@unitsaq.bsky.social
Interested in LC-MS -omics (proteomics, metabolomics, lipidomics, exposomics).
Generally agree about mRNA != Protein but the liver example is a bit unfair as it's the primary tissue supplying plasma, i.e. if the protein representation was liver + plasma this figure would have much higher congruence.
congruence.is
November 12, 2025 at 5:08 PM
Generally agree about mRNA != Protein but the liver example is a bit unfair as it's the primary tissue supplying plasma, i.e. if the protein representation was liver + plasma this figure would have much higher congruence.
Run time determines instrument cost per sample?
November 11, 2025 at 7:29 AM
Run time determines instrument cost per sample?
Agreed at the individual peak level. For the sake of argument, what about n=100 vs 100 compared to 4x slower 50 SPD at n=25 vs 25? The latter is barely enough stat power to get past human variation, and whereas former averages across peptides per protein to make up for low points across peak.
November 11, 2025 at 3:09 AM
Agreed at the individual peak level. For the sake of argument, what about n=100 vs 100 compared to 4x slower 50 SPD at n=25 vs 25? The latter is barely enough stat power to get past human variation, and whereas former averages across peptides per protein to make up for low points across peak.
That is really bad... no substantial mention of LC-MS. Odd because Grok chat mentions it upfront even without search
October 30, 2025 at 1:06 AM
That is really bad... no substantial mention of LC-MS. Odd because Grok chat mentions it upfront even without search
SPOT-1000 and others from divbio.com/labels/cryo-... compatible with laser printers. Once the excel spreadsheet is set up it's easy to populate the sample ids
Diversified Biotech | Laboratory Labeling Solutions & Planet-Safe® Labware
Developers and manufactures of specialized labeling solutions such as cryogenic labels (Cryo-Tags® & Cryo-Babies®), freezer labels (Tough-Tags®), application-specific labels for various labware, as we...
Divbio.com
October 5, 2025 at 9:18 PM
SPOT-1000 and others from divbio.com/labels/cryo-... compatible with laser printers. Once the excel spreadsheet is set up it's easy to populate the sample ids
Afaiu current LLMs can't imagine completely new concepts but they can create novelty via concept shuffling / information transfer. Analogous to translating deja vu to English.
September 17, 2025 at 4:27 PM
Afaiu current LLMs can't imagine completely new concepts but they can create novelty via concept shuffling / information transfer. Analogous to translating deja vu to English.
When I first learned about spectral counting as a way of quantifying proteins I was stunned at how "qualitative" it seemed. Now I think it served it's time--how else are you supposed to "quantify" proteins from hyperfractions across dozens of labs' LC-MS systems eg the Human Plasma Proteome Project.
September 10, 2025 at 3:39 PM
When I first learned about spectral counting as a way of quantifying proteins I was stunned at how "qualitative" it seemed. Now I think it served it's time--how else are you supposed to "quantify" proteins from hyperfractions across dozens of labs' LC-MS systems eg the Human Plasma Proteome Project.
My treatment significantly modulates gene expression machinery!
August 28, 2025 at 4:21 PM
My treatment significantly modulates gene expression machinery!
Remember to say please & thank you (& tip $ if you don't mind potential future payback risk 😜)
Definitely some new LLM-powered bioinformatic tools to be developed with careful engineering e.g. interpreting top hits based on the human knowledgebase (analogous to backgrounded pathway analysis)
Definitely some new LLM-powered bioinformatic tools to be developed with careful engineering e.g. interpreting top hits based on the human knowledgebase (analogous to backgrounded pathway analysis)
August 28, 2025 at 4:19 PM
Remember to say please & thank you (& tip $ if you don't mind potential future payback risk 😜)
Definitely some new LLM-powered bioinformatic tools to be developed with careful engineering e.g. interpreting top hits based on the human knowledgebase (analogous to backgrounded pathway analysis)
Definitely some new LLM-powered bioinformatic tools to be developed with careful engineering e.g. interpreting top hits based on the human knowledgebase (analogous to backgrounded pathway analysis)
It's ironic that people often use/suggest fetus-derived cells eg HEK293 as a ethical substitute for HeLa.
