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PXD004163_Notebooks Public
Re-analysis of PXD004163 using notebooks to compare with Mascot blog.
HTML MIT License UpdatedJun 27, 2020 -
JPR-201712_MS2-MS3 Public
Public TMT data comparing MS2 to MS3 methods
Jupyter Notebook MIT License UpdatedJun 26, 2020 -
E. coli spiked into a human background, 10-plex TMT labeled, MS2 scans, Q Exactive
HTML MIT License UpdatedJun 26, 2020 -
PXD017823_Real-Time-Search Public
Re-analysis of data from PXD017823 exploring real time search for TMT.
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talk_to_repo_example Public
Example of turning a Powerpoint talk into a repo README.md
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RECOMB-CP_2012 Public
PowerPoint from 2012 RECOMB-CP meeting: shotgun analysis tutorial - mods, accurate mass, FDR
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Cascadia_2018 Public
Using Jupyter notebooks in proteomics data analyses talk slides from the 2018 Cascadia Proteomics Symposium
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Cascadia_2013 Public
2013 Cascadia Proteomics Symposium talk about extended parsimony protein grouping.
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An unbiased comparison of peptide identification performance between SEQUEST, Mascot, and X!Tandem (circa 2013).
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ASMS_2018 Public
IRS normalization poster presented at 2018 San Diego ASMS meeting (Thursday #389) .
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SPS-MS3_vs_MS2_TMT Public
Comparison of SPS MS3 TMT data to MS2 TMT data
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utilities Public
Some Python utility scripts for proteomics file management
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annotations Public
GUI tool to add rich annotations to PAW summary files from Swiss-Prot flat text files.
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PXD001077_P-furiosus Public
PAW analysis of Pyrococcus furiosus digest from PXD001077
MIT License UpdatedDec 6, 2019 -
Smith_SpC_2018 Public
A large-scale spectral counting data analysis using PAW pipeline, edgeR, R, and Jupyter notebooks
Jupyter Notebook MIT License UpdatedSep 6, 2019 -
Sea_lion_urine_SpC Public
Sea lion urine comparison with spectral counting.
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IRS_normalization Public
An exploration of internal reference scaling (IRS) normalization in isobaric tagging proteomics experiments.
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ABRF_iPRG_2015_SpC Public
A spectral counting analysis of the ABRF iPRG 2015 study
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BCP-ALL_QE-TMT_Nat-Comm-2019 Public
Re-analysis of data from childhood acute lymphoblastic leukemia study in Nat. Comm. April 2019
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spectrum_utils Public
Forked from bittremieux-lab/spectrum_utilsSimple MS/MS spectrum preprocessing and visualization in Python
Jupyter Notebook Apache License 2.0 UpdatedApr 7, 2019 -
Dilution_series Public
Tandem Mass Tag (TMT) dilution series analysis
Jupyter Notebook MIT License UpdatedMar 27, 2019 -
Plubell_2017_PAW Public
Data from Plubell et al., 2017 processed with the PAW pipeline.
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Multiple_TMT_MQ Public
Developing mouse lens done with MQ
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Reference_Proteome_Manager Public
Forked from lily-liang12/Reference_Proteome_ManagerProgram to allow researchers to download and maintain protein databases from the UniProt database site for proteomics research.
Python MIT License UpdatedNov 18, 2018 -
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RawQuant Public
Forked from kevinkovalchik/RawQuantRawQuant is a Python package for extracting scan meta data and quantification values from Thermo .raw files.
Python MIT License UpdatedOct 5, 2018 -
RawTools Public
Forked from kevinkovalchik/RawToolsRawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis of Thermo Orbitrap raw mass spectrometer files.
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Yeast_triple_KO_TMT Public
R analysis of TMT data from Yeast triple knockout strains (Paulo et al., 2016, JASMS, v27, p1620-25)
Jupyter Notebook MIT License UpdatedSep 29, 2018 -
stats337 Public
Forked from hadley/stats337Readings in applied data science
R Creative Commons Attribution Share Alike 4.0 International UpdatedJun 20, 2018