rah
@rah37ds.bsky.social
Large-scale Proteomics (clincial & single-cell), mass spectrometry, biostatistics, machine learning, multi-omics.
I keep being surprised about how such things end up in a peer-reviewed journal? And how can there be such a lack of statistical understanding in the first place? #peerreview #biostatistics #bioinformatics @nature.com @naturemedicine.bsky.social
July 16, 2025 at 10:04 AM
I keep being surprised about how such things end up in a peer-reviewed journal? And how can there be such a lack of statistical understanding in the first place? #peerreview #biostatistics #bioinformatics @nature.com @naturemedicine.bsky.social
or the emitter is complete crap
July 10, 2025 at 7:21 PM
or the emitter is complete crap
based on your TIC, there does not seem to be any voltage on the source. Is it plugged in correctly?
July 10, 2025 at 7:20 PM
based on your TIC, there does not seem to be any voltage on the source. Is it plugged in correctly?
intentionally left "blank"....
I thought the same, but still just a preprint
I thought the same, but still just a preprint
June 26, 2025 at 8:34 AM
intentionally left "blank"....
I thought the same, but still just a preprint
I thought the same, but still just a preprint
Has anybody seen this BOXmini SCP device in action? How many cells can one prep in what time?
#proteomics #singlecell
#proteomics #singlecell
June 24, 2025 at 10:37 AM
Has anybody seen this BOXmini SCP device in action? How many cells can one prep in what time?
#proteomics #singlecell
#proteomics #singlecell
and, am I correct that without being registered at the UK Biobank (@ukbiobank.bsky.social)
one can not actually access the "input" data? I mean, nice repositories but useless if one cannot access the input data.
one can not actually access the "input" data? I mean, nice repositories but useless if one cannot access the input data.
January 13, 2025 at 8:49 AM
and, am I correct that without being registered at the UK Biobank (@ukbiobank.bsky.social)
one can not actually access the "input" data? I mean, nice repositories but useless if one cannot access the input data.
one can not actually access the "input" data? I mean, nice repositories but useless if one cannot access the input data.
curious to try this out. Is there a timeline for timsTOF support? And what about Astral?
December 14, 2024 at 12:18 PM
curious to try this out. Is there a timeline for timsTOF support? And what about Astral?
the SCoPE2 paper sets the bar even though already 5 years since published genomebiology.biomedcentral.com/articles/10....
Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2 - Genome Biology
Background Macrophages are innate immune cells with diverse functional and molecular phenotypes. This diversity is largely unexplored at the level of single-cell proteomes because of the limitations o...
genomebiology.biomedcentral.com
November 26, 2024 at 9:07 PM
the SCoPE2 paper sets the bar even though already 5 years since published genomebiology.biomedcentral.com/articles/10....
what kind of samples were run on this MS?
November 26, 2024 at 11:01 AM
what kind of samples were run on this MS?
I think in PXD054127 "hybrid" only refers to generating a spectral library from DDA and DIA runs combined. The PRM/DIA was actually data acquisition, right?
November 19, 2024 at 11:56 AM
I think in PXD054127 "hybrid" only refers to generating a spectral library from DDA and DIA runs combined. The PRM/DIA was actually data acquisition, right?
not sure about the concurrence TMT6 and TMTpro - are these different experiments / sample batches?
November 16, 2024 at 9:19 AM
not sure about the concurrence TMT6 and TMTpro - are these different experiments / sample batches?
Usually when establising/running a protocol one does a label check, to see if >98% of peptides are TMT-labelled. For this we set it as variable modification. While for actual quant it seem common run it as "static", i.e. omitting all unlabelled peptides from quant
November 16, 2024 at 9:05 AM
Usually when establising/running a protocol one does a label check, to see if >98% of peptides are TMT-labelled. For this we set it as variable modification. While for actual quant it seem common run it as "static", i.e. omitting all unlabelled peptides from quant
The reactive group group of TMT (NOT iodoTMT) reacts with amine groups. Which are the N-termini as well as Lysine sidechain.
November 16, 2024 at 9:04 AM
The reactive group group of TMT (NOT iodoTMT) reacts with amine groups. Which are the N-termini as well as Lysine sidechain.
Hi Yishai, I see this is quite old post. But curious if RawBeans is still (again?) under active development? I.e. for timsTOFs and Astral? Would be absolutely great to have is back! Even just the functionality to get a matrix of QC parameters #proteomics #teammassspec
November 13, 2024 at 5:39 PM
Hi Yishai, I see this is quite old post. But curious if RawBeans is still (again?) under active development? I.e. for timsTOFs and Astral? Would be absolutely great to have is back! Even just the functionality to get a matrix of QC parameters #proteomics #teammassspec
maybe a daft question, but why does DIA require two CVs? Never heard that. And FAIMS is way too slow for CV switching if you don't run 2h+ gradients
November 12, 2024 at 6:58 PM
maybe a daft question, but why does DIA require two CVs? Never heard that. And FAIMS is way too slow for CV switching if you don't run 2h+ gradients