August 14, 2025 at 3:40 PM
It's ironic that people often use/suggest fetus-derived cells eg HEK293 as a ethical substitute for HeLa.
If you haven't increased the DDA tolerance to 50 mz window and set it to go after off inclusion list ions while waiting, then the instrument may be waiting around for the inclusion list mzs.
August 4, 2025 at 9:12 AM
If you haven't increased the DDA tolerance to 50 mz window and set it to go after off inclusion list ions while waiting, then the instrument may be waiting around for the inclusion list mzs.
Would be interesting to see the effects of constant [trypsin] without normalizing [protein]. May I (or someone else) can compare?
July 28, 2025 at 11:09 PM
Would be interesting to see the effects of constant [trypsin] without normalizing [protein]. May I (or someone else) can compare?
Yes but that conclusion may lead to the misinterpreted addition of the same [trypsin] at wildly different [protein] which I can't imagine will yield the same proteomics profiles due to concentration-dependent effects. Still believe [protein] needs to normalize pre-digestion AFAIU.
July 28, 2025 at 11:00 PM
Yes but that conclusion may lead to the misinterpreted addition of the same [trypsin] at wildly different [protein] which I can't imagine will yield the same proteomics profiles due to concentration-dependent effects. Still believe [protein] needs to normalize pre-digestion AFAIU.
Are these all these sentimentals just about the affinity platforms, or LC-MS too? I thought large plasma datasets would be helpful for filtering noise a la GWAS. AFAIR the UK Biobank plasma disease studies were anti-hopium with mostly minor improvements of Dx accuracy vs traditional biomarkers.
July 19, 2025 at 8:25 PM
Are these all these sentimentals just about the affinity platforms, or LC-MS too? I thought large plasma datasets would be helpful for filtering noise a la GWAS. AFAIR the UK Biobank plasma disease studies were anti-hopium with mostly minor improvements of Dx accuracy vs traditional biomarkers.
Do the splitting ones have any special characteristics eg reduced solubility or amphipathic nature? How big is the first vs second peak? Speculating, maybe the first elution point doesn't have enough time/flow to elute everything and the second elution point cleans up the rest?
July 7, 2025 at 3:56 PM
Do the splitting ones have any special characteristics eg reduced solubility or amphipathic nature? How big is the first vs second peak? Speculating, maybe the first elution point doesn't have enough time/flow to elute everything and the second elution point cleans up the rest?
I was never able to get two scan boxcar-DDA to ID more proteins than a vanilla top 15 DDA on my QEP. Probably could do better with maxIT > 5 ms for the 10x 50mz msx tsim MS1 scan but then it would start eating MS2 time so I never ventured.
July 1, 2025 at 1:18 AM
I was never able to get two scan boxcar-DDA to ID more proteins than a vanilla top 15 DDA on my QEP. Probably could do better with maxIT > 5 ms for the 10x 50mz msx tsim MS1 scan but then it would start eating MS2 time so I never ventured.
Supposedly Edison and others held objects in hand that would drop as they fell asleep, wakimg them in a creative cognitive interphase, aka using a "hypnagogia catcher"
June 27, 2025 at 8:25 PM
Supposedly Edison and others held objects in hand that would drop as they fell asleep, wakimg them in a creative cognitive interphase, aka using a "hypnagogia catcher"
Diabetic fasting glucose is 1.3x
May 13, 2025 at 11:20 PM
Diabetic fasting glucose is 1.3x
doi.org/10.1101/2025... unbroken link
An adaptive, continuous-learning framework for clinical decision-making from proteome-wide biofluid data
Mass spectrometry (MS)-based proteomics provides deep molecular insights from patient samples, but clinical use has been limited by missing values, static biomarker panels, and the need for targeted a...
doi.org
May 8, 2025 at 4:17 PM
doi.org/10.1101/2025... unbroken link