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Karel Stejskal

@karelstejskal.bsky.social

LC-MSMS troubleshooting enthusiast in VBCF - Proteomics facility Cycling commuter

96 Followers  |  171 Following  |  2 Posts  |  Joined: 10.10.2023  |  1.524

Latest posts by karelstejskal.bsky.social on Bluesky

The Need for Guidelines in Publication of Peptide and Protein Identification Data Over the past few years, the number and size of proteomic datasets composed of mass spectrometry-derived protein identifications reported in the literature have grown dramatically. This is a direct result of the widespread availability of instruments, methods, and easy-to-use software for collecting large amounts of data and for converting the observed peptide and fragment-ion masses to peptide and then protein identities. In particular, the analysis of samples containing large numbers of proteins by multidimensional liquid chromatography (LC/LC)1 coupled on-line with tandem mass spectrometry (MS/MS) is now a common component of many biological projects.

DDA was a mess 20 years ago, but the field converged to certain accepted principles rather quickly. The MCP guidelines were useful. DIA is more complex as it blurs the line between ID and quant a lot more than DDA. Still, we can come up with a set of guidelines. www.mcponline.org/article/S153...

12.12.2024 23:57 — 👍 21    🔁 2    💬 1    📌 0

I have a radical idea. All DIA tool developers meet in Geneva for a convention and agree to apply certain additional conservative quality filters by default (so yeah, not 10k proteins but “just” 8k…). And then provide users an option to relax the filters at their own risk. Not the other way around.

12.12.2024 13:56 — 👍 60    🔁 9    💬 12    📌 2

I am really worried about DIA approach trustworthiness in the field if something like this will not be done. If there will not be free seminar room in Geneva you are invited to come to Vienna!

13.12.2024 10:11 — 👍 5    🔁 0    💬 0    📌 0

Sorry for joinning so late. Funny fact under the line - RSLC can manage most problematic samples without any problems... There is always a posibility to try to improve sample prep... But it turns me crazy to know RSLC makes it better and not finding why so far

15.11.2023 20:16 — 👍 1    🔁 0    💬 1    📌 0

We are having issues with our Vanquish Neos recently. The most annoying is quite obvious peak tailing in samples that are fine when run on a U3000. Problem is that the HeLa QC is OK, so it seems to be a combination of samples and Neo. We use a trap column, prior desalting does not help. Any ideas?

06.10.2023 16:20 — 👍 3    🔁 4    💬 5    📌 0

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