Karel Stejskal
@karelstejskal.bsky.social
LC-MSMS troubleshooting enthusiast in VBCF - Proteomics facility
Cycling commuter
Cycling commuter
Reposted by Karel Stejskal
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...
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.
www.mcponline.org
December 12, 2024 at 11:57 PM
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...
Reposted by Karel Stejskal
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.
December 12, 2024 at 1:56 PM
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.
Reposted by Karel Stejskal
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?
October 6, 2023 at 4:20 PM
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?