Protocols

Before you hand in samples for proteome analysis (see sample submission), it is advised to check sample quality on a coomassie gel if sample amount allows. Your samples are lysed in a buffer appropriate for the desired workflow (discuss if you are not sure) with a protein determination aiming for equal protein in all samples.

General protocols

Tools

Inkascore.org for kinase activity scoring. Cite the following paper Please cite the following papers when using the tool:

Beekhof R, van Alphen C, Henneman AA, Knol JC, Pham TV, Rolfs F, Labots M, Henneberry E, Le Large TY, de Haas RR, Piersma SR, Vurchio V, Bertotti A, Trusolino L, Verheul HM, Jimenez CR. INKA, an integrative data analysis pipeline for phosphoproteomic inference of active kinases. Mol Syst Biol. 2019 Apr 12;15(4):e8250. doi: 10.15252/msb.20188250. PubMed PMID: 30979792; PubMed Central PMCID: PMC6461034.

Software

R package iq for protein quantification
Pham TV, Tran CTM, Henneman AA, Pham LHC, Le DG, Can AH, Bui PHL, Piersma SR, Jimenez CR. Boosting the Speed and Accuracy of Protein Quantification Algorithms in Mass Spectrometry-Based Proteomics. J Proteome Res. 2026 Feb 6;25(2):1198-1203.
Pham TV, Henneman AA, Jimenez CR. iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics. Bioinformatics. 2020 Apr 15;36(8):2611-2613.

Python package msproteomics for phosphoDIA site report
Pham TV, Henneman AA, Truong NX, Jimenez CR. msproteomics sitereport: reporting DIA-MS phosphoproteomics experiments at site level with ease. Bioinformatics. 2024 Jul 1;40(7):btae432.

Python package aiproteomics for peptide properties prediction
Pham TV, Nguyen VV, Vu D, Henneman AA, Richardson RA, Piersma SR, Jimenez CR. A transformer architecture for retention time prediction in liquid chromatography mass spectrometry-based proteomics. Proteomics. 2023 Apr;23(7-8):e2200041.

R package countdata for the beta binomial test
Pham TV, Jimenez CR. An accurate paired sample test for count data. Bioinformatics. 2012 Sep 15;28(18):i596-i602.
Pham TV, Piersma SR, Warmoes M, Jimenez CR. On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics. Bioinformatics. 2010 Feb 1;26(3):363-9.

R script for the s-test
Pham TV, Jimenez CR. Simulated linear test applied to quantitative proteomics. Bioinformatics. 2016 Sep 1;32(17):i702-i709.

Training/ Education

We offer one-on-one training in sample preparation and education in an annual elective course “Biomedical Proteomics” for master students (2 weeks/ 3 ECTs) and PhD students (1 week/ 1,5 ECTs) (link to OAA and doctoral school) Click here for the program: Page 1 Page 2