very happy that the iq 2.0 paper is published. Boosting the Speed and Accuracy of Protein Quantification Algorithms in Mass Spectrometry-Based Proteomics | Journal of Proteome Research pubs.acs.org/doi/10.1021/...

Very happy to introduce the maxlfq-bit algorithm, a much better way to implement the maxlfq protein quantification method than before in both speed and memory requirement. Now available in the R package iq. www.biorxiv.org/content/10.1...

DIA-NN 2.2.0 is released! The new DIA-NN 2.2.0 Enterprise achieves up to ~1.6x median speedup on 64-cores under Windows (please see benchmark below). Release notes: github.com/vdemichev/Di..., download (Academia): github.com/vdemichev/Di...

Very happy to share our latest publication in Cancer Cell on a pan-cancer landscape using #DIA-MS. #TeamMassSpec #Proteomics doi.org/10.1016/j.cc...

#TeamMassSpec #Proteomics #DIA-MS #Phosphoproteomics Curious about the performance of the latest version of DIA-NN (v2.0.2) for phosphoproteomics? We have some numbers for you here digitalbiologylab.github.io/posts/250310...

Amsterdam morning, -1 °C.

#TeamMassSpec #Proteomics It is simple to convert the DIA-NN parquet file to the tsv text format if your downstream tool requires tsv. Note that if you want to perform quantification at fragment level, remember to turn on the --export-quant switch. digitalbiologylab.github.io/posts/220301...

This is mostly for Excel users who want to do statistics in R. digitalbiologylab.github.io/posts/250224...

A single command to zip all #timsTOF .d folders for #ProteomeXchange upload. #proteomics digitalbiologylab.github.io/posts/250215...

Some documentation on processing DIA-NN 1.8.1 output. #TeamMassSpec #Proteomics digitalbiologylab.github.io/posts/250206...

The R package iq has been updated to support the parquet file format. New versions of DIA-NN produce the main report in this format. If you use DIA-NN for your dia-ms data processing, please give it a try. #TeamMassSpec #Proteomics github.com/tvpham/iq/