) Join a vibrant department: we are also recruiting three new faculty in epigenetics and neuroscience! Labs actively recruiting grad students are here: artsandsciences.syracuse.edu/biology/grad...

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Tonya Zeczycki @tnzeczycki.bsky.social · 22/12/2023

Ohhhh, that would be great! Will send email later this evening so you can get to it when you have the time....

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Tonya Zeczycki @tnzeczycki.bsky.social · 22/12/2023

I now have some lab listening for tomorrow. Hee hee hee.

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Tonya Zeczycki @tnzeczycki.bsky.social · 22/12/2023

So agree. It was like sending up the batsignal! This is why I stand by my comments on the mass spec community being amazing people who don't eat their young (or noobies).

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Tonya Zeczycki @tnzeczycki.bsky.social · 22/12/2023

I was wondering the same thing-if morephus doesn't do it, I wonder if MetaMorpheus would. Hmmmm....

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Tonya Zeczycki @tnzeczycki.bsky.social · 22/12/2023

Ehhhhhhh....yes and no. I've tried.

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Tonya Zeczycki @tnzeczycki.bsky.social · 22/12/2023

Phenomenal! Thank you. I'll see how it goes- fingers crossed!!!

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Tonya Zeczycki @tnzeczycki.bsky.social · 21/12/2023

Thanks guys for the fast replies! I appreciate you all!

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Tonya Zeczycki @tnzeczycki.bsky.social · 21/12/2023

Yup. DDA, purified protein. I'll give this a shot.

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Tonya Zeczycki @tnzeczycki.bsky.social · 21/12/2023

Yah, used this. Staying away from $$. I should have probably mentioned freeware.

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Tonya Zeczycki @tnzeczycki.bsky.social · 21/12/2023

True true. Actually much better idea for some of things we are doing. But let's say we've already ran the DDA.

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Tonya Zeczycki @tnzeczycki.bsky.social · 21/12/2023

#massspecsos Best way/software for peptide mapping from limited proteolysis or full proteolysis experiments for a single, purified recombinant protein? Something that I can use/search against the Fasta for so the search would be our protein and contaminants with Thermo data.

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Tonya Zeczycki @tnzeczycki.bsky.social · 18/12/2023

Maybe next weekend. At the finish point, I was just excited to see flames where there was supposed to be and the only smoke I smelled was coming from the pellets.

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Tonya Zeczycki @tnzeczycki.bsky.social · 17/12/2023

Just finished replacing the hot rod and the fan (might as well since I had everything torn up). 4 hrs, 3 YouTube videos and enough cursing to make a sailor blush and we are back in business.

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Reposted by Tonya Zeczycki

Ben Neely @benneely.com · 01/12/2023

A new season of #TheProteomicsShow with me and @proteomicsnews.bsky.social?!!! Find it wherever you podcast and expect a weekly-ish release schedule to bath your ears in proteomic goodness.

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Tonya Zeczycki @tnzeczycki.bsky.social · 26/11/2023

Wait. What? Oh, I don't know if I like that. (Note I'm not a total luddite, but I was also leary of setting up any biometric-type login on my phone until about a year ago- fingerprint login? Life changing...)

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Tonya Zeczycki @tnzeczycki.bsky.social · 24/11/2023

We have a pellet smoker. Turkey prepared for said smoker. Said smoker's heat rod decided that, after 7 years of faithful use, today was the day it would give out. Not enough charcoal /wood chunks to improvise. Good thing we have another turkey in the freezer for after I replace the heat rod.

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Tonya Zeczycki @tnzeczycki.bsky.social · 24/11/2023

Uggghhhh. They both look shiny to me!!! is this like that what color is the dress thing that was all over the internet a few years ago?!?

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Reposted by Tonya Zeczycki

Castañeda Lab at SU @castanedalab.bsky.social · 22/11/2023

Learning my way around Bluesky; hoping to re-establish the many awesome scientific connections from X! We are a molecular biophysics lab also doing cell biology to better understand protein quality control mechanisms in ALS and other neurodegenerative disorders; keen on IDPs, condensates, and NMR!

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Reposted by Tonya Zeczycki

PastelBio @pastelbio.bsky.social · 23/11/2023

A Review of Fifteen Years Developing Computational Tools to Study Protein Aggregation www.mdpi.com/2673-41... --- #proteomics #prot-paper

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Tonya Zeczycki @tnzeczycki.bsky.social · 23/11/2023

Ugh had a meeting run late today and got hung up. And I even had questions about things this week too! Next time next time......

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Tonya Zeczycki @tnzeczycki.bsky.social · 22/11/2023

Also also, am I the only one that calls it "tin foil"? Is this a midwest thing? (Why yes, I'm procrastinating on working on 2 problematic data sets, my own grant, and our half-finished manuscript why do you ask?)

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Tonya Zeczycki @tnzeczycki.bsky.social · 21/11/2023

Ohhhhh i was going to ask about this.... Can you use ambic instead of TEAB for one pot or s-trap? (Let's say i only have ambic on hand and wanna try s-trap and already am buying columns and...yeh).

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Tonya Zeczycki @tnzeczycki.bsky.social · 21/11/2023

Also, they both look shiny to me...

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Tonya Zeczycki @tnzeczycki.bsky.social · 21/11/2023

I just went and looked at my foil and was dumbfounded because I couldn't figure out which side was shiny. Then thought maybe I shouldn't be touching the mass specs if I can't figure out if things are shiny. Then realized I buy cheap foil. You saved my from my mini-existential crisis...

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Tonya Zeczycki @tnzeczycki.bsky.social · 18/11/2023

This might be what I was thinking about! I think this might lower limits to threshold the "fold-change". Again, from a statistical sig, not biological sig, standpoint. Using both adjusted p-value and equivalence testing on the data set. Need to read your github more to see but it might be it.

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Tonya Zeczycki @tnzeczycki.bsky.social · 18/11/2023

Yup been reading this the past few days....

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Reposted by Tonya Zeczycki

Ben Neely @benneely.com · 16/11/2023

To all you #TeamMassSpec and proteomics tweeps who came over, or maybe came over and left, read this blog post: federation is real.

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Tonya Zeczycki @tnzeczycki.bsky.social · 17/11/2023

Ugh. Power analysis...this wasn't what I was thinking. But I was looking for a way to do this for something else so THANK YOU!

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Tonya Zeczycki @tnzeczycki.bsky.social · 16/11/2023

Yah. I lump that into the bio end of things and I think is/can linked with the "importance", redundancy, cost (big protein vs. Small), need (think bacteria biofilm vs planktonic conditions) sort of thing. I was looking at a purely stats threshold based on a data set/CI, before delving into the bio.

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