We recently got to have Jennifer Geddes-McAlister on #THEProteomicsShow to chat with me and Ben @proteomicsnews.bsky.social about #HUPO2025, T-O and her research. Super fun and definitely check it out. Find it wherever you find fine podcasts, or here anchor.fm/theproteomic...

Lazy Sunday (or manic Monday depending on when you look) question to proteomics skywalkers: does/can fragpipe make mzID files for a full PRIDE dataset? Surely, right, but all I see are pep.xml.

In 1988, a heat wave in the US killed thousands and caused $80B in damage. Congress turned to scientists for answers. James Hansen, then a director at NASA, testified that “the greenhouse effect has been detected, and it is changing our climate now.”

Proteomics Webinar: DIA with FragPipe, DIA-NN, and Skyline Presenters: Eduard Sabidó and Brendan MacLean When: Tuesday, September 16, 8am (Pacific Time) Register Now ... skyline.ms/project/home... #massspec #proteomics

On proteomics normalization methods: so we've various weighting and normalization of counts and intensity, and even fancier things like IBAQ, MaxLFQ and the molecular ruler. Came across total protein approach. Pretty simple but workable. www.sciencedirect.com/science/arti...

We heard there were some wannabe pirates at the mass spectrometry conference in Baltimore last summer. Somehow their banner ended up in the Bermuda Triangle... (From one robot to another @evosep.bsky.social, I blame the humans.) #piratesoftheproteome #ASMS2025

The promise of AI searching is huge, but sometimes it’s laughable. Ex. From the basic AI gen answer to me clicking dive deeper and the answer is the opposite. I enjoy benign examples, but this can and does play out in very important questions. Also, I still don’t know if Slo Mo dies.

Finally!

Maybe today’s #THEProtemicsShow with me and Ben @proteomicsnews.bsky.social should be called the Genomics Show, but it’s great, for real. Olga Dudchenko from THE DNA zoo sat down with us and let us ask all sorts of dumb questions. Maybe we understand structural genomics now? Find it wherever!

I am *very* belatedly finalizing my COMPARE Phase 1 analysis, and was looking for these 8 species I swear we ran. Whelp, found the SST raws on 2020-3-2, but no actual runs of my samples. What happened... oh yeah. So that is why compare phase 1 is 31 species and not 39. whomp whomp COVID.

Join us for our 19th YPIC Webinar – “Transition from Academia to Start-Up” Ever wondered what it takes to turn your research into a company?! 🧪 Information in comments! 1/3 #YPIC #Proteomics #ScienceToStartup #ScienceCareers #Entrepreneurship #Biotech #AcademicTransition #Webinar #StartUpScience

Things that are 100% going on in corporate land (or maybe all lands): employee feeds light notes and prompt to generate 10 page report. Management makes and reads a bullet point summary of 10 page report.

Alright, help from my "wider" mass tolerance peeps ( @pwilmarth.bsky.social @ypriverol.bsky.social @michaellazear.bsky.social): I have confirmed what you all said that 1.25 Da MS1 and 20 ppm MS2 is a winning DDA combination. But I see in MSFragger I can do an upper and lower. Do +- 1.25 Da on MS1?

For anyone still on blue sky, if you want to help me out with a list, I’d take it. (Might be that Alfaro 2021 paper?) Terms like single molecule protein detection/sequencing, “Recognizer-based sequencing” (from this paper), aptamer based, etc. But I need a better terms with correct hierarchy.

I was wondering when we would hear the proteomics equivalent to NGS, and I guess here is an attempt (not saying it’s the first use): NGPS. As a field, there’s still a need for agreed upon easy to use/understand labels to further delineate the different NGPS approaches. pubs.acs.org/doi/10.1021/...

Real question: do you ever legit think about work life if you moved to a job that had nothing to do with your current field (ex. proteomics or biotech), so just walking away from all accumulated expertise and cred? Like mentally, can you cope with that, even if it pays the bills?

