Fex's Modelling Toolbox

Proteomics database searches

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Data Reduction System (DRS) for the Thirty Meter Telescope IRIS imager/spectrograph

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

A Comet-based, best practices proteomics pipeline.

Yeast TMT data - 3 different carbon sources (from Gygi lab) analyzed with PAW pipeline and MaxQuant

Examples of TMT data analyses using R. Links to notebooks and repositories. Also a few spectral counting analyses.

Analysis of technical replicate channels to more fully validate the internal reference scaling (IRS) method.

Converter from Census TMT output file to the input of MSstatsTMT

Compares PAW and MQ for a 7-channel TMT experiment; compares edgeR to two-sample t-test

Public TMT data comparing MS2 to MS3 methods

Generic Fedora CI tests FMF defintions

Comparison of SPS MS3 TMT data to MS2 TMT data

An exploration of internal reference scaling (IRS) normalization in isobaric tagging proteomics experiments.

Re-analysis of data from childhood acute lymphoblastic leukemia study in Nat. Comm. April 2019

Tandem Mass Tag (TMT) dilution series analysis

Data from Plubell et al., 2017 processed with the PAW pipeline.

Developing mouse lens done with MQ