Research funding from VNU University of Engineering and Technology approved

news
We are happy to share that we have received a research funding from VNU University of Engineering and Technology. This grant enables us to focus on developing computational…
Mar 29, 2025
Thang V. Pham

Phosphorylation site report from a DIA-MS experiment

phosphoproteomics
DIA-MS
msproteomics
sitereport
script
Skowronek et al. 2022 reported a large difference between the performance of Spectronaut and DIA-NN. For DIA-MS-based phosphoproteomics, one of the issues was that it was…
Mar 10, 2025
Thang V. Pham & Pham Huy Chau Long

DIA-NN 2.0 and tsv file output

iq
protein quantification
R
script
From version 2.0, DIA-NN stops producing output in the tab-delimited text format (.tsv). It uses the parquet data format. In our experiments, a .parquet file output is about…
Mar 1, 2025
Thang V. Pham

A Kruskal-Wallis test is added to ion

ion
R
script
statistics
I’ve added a script to ion to perform a Kruskal-Wallis test for each row in a data matrix (ion$kruskal_test_3g). This statistical test is a non-parametric test and can be…
Feb 25, 2025
Thang V. Pham

 

One command to zip them all

script
To upload timsTOF data to ProteomeXchange, we have to create a single file for each .d data folder. One can zip each folder by right-click and send-to a compressed zipped…
Feb 15, 2025
Thang V. Pham

Processing DIA-NN 1.8.1 output

iq
protein quantification
We processed the Bruderer15 dataset (Bruderer et al., MCP 2015) using DIA-NN 1.8.1 (Demichev et al., Nature Methods 2020) with the switch --report-lib-info turned on. The…
Feb 6, 2025
Thang V. Pham

Hello world

news
Dec 28, 2024
Thang V. Pham
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