From chefs to forensic scientists, #THEProteomicsShow is coming at you hard. This week of Alt Proteomics had Ben @proteomicsnews.bsky.social and I talking to Ashley Spicer about proteomics in wildlife forensics… and rhino capers. Find it wherever you find fine podcast or anchor.fm/theproteomic...

Native mass spectrometry” united with “top-down proteomics” 😀🤗👍👏 @hecklab.bsky.social @nlkproteomics.bsky.social @proteoforms.bsky.social ❤️

Side observation: there has been a trend towards more screens and gamification of learning, but this year (k-8) I’m seeing a lot more analog work and less screen time (workbooks are making a comeback!) and I’m super stoked. Is it pushback against the ease of using LLMs when already on laptop, maybe?

So part of my "new" job is getting into legit prompt engineering. Boy is it more than I expected. It blends logic and directions with awareness of word connotations (basically moving between word clouds). Constructing and testing prompts more rigorous than it sounds, but its definitely magic.

We’re excited to present this integrative analysis of single-cell proteomics and transcriptomics of the human HSPC hierarchy. Now published in @science.org together with @fabiantheis.bsky.social, @erwinschoof.bsky.social, @porsebo.bsky.social. www.science.org/doi/10.1126/... 🧵

Today’s episode of #THEProteomicsShow with me and Ben @proteomicsnews.bsky.social had on Chef Michael Toscano, cause you know, protein. Actually had a ton more overlap with science than you might expect. 100% worth a listen. Find it wherever you find fine podcasts.

Take note proteomics companies, this ad campaign from Qiagen is spot on (imo). www.reddit.com/user/QIAGEN/...

Yu Gao @gao_lab are hosting the 3rd International Single-cell Mass Spectrometry meeting in Chicago Sep 25-27, singlecellms.org, co-hosting the meeting with @LingjunLi2 . Keynote speakers: @JesperOlsenLab @LabLaskin and @jbsweedler There will be a hackathon as well, register today!

Reminder 📣 still time to apply to the position in my team! - statistical modeling - large scale #metabolomics and #proteomics data - #rstats , #python 📍 Bolzano, ⛰️, 🇮🇹 🔗https://eurac.onboard.org/jobs/Q4301nGV

“Larry, cancel my meetings for the week, we’ve got a fistful of barrels showing up.” * we have two pods this week and I’m keeping those on schedule. Larry is my fictitious admin assistant, also know for brothers Daryl.

Too often, I see people talk about a replication as if the first study has established something, and the replication study is a double-check. What people often fail to understand is that we do not do replication studies to *check* a finding, but to *establish* a finding. 1/x

Though not the focus of the episode, we touch on HUPO PSI. Since sometimes satire is not obvious, do know this group does essential and foundational proteomics work. Here is 2023 review paper, but also their current efforts can be seen on their website www.psidev.info . pubs.acs.org/doi/10.1021/...

This week’s #THEProteomicsShow continues to explore #AltProteomics, but this time more about the data. Ben @proteomicsnews.bsky.social and I sat down with Yasset @ypriverol.bsky.social and talked about non-mass spec data and related aspects. Find it wherever you find fine podcasts and enjoy!

Not science: as a father of 3, my world revolves around kids and now school. My kids ride the bus and the drivers are great, but boy does it take a while to get the routes and timing straight (toss in a high tide rain and it’s carmageddon). First week partay starts tomorrow!!!!

Not to pile on, but it’s an interesting example (fancy LLM still can’t count letters) in that Gemini is like “whoa, that’s one of those arithmetic things that messes me up, let’s write code to solve it instead”. That’s scarier than stump the chump.

“What does a cell know of itself?” Molecular philosophy... I am feeling my biases here when asking what exactly memory is, if these aren't "tropisms", but these experiments are pretty crafty and is a fun road to venture down.

There’s a glycan reference squiggle database, @jeffnivala.bsky.social, but they forgot to call it that. www.biorxiv.org/content/10.1...

