abrf_2020

Content for ARBF 2020 meeting talk

abrf_iprg_2015_spc

A spectral counting analysis of the ABRF iPRG 2015 study

annotations

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

asms-2013_search-engine-comparison

An unbiased comparison of peptide identification performance between SEQUEST, Mascot, and X!Tandem (circa 2013).

asms_2018

IRS normalization poster presented at 2018 San Diego ASMS meeting (Thursday #389) .

bcp-all_qe-tmt_nat-comm-2019

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

cascadia_2013

2013 Cascadia Proteomics Symposium talk about extended parsimony protein grouping.

cascadia_2018

Using Jupyter notebooks in proteomics data analyses talk slides from the 2018 Cascadia Proteomics Symposium

cloud_desktop_benchmarks

Benchmarking proteomics analyses on desktop computers and in the cloud.

dilution_series

Tandem Mass Tag (TMT) dilution series analysis

fasta_utilities

Utilities for downloading and managing protein FASTA files.

human-plasma_dia-vs-tmt

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

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

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.

jpr-201712_ms2-ms3

Public TMT data comparing MS2 to MS3 methods

mammalian_sperm_pxd003164

maxquant_and_paw

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

metaplastic-bc_pxd014414

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

mouse_lens_development_khan2018_reanalysis

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

multiple_tmt_mq

Developing mouse lens done with MQ

paw_blast

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

paw_phospho

Phospho peptide software for processing Proteome Discoverer PSM export files.

paw_pipeline

A Comet-based, best practices proteomics pipeline.

plubell_2017_paw

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

precisionprodb_references

precursor_mass_corrections

Explores precursor mass correction algorithm assumptions and claims

proteomics_best_practices

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

pwilmart