pwilmart
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TMT_channel_cross_talk Public
An exploration of how much TMT channels cross-talk with each other
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PAW_pipeline Public
A Comet-based, best practices proteomics pipeline.
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fasta_utilities Public
Utilities for downloading and managing protein FASTA files.
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Proteomics_best_practices Public
An exploration of how best practices for bottom-up, data-dependent acquisition proteomics are ignored
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PAW_phospho Public
Phospho peptide software for processing Proteome Discoverer PSM export files.
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Start_Here Public
Navigation links (and brief descriptions) to my repositories.
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Re-analysis of Khan 2018 developing mouse lens TMT study (PXD006381)
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Re-analysis of human tear data from PXD030990
MIT License UpdatedNov 23, 2023 -
Human_rhesus_TMT Public
Analysis discussion of a multi-sample, multi-fraction, multi-kit, multi-species TMTpro experiment
MIT License UpdatedOct 9, 2023 -
A discussion of basic data cleaning concepts for quantitative proteomics data.
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Yeast_CarbonSources Public
Yeast TMT data - 3 different carbon sources (from Gygi lab) analyzed with PAW pipeline and MaxQuant
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PXD011691_reanalysis Public
Reanalysis of data from PXD011691 - another DIA versus TMT experiment
Jupyter Notebook MIT License UpdatedFeb 24, 2023 -
Human-plasma_DIA-vs-TMT Public
An apples-to-aardvarks comparison of human plasma proteomes from DIA and TMT
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TMT_PAW_pipeline Public
Details about how TMT labeling is handled in PAW pipeline
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TMT_analysis_examples Public
Examples of TMT data analyses using R. Links to notebooks and repositories. Also a few spectral counting analyses.
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IRS_validation Public
Analysis of technical replicate channels to more fully validate the internal reference scaling (IRS) method.
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human_tear_references Public
Review of 80 or so human tear quantitative proteomics studies
MIT License UpdatedApr 23, 2022 -
PAW_BLAST Public
A utility for blasting one protein FASTA file against another FASTA file to find orthologs.
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R-Jupyter-notebook_setup Public
How to setup Jupyter notebooks to run an R kernel
MIT License UpdatedAug 29, 2021 -
Cloud_desktop_benchmarks Public
Benchmarking proteomics analyses on desktop computers and in the cloud.
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precursor_mass_corrections Public
Explores precursor mass correction algorithm assumptions and claims
MIT License UpdatedApr 22, 2021 -
score_distributions_FDR Public
How relative sizes of incorrect and correct score distributions affect FDR thresholds.
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PrecisionProDB_references Public
Forked from ATPs/PrecisionProDB_referencesMIT License UpdatedJan 4, 2021 -
MaxQuant_and_PAW Public
Compares PAW and MQ for a 7-channel TMT experiment; compares edgeR to two-sample t-test
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Metaplastic-BC_PXD014414 Public
Re-analysis of metaplastic breast cancer 27-sample TMT data from the PXD014414 archive.
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Z-score_GUI Public
GUI app for doing sliding window Z-score transformations of quantitative proteomics data