Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
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Dec 9, 2025 - Nextflow
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tmt
Here are 23 public repositories matching this topic...
R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
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Jul 28, 2025 - R
An exploration of internal reference scaling (IRS) normalization in isobaric tagging proteomics experiments.
r jupyter-notebook ipynb proteomics mass-spectrometry proteomics-data normalization irs-normalization tmt
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Aug 6, 2019 - Jupyter Notebook
A Comet-based, best practices proteomics pipeline.
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Mar 21, 2024 - Python
Data Reduction System (DRS) for the Thirty Meter Telescope IRIS imager/spectrograph
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Dec 2, 2025 - Python
Examples of TMT data analyses using R. Links to notebooks and repositories. Also a few spectral counting analyses.
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May 27, 2022
Compares PAW and MQ for a 7-channel TMT experiment; compares edgeR to two-sample t-test
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Sep 17, 2020 - HTML
Converter from Census TMT output file to the input of MSstatsTMT
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Aug 2, 2021 - Java
An open-source Python package for accurate and sensitive peptide and protein quantification.
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Nov 14, 2025 - Python
Developing mouse lens done with MQ
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Dec 10, 2018 - HTML
R analysis of TMT data from Yeast triple knockout strains (Paulo et al., 2016, JASMS, v27, p1620-25)
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Sep 29, 2018 - Jupyter Notebook
Yeast TMT data - 3 different carbon sources (from Gygi lab) analyzed with PAW pipeline and MaxQuant
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Mar 27, 2023 - Jupyter Notebook
Tandem Mass Tag (TMT) dilution series analysis
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Mar 27, 2019 - Jupyter Notebook
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
workflow pipeline nextflow proteomics dia mass-spectrometry openms proteogenomics tmt nf-core mass-spec lfq
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May 6, 2024 - Nextflow
Data from Plubell et al., 2017 processed with the PAW pipeline.
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Jan 3, 2019 - Jupyter Notebook
Re-analysis of data from childhood acute lymphoblastic leukemia study in Nat. Comm. April 2019
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Apr 11, 2019 - HTML
Comparison of SPS MS3 TMT data to MS2 TMT data
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Feb 8, 2020 - HTML
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