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Thang Pham

@tvpham.bsky.social
79 followers 235 following 13 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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Thang Pham @tvpham.bsky.social · 20/06/2026
just finished the first #ProteomeXchange submission using globus. A few lessons learned or re-learned: space in file names, sub-folders, incorrect checksum, local file permission, files not in .px file uploaded.
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Thang Pham @tvpham.bsky.social · 15/05/2026
Come do proteomics with us. Advertising mass spec-based proteomics to colleagues at Amsterdam UMC.
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Thang Pham @tvpham.bsky.social · 22/03/2026
Back to software maintainance mode. Update the iq package. Thanks to the users who reported the problem. digitalbiologylab.github.io/posts/260322...
digitalbiologylab.github.io
Reading a parquet file to an R data frame – Digital Biology Lab
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Thang Pham @tvpham.bsky.social · 20/01/2026
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/...
pubs.acs.org
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 ...
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Thang Pham @tvpham.bsky.social · 08/10/2025
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...
biorxiv.org
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....
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Reposted by Thang Pham
Vadim Demichev @vadim-demichev.bsky.social · 30/05/2025
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...
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Thang Pham @tvpham.bsky.social · 30/05/2025
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...
doi.org
Redirecting
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Thang Pham @tvpham.bsky.social · 10/03/2025
#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...
digitalbiologylab.github.io
Phosphorylation site report from a DIA-MS experiment – Digital Biology Lab
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Thang Pham @tvpham.bsky.social · 04/03/2025
Amsterdam morning, -1 °C.
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Thang Pham @tvpham.bsky.social · 01/03/2025
#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...
digitalbiologylab.github.io
DIA-NN 2.0 and tsv file output – Digital Biology Lab
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Thang Pham @tvpham.bsky.social · 25/02/2025
This is mostly for Excel users who want to do statistics in R. digitalbiologylab.github.io/posts/250224...
digitalbiologylab.github.io
A Kruskal-Wallis test is added to ion – Digital Biology Lab
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Thang Pham @tvpham.bsky.social · 15/02/2025
A single command to zip all #timsTOF .d folders for #ProteomeXchange upload. #proteomics digitalbiologylab.github.io/posts/250215...
digitalbiologylab.github.io
One command to zip them all – Digital Biology Lab
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Thang Pham @tvpham.bsky.social · 08/02/2025
Some documentation on processing DIA-NN 1.8.1 output. #TeamMassSpec #Proteomics digitalbiologylab.github.io/posts/250206...
digitalbiologylab.github.io
Processing DIA-NN 1.8.1 output – Digital Biology Lab
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Thang Pham @tvpham.bsky.social · 14/12/2024
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.com
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
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