Thang Pham
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tvpham.bsky.social
Thang Pham
@tvpham.bsky.social
66 followers 210 following 9 posts
Computer scientist at OncoProteomics Lab, Amsterdam UMC, the Netherlands; visiting scholar at Vietnam National University, Hanoi; working on mass spectrometry-based proteomics data analysis and biomedical applications.
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tvpham.bsky.social
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...
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....
www.biorxiv.org
October 8, 2025 at 7:57 PM
Reposted by Thang Pham
vadim-demichev.bsky.social
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...
May 30, 2025 at 8:36 AM
tvpham.bsky.social
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...
Redirecting
doi.org
May 30, 2025 at 6:43 AM
tvpham.bsky.social
#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...
Phosphorylation site report from a DIA-MS experiment – Digital Biology Lab
digitalbiologylab.github.io
March 10, 2025 at 9:46 PM
tvpham.bsky.social
Amsterdam morning, -1 °C.
March 4, 2025 at 9:03 PM
tvpham.bsky.social
#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...
DIA-NN 2.0 and tsv file output – Digital Biology Lab
digitalbiologylab.github.io
March 1, 2025 at 2:14 PM
tvpham.bsky.social
This is mostly for Excel users who want to do statistics in R.

digitalbiologylab.github.io/posts/250224...
A Kruskal-Wallis test is added to ion – Digital Biology Lab
digitalbiologylab.github.io
February 25, 2025 at 11:47 AM
tvpham.bsky.social
A single command to zip all #timsTOF .d folders for #ProteomeXchange upload.

#proteomics

digitalbiologylab.github.io/posts/250215...
One command to zip them all – Digital Biology Lab
digitalbiologylab.github.io
February 15, 2025 at 5:19 PM
tvpham.bsky.social
Some documentation on processing DIA-NN 1.8.1 output.

#TeamMassSpec #Proteomics

digitalbiologylab.github.io/posts/250206...
Processing DIA-NN 1.8.1 output – Digital Biology Lab
digitalbiologylab.github.io
February 8, 2025 at 5:39 AM
tvpham.bsky.social
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/
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
github.com
December 14, 2024 at 2:34 PM