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.

High quality in silico spectral library generation for data-independent acquisition proteomics

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

A software tool for omics-agnostic automated quality control of mass spectrometry data.

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".