Thang Pham

Boosting the Speed and Accuracy of Protein Quantification Algorithms in Mass Spectrometry-Based Proteomics Protein quantification is a crucial data processing step that combines quantitative values at the peptide or fragment level into protein levels in mass spectrometry-based proteomics. However, many of ...

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/...

Boosting the speed and accuracy of protein quantification algorithms in mass spectrometry-based proteomics Current methods for protein level quantification in mass spectrometry-based proteomics do not scale with the increasing number of samples because of limited system memory and algorithmic complexities....

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...

GitHub - tvpham/iq: An R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics An R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics - tvpham/iq

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/