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

Developing mouse lens done with MQ

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

Tandem Mass Tag (TMT) dilution series analysis

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

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

Comparison of SPS MS3 TMT data to MS2 TMT data

Generic Fedora CI tests FMF defintions

Public TMT data comparing MS2 to MS3 methods

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

Converter from Census TMT output file to the input of MSstatsTMT

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

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

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

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.

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

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

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

Fex's Modelling Toolbox