Phillip Wilmarth's repositories
PAW_pipeline
A Comet-based, best practices proteomics pipeline.
TMT_analysis_examples
Examples of TMT data analyses using R. Links to notebooks and repositories. Also a few spectral counting analyses.
Start_Here
Navigation links (and brief descriptions) to my repositories.
fasta_utilities
Utilities for downloading and managing protein FASTA files.
IRS_validation
Analysis of technical replicate channels to more fully validate the internal reference scaling (IRS) method.
score_distributions_FDR
How relative sizes of incorrect and correct score distributions affect FDR thresholds.
Human-plasma_DIA-vs-TMT
An apples-to-aardvarks comparison of human plasma proteomes from DIA and TMT
quantitative_proteomics_data_cleaning
A discussion of basic data cleaning concepts for quantitative proteomics data.
Cloud_desktop_benchmarks
Benchmarking proteomics analyses on desktop computers and in the cloud.
MaxQuant_and_PAW
Compares PAW and MQ for a 7-channel TMT experiment; compares edgeR to two-sample t-test
mouse_lens_development_Khan2018_reanalysis
Re-analysis of Khan 2018 developing mouse lens TMT study (PXD006381)
Proteomics_best_practices
An exploration of how best practices for bottom-up, data-dependent acquisition proteomics are ignored
TMT_channel_cross_talk
An exploration of how much TMT channels cross-talk with each other
TMT_PAW_pipeline
Details about how TMT labeling is handled in PAW pipeline
Yeast_CarbonSources
Yeast TMT data - 3 different carbon sources (from Gygi lab) analyzed with PAW pipeline and MaxQuant
Z-score_GUI
GUI app for doing sliding window Z-score transformations of quantitative proteomics data
Human_rhesus_TMT
Analysis discussion of a multi-sample, multi-fraction, multi-kit, multi-species TMTpro experiment
human_tear_references
Review of 80 or so human tear quantitative proteomics studies
Metaplastic-BC_PXD014414
Re-analysis of metaplastic breast cancer 27-sample TMT data from the PXD014414 archive.
PAW_phospho
Phospho peptide software for processing Proteome Discoverer PSM export files.
precursor_mass_corrections
Explores precursor mass correction algorithm assumptions and claims
pwilmart.github.io
Thinking outside of the black box.
PXD011691_reanalysis
Reanalysis of data from PXD011691 - another DIA versus TMT experiment
PXD030990_human-tear_re-analysis
Re-analysis of human tear data from PXD030990
R-Jupyter-notebook_setup
How to setup Jupyter notebooks to run an R kernel