pwilmart

annotations

GUI tool to add rich annotations to PAW summary files from Swiss-Prot flat text files.

fasta_utilities

Utilities for downloading and managing protein FASTA files.

IRS_normalization

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

IRS_validation

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

PAW_BLAST

A utility for blasting one protein FASTA file against another FASTA file to find orthologs.

PAW_pipeline

A Comet-based, best practices proteomics pipeline.

RECOMB-CP_2012

PowerPoint from 2012 RECOMB-CP meeting: shotgun analysis tutorial - mods, accurate mass, FDR

score_distributions_FDR

How relative sizes of incorrect and correct score distributions affect FDR thresholds.

Start_Here

Navigation links (and brief descriptions) to my repositories.

TMT_analysis_examples

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

pwilmart/PAW_pipeline

A Comet-based, best practices proteomics pipeline.

pwilmart/TMT_analysis_examples

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

pwilmart/Start_Here

Navigation links (and brief descriptions) to my repositories.

pwilmart/fasta_utilities

Utilities for downloading and managing protein FASTA files.

pwilmart/PAW_BLAST

A utility for blasting one protein FASTA file against another FASTA file to find orthologs.

pwilmart/IRS_validation

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

pwilmart/score_distributions_FDR

How relative sizes of incorrect and correct score distributions affect FDR thresholds.

pwilmart/Human-plasma_DIA-vs-TMT

An apples-to-aardvarks comparison of human plasma proteomes from DIA and TMT

pwilmart/quantitative_proteomics_data_cleaning

A discussion of basic data cleaning concepts for quantitative proteomics data.

pwilmart/Cloud_desktop_benchmarks

Benchmarking proteomics analyses on desktop computers and in the cloud.

pwilmart/MaxQuant_and_PAW

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

pwilmart/mouse_lens_development_Khan2018_reanalysis

Re-analysis of Khan 2018 developing mouse lens TMT study (PXD006381)

pwilmart/Proteomics_best_practices

An exploration of how best practices for bottom-up, data-dependent acquisition proteomics are ignored

pwilmart/TMT_channel_cross_talk

An exploration of how much TMT channels cross-talk with each other

pwilmart/TMT_PAW_pipeline

Details about how TMT labeling is handled in PAW pipeline

pwilmart/Yeast_CarbonSources

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

pwilmart/Z-score_GUI

GUI app for doing sliding window Z-score transformations of quantitative proteomics data

pwilmart/ABRF_2020

Content for ARBF 2020 meeting talk

pwilmart/Human_rhesus_TMT

Analysis discussion of a multi-sample, multi-fraction, multi-kit, multi-species TMTpro experiment

pwilmart/human_tear_references

Review of 80 or so human tear quantitative proteomics studies

pwilmart/Mammalian_sperm_PXD003164

pwilmart/Metaplastic-BC_PXD014414

Re-analysis of metaplastic breast cancer 27-sample TMT data from the PXD014414 archive.

pwilmart/PAW_phospho

Phospho peptide software for processing Proteome Discoverer PSM export files.

pwilmart/PrecisionProDB_references

pwilmart/precursor_mass_corrections

Explores precursor mass correction algorithm assumptions and claims

pwilmart/pwilmart

pwilmart/pwilmart.github.io

Thinking outside of the black box.

pwilmart/PXD011691_reanalysis

Reanalysis of data from PXD011691 - another DIA versus TMT experiment

pwilmart/PXD030990_human-tear_re-analysis

Re-analysis of human tear data from PXD030990

pwilmart/R-Jupyter-notebook_setup

How to setup Jupyter notebooks to run an R kernel