DrAndyFrey
@drandyfrey.bsky.social
Electric biomancer: Microbiologist turned mass spectrometrist with a hefty emphasis on all things proteomics!
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!
September 5, 2025 at 10:34 AM
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!
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...
August 24, 2025 at 10:10 AM
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...
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. 😁
August 11, 2025 at 6:39 AM
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. 😁
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.
July 22, 2025 at 9:27 AM
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?
July 15, 2025 at 7:13 AM
*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.
July 12, 2025 at 1:09 PM
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? :)
July 11, 2025 at 7:30 PM
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!
July 9, 2025 at 10:08 AM
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
June 26, 2025 at 6:05 PM
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
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!
June 19, 2025 at 8:43 AM
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
June 17, 2025 at 2:58 PM
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...
www.biorxiv.org
May 22, 2025 at 7:40 AM
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!
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...
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
May 15, 2025 at 10:47 AM
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...
May 15, 2025 at 7:03 AM
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!
May 14, 2025 at 10:01 AM
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?
May 14, 2025 at 9:56 AM
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!
April 3, 2025 at 1:09 PM
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".
March 10, 2025 at 9:50 AM
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.
February 21, 2025 at 2:15 PM
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?
February 21, 2025 at 10:08 AM
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
February 21, 2025 at 8:15 AM
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 🙏
February 19, 2025 at 5:23 PM
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.
February 19, 2025 at 11:29 AM
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.
February 19, 2025 at 10:45 AM
Likewise, EuPA is very much on our radar. Its a shame, we love going to ASMS when we can.