tmt

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.

A Comet-based, best practices proteomics pipeline.

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.

An open-source Python package for accurate and sensitive peptide and protein quantification.

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.

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

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

Developing mouse lens done with MQ

Proteomics database searches

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

Quality Control Pipeline Server for Large-Cohort Quantitative Proteomics (TMT)

Comparison of SPS MS3 TMT data to MS2 TMT data

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

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

Generic Fedora CI tests FMF defintions

Exploratory CPTAC breast cancer proteomics analysis of tumor state, age, and self-reported race