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DrAndyFrey @drandyfrey.bsky.social · 01/05/2026

Metadata is so crucial but making it just right for the deposition seems like such a task, so many people don't do it and that deposition just becomes so much less accessible. Will definitely play around with this next time.

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Yasset Perez-Riverol @ypriverol.bsky.social · 30/04/2026

🚀 SDRF Validator is LIVE! Check it out 👉 www.ebi.ac.uk/pride/servic... With #SDRF v1.1.0, we’ve rolled out tailored templates for different experiment types - from Single Cell proteomics #SCP to Crosslinking, & more. The new validator + web interface makes it easy to catch issues before submission.

ebi.ac.uk

SDRF Validator

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DrAndyFrey @drandyfrey.bsky.social · 10/03/2026

Wow. Is this real? It's not April 1st yet right?

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DrAndyFrey @drandyfrey.bsky.social · 05/09/2025

Thanks to you and the team! Can I ask: I find I have to zip bruker.d raw files (which to be fair look like folders), the tool thinks they are folders and it tries to upload the contents as separate files. Is there a work around to this? I did check the troubleshooting docs. A while ago admittedly!

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DrAndyFrey @drandyfrey.bsky.social · 24/08/2025

I suppose this correlation shouldn't be too surprising... I'm always thinking about how dynamic the transcriptome is. To me it's not massively surprising it doesn't correlate all that well with the proteome for this reason alone. Nevermind all the proteasome buffering, translational magic etc...

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DrAndyFrey @drandyfrey.bsky.social · 11/08/2025

Off to @babrahaminst.bsky.social for an incredibly productive week with @harveyejohnston.bsky.social and the @babraham-bioinf.bsky.social crew, featuring multiomics and... casual cycling amongst other things. 😁

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DrAndyFrey @drandyfrey.bsky.social · 22/07/2025

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.

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DrAndyFrey @drandyfrey.bsky.social · 15/07/2025

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

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DrAndyFrey @drandyfrey.bsky.social · 12/07/2025

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.

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DrAndyFrey @drandyfrey.bsky.social · 11/07/2025

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? :)

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DrAndyFrey @drandyfrey.bsky.social · 09/07/2025

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!

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DrAndyFrey @drandyfrey.bsky.social · 26/06/2025

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

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DrAndyFrey @drandyfrey.bsky.social · 19/06/2025

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!

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DrAndyFrey @drandyfrey.bsky.social · 17/06/2025

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

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DrAndyFrey @drandyfrey.bsky.social · 22/05/2025

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...

biorxiv.org

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DrAndyFrey @drandyfrey.bsky.social · 15/05/2025

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!

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DrAndyFrey @drandyfrey.bsky.social · 15/05/2025

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...

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DrAndyFrey @drandyfrey.bsky.social · 14/05/2025

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

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DrAndyFrey @drandyfrey.bsky.social · 14/05/2025

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

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DrAndyFrey @drandyfrey.bsky.social · 03/04/2025

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

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DrAndyFrey @drandyfrey.bsky.social · 10/03/2025

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".

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DrAndyFrey @drandyfrey.bsky.social · 21/02/2025

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

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DrAndyFrey @drandyfrey.bsky.social · 21/02/2025

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?

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DrAndyFrey @drandyfrey.bsky.social · 19/02/2025

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 🙏

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DrAndyFrey @drandyfrey.bsky.social · 19/02/2025

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

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DrAndyFrey @drandyfrey.bsky.social · 19/02/2025

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

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DrAndyFrey @drandyfrey.bsky.social · 19/02/2025

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.

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DrAndyFrey @drandyfrey.bsky.social · 19/02/2025

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

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DrAndyFrey @drandyfrey.bsky.social · 19/02/2025

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.

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Matthias Trost @mtrost.bsky.social · 17/02/2025

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.

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DrAndyFrey @drandyfrey.bsky.social · 24/01/2025

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

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DrAndyFrey @drandyfrey.bsky.social · 24/01/2025

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?

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DrAndyFrey @drandyfrey.bsky.social · 07/01/2025

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

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DrAndyFrey @drandyfrey.bsky.social · 19/12/2024

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.

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DrAndyFrey @drandyfrey.bsky.social · 06/12/2024

The FASTA ORFs without trypsin cleavage sites essentially won't be digested in silico, so if you have good spectra that match these you will find them. Suggest trying the search with trypsin enabled. Just watch out for peptide lengths specified since I'm guessing these will be quite long!

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DrAndyFrey @drandyfrey.bsky.social · 06/12/2024

Can I ask, is there some reason this has to be unspecific digest, when you have actually used trypsin?

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DrAndyFrey @drandyfrey.bsky.social · 05/12/2024

Sample type dependent surely... Serum: 1000 = good. Most other sample types... not so much.

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Reposted by DrAndyFrey

Alejandro Brenes @ajbrenes.com · 10/11/2024

#teamMassSpec here is a starting pack in case you just moved over, or in case you've been absent for a while. This is #proteomics or #massspec related. The pack is not comprehensive but it's a start. go.bsky.app/HH7kqEh

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