A cross-platform proteomics data analysis suite
PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
MassDash: A web-based dashboard for streamlined DIA-MS visualization, analysis, prototyping, and optimization
A workflow for metabolite identification and accurate profiling in multidimensional LC-IM-MS-DIA measurements. DOI: 10.5281/zenodo.
Avant-garde (AvG) is a new tool to refine Data-Independent Acquisition (and Parallel Reaction Monitoring) by removing interfered transitions, adjusting integration boundaries and scoring peaks to control the FDR.
Size-Exclusion Chromatography Algorithmic Toolkit
A NextFlow pipeline for chromatogram library DIA proteomics workflows
Composite Spectra Analysis
A Framework for IMS-MS Raw Data Processing written in Rust and Python.
Extracts the features of peptide spectral library for better understanding and its efficient usage in DIA database search
This repository is associated with a bioRxiv preprint describing the MacCoss laboratory's quality control measures for sample preparation, system suitability, and assessing results.
Extract the identified peptides and proteins from spectral library search of DIA proteomic data in Skyline
CRISP-DIA is a software for liquid chromatography-tandem mass spectrometry (LC-MS/MS) based proteomics data processing, which enables accurate and reliable quantification for data-independent acquisition (DIA) proteomics.
Code building for workflow package
Reproducibility repo for Shashikadze et al. "Multi-omics profiling of lungs from genetically diabetic pigs reveals reduced ALOX15 levels and impaired eicosanoid switching as mechanisms contributing to a proinflammatory milieu".
A software tool for omics-agnostic automated quality control of mass spectrometry data.
Add a description, image, and links to the data-independent-acquisition topic page so that developers can more easily learn about it.
To associate your repository with the data-independent-acquisition topic, visit your repo's landing page and select "manage topics."