Q2C: A software for managing mass spectrometry facilities www.sciencedirect.co... --- #proteomics #prot-paper

As many of you know, I’ve been feeling out the job market and hoping to get a bite one day. Well, wait no more, for this sweet message came today. Costco here I come!

Not science: I can’t believe he’s not in more shows, but The Pie Maker (Lee Pace) is exceptional and so far his acting in 3rd season of Foundation is perfection. I had to look up the rest of his filmography to see what else was there, beyond his these and his Marvel role. Answer: not a lot. Driven?

This week’s #THEProteomicsShow with me and Ben @proteomicsnews.bsky.social continues to explore Alt Proteomics, this time optoproteomics with @lungucristiana.bsky.social. Super fun and super cool. Check it out wherever you find fine podcasts, and also the webinar she just gave too (link below).

A little PSA for folks with animals or wildlife pics. This prompt into an LLM with a pic works wonders. Won’t do humans. Focus on the bird — high contrast black & white close-up of face. 35mm lens, 4K HD, black shadow background, sharp profile, 4:3 ratio.

Very happy that our paper on how 'thoughtful frequentists' should use hypothesis testing is now an award winning paper. It was very nice to have @laabho.bsky.social over for a visit in Eindhoven during his PhD to start this project! www.linkedin.com/posts/aom-rm...

Excellent work!! I just love the term Mini-Bulk so I had chatGPT help me whip something up

Spotted lanternfly protein fasta is alive, @proteomicsnews.bsky.social !!! About 1 month from request to done. RefSeq will always be my fav thing. Great people, awesome work. For download: www.ncbi.nlm.nih.gov/datasets/gen... Annotation report: www.ncbi.nlm.nih.gov/refseq/annot...

What is next, @proteomicsnews.bsky.social? Well, it starts with 'opto' and ends with 'proteomics'. We have some good ones still to record. proteomicsnews.blogspot.com/2025/07/the-...

I spent 3-5 days working on modifying a js/php/mysql website, and spoiler, I know none of these things so it was me and LLMs, and I got to where I needed. A real programmer took my merge and maybe did 1 day of work on top of it and it is super obvious how much better his product is than mine.

This week’s AltProteomics #THEProteomicsShow is Graham Wiley @gbw42.bsky.social letting me and Ben @proteomicsnews.bsky.social ask all questions about Olink, and we learned a ton along the way. It’s a short day on Le Tour, so listen now! Find it wherever you find fine podcasts.

This week’s Alt Proteomics on #THEProteomicsShow is @jeffnivala.bsky.social talking to me and Ben @proteomicsnews.bsky.social about nanopores and how they might “fill the gaps in proteomics”… which might be a biophysics pun? Find it wherever you find fine podcasts, and enjoy!

This is still the picture Harry Potter uses for his lab website

10 years ago I was looking at non science jobs and talked to a marketing person. They asked what I wanted in a job I said exciting, creative and impactful and their response was that wasn’t really a job. We scientists have a privileged daily “grind” that isn’t easily replaced doing something else.

🚀 Attention DIA/DDA proteomics users! Whether you're using #DIA-NN, #MaxQuant, #quantms, or any tool that outputs mzIdentML and mzML, the NEW pmultiqc v0.0.29 is here! 💡 Create stunning, shareable HTML reports for your collaborators in seconds. ✨ Try pmultiqc.quantms.org Examples👇 #Proteomics #QC

Not science: I was heart broken when Paul Sherwen died years back, since Le Tour just wasn’t the same (think Frank Muller and audiobooks). Eventually Nico and Ant made me love the coverage again. But it’s the 2nd year without them (in US) and I really dislike the coverage. That’s my rant.

Today’s #THEProteomicsShow AltProteomics episode we are talking pores, proteins, and biophysics! Me and @proteomicsnews.bsky.social talk with Alek Aksimentiev and get schooled along the way. Take notes, there will be a test a few episodes from now. Find it wherever you find fine podcasts. Enjoy!