Luke Gamon
@lgamon.bsky.social
All things teammassspec/realtimechem. Survives on only the fanciest coffee and beer.
Laser capture microdissection | spatial proteomics | protein modification | atherosclerosis | inflammation and oxidation
Laser capture microdissection | spatial proteomics | protein modification | atherosclerosis | inflammation and oxidation
Haven’t seen it on a Peaks generator but we did have it recently on our separate compressor/generator combo. One of the physical control valves was faulty.
December 3, 2025 at 5:52 AM
Haven’t seen it on a Peaks generator but we did have it recently on our separate compressor/generator combo. One of the physical control valves was faulty.
Bleurgh! I’m waiting on 4 grant responses by Christmas. Not sure if all the Glögg in Denmark will negate the effects of 0/4 🙃
December 3, 2025 at 5:24 AM
Bleurgh! I’m waiting on 4 grant responses by Christmas. Not sure if all the Glögg in Denmark will negate the effects of 0/4 🙃
Definitely the critical O-ring for a Bruker CaptiveSpray ion transfer interface (specifically the newer version but not the new newest version). I wish I was joking.
November 28, 2025 at 5:55 AM
Definitely the critical O-ring for a Bruker CaptiveSpray ion transfer interface (specifically the newer version but not the new newest version). I wish I was joking.
Important to post-validate of course but I can say LLMs are shockingly good at this. I used it recently to identify likely contaminants in a very specific cell culture experiment.
November 25, 2025 at 6:06 AM
Important to post-validate of course but I can say LLMs are shockingly good at this. I used it recently to identify likely contaminants in a very specific cell culture experiment.
I’m still a pseudo-PI and definitely winging it but the EMBO courses come highly recommended:
www.embolableadership.org
www.embolableadership.org
Home - EMBO Lab Leadership
www.embolableadership.org
November 11, 2025 at 8:01 AM
I’m still a pseudo-PI and definitely winging it but the EMBO courses come highly recommended:
www.embolableadership.org
www.embolableadership.org
Now that would be an absolute steal
November 11, 2025 at 7:53 AM
Now that would be an absolute steal
Yeah no way is that just an astral 😅
November 11, 2025 at 6:59 AM
Yeah no way is that just an astral 😅
DUDE!!! Absolutely epic! Congratulations my friend 👏
November 7, 2025 at 6:13 AM
DUDE!!! Absolutely epic! Congratulations my friend 👏
Try €500 for a Dionex syringe 🤯 Very happy with a substitute from a german supplier that is €100 a pop.
October 30, 2025 at 6:31 PM
Try €500 for a Dionex syringe 🤯 Very happy with a substitute from a german supplier that is €100 a pop.
Not at all. The next comment seemed to be a complete misunderstanding of the proposal. A few fair criticisms like mice ≠ people but TBH that’s a bit of a low blow too.
At least reviewer 2 said it was a major improvement on the previous submission.
At least reviewer 2 said it was a major improvement on the previous submission.
October 30, 2025 at 1:22 PM
Not at all. The next comment seemed to be a complete misunderstanding of the proposal. A few fair criticisms like mice ≠ people but TBH that’s a bit of a low blow too.
At least reviewer 2 said it was a major improvement on the previous submission.
At least reviewer 2 said it was a major improvement on the previous submission.
Sure - there will be considerable artefactual protein degradation in any laser capture experiment - but we and others have shown conclusively there is plenty of biological insight to be obtained even with these limitations.
October 30, 2025 at 1:16 PM
Sure - there will be considerable artefactual protein degradation in any laser capture experiment - but we and others have shown conclusively there is plenty of biological insight to be obtained even with these limitations.
There’s a discussion on the GitHub about DIANN support being ‘experimental’ but seems to work well for everything we’ve used it for so far. At least I like that you can have differential detection in the model rather than relying on a janky UpSet plot.
October 29, 2025 at 6:43 PM
There’s a discussion on the GitHub about DIANN support being ‘experimental’ but seems to work well for everything we’ve used it for so far. At least I like that you can have differential detection in the model rather than relying on a janky UpSet plot.
Ha whoops partially my fault. Great tool which extends MSqRob for modeling both differential abundance and differential detection. They have some nice examples in the supp into for each case compared to imputation, standard MSqRob etc
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
MSqRob Takes the Missing Hurdle: Uniting Intensity- and Count-Based Proteomics
Missing values are a major issue in quantitative data-dependent mass spectrometry-based proteomics. We therefore present an innovative solution to this key issue by introducing a hurdle model, which is a mixture between a binomial peptide count and a peptide intensity-based model component. It enables dramatically enhanced quantification of proteins with many missing values without having to resort to harmful assumptions for missingness. We demonstrate the superior performance of our method by comparing it with state-of-the-art methods in the field.
pubs.acs.org
October 29, 2025 at 6:36 PM
Ha whoops partially my fault. Great tool which extends MSqRob for modeling both differential abundance and differential detection. They have some nice examples in the supp into for each case compared to imputation, standard MSqRob etc
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
Oh very cool! We are doing a lot of msqrob and mqrobhurdle workflows these days
October 29, 2025 at 4:57 AM
Oh very cool! We are doing a lot of msqrob and mqrobhurdle workflows these days
Nice video by the way!
October 28, 2025 at 6:41 PM
Nice video by the way!
In terms of user-friendly-ness how do you think it compares to something like DIA-Analyst? We do mostly custom R scripts because of complicated experimental designs and visualisations but I often send collaborators with standard differential expression straight to Frapipe- or DIA-Analyst.
October 28, 2025 at 6:41 PM
In terms of user-friendly-ness how do you think it compares to something like DIA-Analyst? We do mostly custom R scripts because of complicated experimental designs and visualisations but I often send collaborators with standard differential expression straight to Frapipe- or DIA-Analyst.
I love how it always says ‘would you like me to make an overview or workflow figure’ as if it’s not going to hallucinate absolute BS
October 28, 2025 at 6:38 PM
I love how it always says ‘would you like me to make an overview or workflow figure’ as if it’s not going to hallucinate absolute BS
Figured that was the case. Thanks for clarifying!
October 25, 2025 at 7:13 PM
Figured that was the case. Thanks for clarifying!
So let’s say there is a peptide which is present in a 50:50 ratio at two different RT, gives almost identical MSMS, but doesn’t have a delta mass for PTM localisation, DIANN is unlikely to ID it and report it?
October 25, 2025 at 5:20 PM
So let’s say there is a peptide which is present in a 50:50 ratio at two different RT, gives almost identical MSMS, but doesn’t have a delta mass for PTM localisation, DIANN is unlikely to ID it and report it?
What if I’m looking for isobaric isomers that don’t have a localised PTM delta mass (specifically, IsoAsp which has different RT and slightly different IM)?
October 25, 2025 at 5:06 PM
What if I’m looking for isobaric isomers that don’t have a localised PTM delta mass (specifically, IsoAsp which has different RT and slightly different IM)?