The case against the Excel for data analysis! A summary from 2004 to 2022.

I had a great time in Ponta Grossa (PR) city at I Escola Integrada de Ciências Ômicas dos Campos Gerais. Lovely town, great university (UEPG), and new friends. Thanks for having me there.

Nice algorithm. It caught my attention that the Astral seems quite bad in the quantification.

This is the feature I'm using.

You can do nice things, such as this one. I will have something really cool to share soon.

DIANN users: making your life easier when evaluating your DIANN search results. QC4DIANN_v1.1.0 has new visualizations and now accepts the fasta you used to generate the speclib as a reference for calculating the proportion of proteotypic peptides per sample. Release 👉 github.com/41ison/QC4DI...

FragPipe users: I've updated PSManalyst shiny app. Check it out and enjoy the easiest way to evaluate the quality of your runs. Now you can map peptides to protein coverage counting PSMs. github.com/41ison/PSMan...

I've seen several recent preprints using DIANN v1.9. DIANN is great and stable in several versions, except for v1.9. We tested at least 7 different versions in a publication 👉 pubs.acs.org/doi/10.1021/... v1.9 will likely provide more IDs, but at the cost of precision.

Absence of correlation between mRNA and protein levels. Probably some reviewer asked for validation of RNAseq results by qPCR. TMT analysis failed because the authors used MS2 resolution of 17,500 on a QE! The reviewer had no idea what they were evaluating.🥲 www.frontiersin.org/journals/imm...

PEA-based proteomics (Olink) is something we should pay more attention to. Apparently, people don't know how to properly normalize and do the stats in this kind of dataset. You should never live the statistic in the hands of core facilities.

I'm surprised that the authors declared that "Quality control measures and normalization of protein concentration were performed at the Firalis facility" and the reviewers were OK with it. It is probable that there is a normalization issue here.

I'm going to tell a bit of history in an introductory course for graduate students beginning in proteomics. Is there anything I'm missing in this specific comparison? Other search engines will be introduced, of course.

Do you want to display your peptide sequences from peptidomics experiments as an overrepresentation analysis? Try this script. link: github.com/41ison/WordC...

I am preparing material for a guided study of the basic physics behind the space charge effect, namely Coulomb's Law. github.com/41ison/space...

I plotted the data from table 1 to highlight this clearly. Can you imagine a direct comparison between several instruments?

#proteomics people, this figure has been around for some years. I'm trying to track the original source to give credit. Any idea? Found this publication pubs.rsc.org/en/content/a... www.crownbio.com/hs-fs/hubfs/...

This is how the block look like if you remove it.

In your picture, the needle seat is marked in the red box. The needle goes in the blue arrow. You can check this keeping the autosampler doors open, manually remove the insulator (black polystyrene part), then click the button wash in the low panel of the autosampler.

Once we are here, another thing that we should be ware of is the needle position at the needle seat. In this system, you need to realign the needle move periodically (usually they only tell you when the problem is there). See our picture and check your needle.

You found the culprit. If you have the same error in the leak test and are not able to find the broken line, check the part marked in red in the figure with a magnifying glass: We had one of these fractured in the loop connection.

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