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DrAndyFrey @drandyfrey.bsky.social · Sep 5

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 · Aug 24

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 · Aug 11

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 · Jul 22

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 · Jul 15

*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 · Jul 12

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.

DrAndyFrey @drandyfrey.bsky.social · Jul 11

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 · Jul 9

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 · Jun 26

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 · Jun 19

P.s. poster F42

DrAndyFrey @drandyfrey.bsky.social · Jun 19

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 · Jun 17

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 · May 22

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...

www.biorxiv.org

DrAndyFrey @drandyfrey.bsky.social · May 15

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!

Matthias Trost @mtrost.bsky.social · Apr 29

I would like to share our latest work: After years of optimisation, we have developed a flow cytometry-based method to isolate pathogen-containing phagosomes. Paired with sensitive proteomics, this provides exciting new insights into host-pathogen interactions!

www.biorxiv.org/content/10.1...

Flow cytometry-based isolation combined with ultra-sensitive proteomics of Salmonella-containing phagosomes reveals novel insights into host-pathogen interactions

Macrophages engulf pathogens into dynamic phagosomes, which many bacteria manipulate for survival. However, isolating pure pathogen-containing phagosomes remains challenging. Here, we developed a nove...

www.biorxiv.org

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DrAndyFrey @drandyfrey.bsky.social · May 15

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 · May 14

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

DrAndyFrey @drandyfrey.bsky.social · May 14

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 · Apr 3

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

DrAndyFrey @drandyfrey.bsky.social · Mar 10

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 · Feb 21

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 · Feb 21

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 · Feb 21

Library free??? If so WOW

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DrAndyFrey @drandyfrey.bsky.social · Feb 19

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 · Feb 19

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

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DrAndyFrey @drandyfrey.bsky.social · Feb 19

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

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