A Comet-based, best practices proteomics pipeline.

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

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

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

Fex's Modelling Toolbox

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

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

Developing mouse lens done with MQ

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

Proteomics database searches

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

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

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

Comparison of SPS MS3 TMT data to MS2 TMT data

R analysis of TMT data from Yeast triple knockout strains (Paulo et al., 2016, JASMS, v27, p1620-25)

Generic Fedora CI tests FMF defintions

Converter from Census TMT output file to the input of MSstatsTMT

Tandem Mass Tag (TMT) dilution series analysis

Public TMT data comparing MS2 to MS3 methods