DrAndyFrey

Our mixed species experiments (aka. CQE, LFQ bench) show excluding precursors below any PPP thresholds can make protein quant objectively worse (and cuts IDs). In short-using more precursors is better than excluding some. Average PPP overall might be useful though- I wouldn't want this to be low.

*Ignorant blueskyer* why do we hate RG now? Is it a colourblindness issue? What to do instead?

It's a problem with people not adding it for sure. Most people use some sort of alkylation but don't always add mods they aren't explicitly studying.

This put me down a small rabbit hole which led me to the quantms-utils github, where I found this gem "diann2mztab". Am I right in thinking this will allow complete depositions of DIANN results with proteomeXchange tool? Do you happen to know? :)

Had a great time presenting on phagosomes and ubiquitylation at #BSPR2025 @mtrost.bsky.social @ukbspr.bsky.social , not much time left but if you wany to I hope we can chat about it over coffee!

A nice trip to Edinburgh for the @brukercorporation.bsky.social (bruker mass spec) meetup! Great to see the North UK proteomics community! @analbant.bsky.social @ajbrenes.com

P.s. poster F42

I am presenting at #EuPA2025, flash talk and poster in quantitative proteomics! Come chat about DIA, methods, and how sure can you be about quantitation!

Tempting to go outside here at #eupa2025 St. Malo is brilliant. But so are the sessions! @mtrost.bsky.social

This one is an exciting application of timsToF and triple quad for truly deep plasma proteomics, I fully intend to deep dive into this dataset, hopefully the reviewers do too, its going to require some extremely technical evaluation to do peer review any justice. www.biorxiv.org/content/10.1...

I am so proud to have worked on this project @newcastleuni.bsky.social @mtrost.bsky.social, it was a really tricky set of samples and method development (for everyone involved, at all stages) to work on, really hope the immunology community can get something useful out of this!

Don't know these guys but a "$50 proteome" when you read the press release is actually 1000 targeted proteins. I hope decision makers know that this probably means they are missing things...

Turns out Humpty Doo is a place. Which is fair enough!

I thought I had some grasp on this but I'm not sure anymore, can someone explain bacterial naming conventions please?

Oooooo new option in PRIDE proteomeXchange tool, truly these approaches are gaining traction!

We see this sort of thing all the time... our general rule with this is "if you're comparing conditions just assume the most extreme ones on the volcano plot are almost certainly correct, be cautious about the others".

Yes, of course a predicted library is still a library 😅 especially after MBR... yes, then that is crazy fast.

If one says "our LC-MS is amazing compared to others", one should be 100 % certain they are doing everything correctly. Your point on double normalisation is also well noted, I think people do often use normalisation with software followed by median normalisation. Is this good practice?

Library free??? If so WOW

That's great-thanks for showing this, will definitely keep an eye on the m/z delta, I noticed there are a lot more plots in the QC report pdf, will definitely check this if we get low IDs! Thanks to you and your team for the hard work on this amazing community resource 🙏

I have some colleagues who use the Orbis more than me, I will mention this.

Likewise, EuPA is very much on our radar. Its a shame, we love going to ASMS when we can.

Oh dear! I suppose I will have to continue using both versions. I know it's meant be a major overhaul compared to 1.9.2, I think the release notes said it puts more emphasis on Q1 features for diaPASEF.

Another ASMS abstract extension... did something happen recently that means less people want to/can go? Does @asms.org collect metrics on international delegates?

Honest question: What have you seen to say that it's not as good? We tested some versions (diaPASEF data), 2.0.1 slightly
outperformed 1.9.2: a small increase in protein IDs for the same QCs searched in both versions, and more PTMs in some samples searched with both versions.

Just wanted to see what UCU is doing regarding all the job losses within the Higher Education Sector in the UK (an expected 10,000).

It seems asking for a ceasefire in Gaza is of higher importance than providing meaningful strategies out of the funding crisis of UK universities.

Oh I see it, and a little black box underneath....alternatively, looks like 2 mini fridges with a source on the front!

No Astral mass spectrometer on @biorender.bsky.social ?!?!?! Can't believe it, does that mean people actually drew all those Astral cartoons in their various publications??? Or am I missing it?

Maybe start refering to them as 2D PSMs? See if it catches on?

This is gonna sound super weird but I once solved this by changing the charcoal filter on the captivespray. Give it a go! Otherwise, possibly something just not quite sitting right with the captivespray has caused these sorts of issues for me before.