Thermo users, have you ever seen this type of error on the Exploris series? I've heard it's common and may require replacing some PCB. Any tips?
#MS

Quick check: Is it common for your institutions for the competition announcement to require candidates to collaborate with very specific people (including their names)? Apparently, USP in São Paulo-Brazil has a very specific interest for faculty position as assistant professor.

Another trivial and still useful application for routine protein estimation calculations. Pay attention to the input files. The standard curve and samples values must be provided separately, and the blank absorbances must be declared manually. It can help your students.
github.com/41ison/Prote...

Trivial, but still useful. A quick code for limma analysis from DIANN data with annotated volcano and MD plots.
github.com/41ison/limma...

If you want to visualize the family-wise error rate and the adjusted p-values using Bonferroni correction for multiple comparisons, you can check the code here: github.com/41ison/FWER/...
It is more for self-learning.
Enjoy :)

Well, I'm trying to make life easier to produce 3D plots for LC-MS/MS. If you find a better way to generate this without binning the data, please let me know. If you want to have a 3D plot including the retention time, precursor m/z and intensity values, give it a try.
github.com/41ison/Binne...

Well, this should not be something to celebrate.

If you set the "--mass-acc-cal" parameter to the same value (30 in the example), you will have comparable overall results. [2/3]

I can explain. If we search the same files, we should have roughly the same numbers. But if you look at the same files in different DIANN versions, this is what you see. So, for Orbitrap data I would say something went wrong with the version 2.0

American Society for Microbiology, your compliance and complicity with far right politics will be remembered!
Until you behave respectfully again, don't send me requests to review again.
#ASM #microbiology

www.nature.com/articles/nat...

This is something super nice when people actually pay attention to this kind of details. Most of the people in core facilities just use something like 300-1200 m/z or whatever. The narrower the mass range the better the IDs, what is not new by the way.

4. Exploris 480 should have comparable results with the TimsTOFHT using 500ng. 1 µg is too much!
5. not quite convinced about the CVs in TimsTOF HT. In HUPO there was a poster showing the opposite of it. TimsTOF HT was the worst in quantification.

You may want to check the search results from DIANN with different filters of quality. Now you can do it easily with a Shiny App that takes your report.parquet file as input and that is it! There is a .qmd more in details if you prefer. Enjoy :)
#MassSpec
#proteomics

github.com/41ison/QC4DI...

You can check the Nterm and Cterm fingerprint of peptides separately on seqlogos or everything together in a heatmap. If you are in proteolysis filed, you can benefit of this code. enjoy it :)