artMS

artMS provides a set of tools for the analysis of proteomics label-free datasets.

Key Features:

• Input Processing: Takes as input the MaxQuant search result output (evidence.txt file).
• Quality Control: Performs quality control on proteomics label-free datasets.
• Relative Quantification: Performs relative quantification using MSstats.
• Downstream Analysis and Integration: Performs downstream analysis and integration of proteomics data.
• Tool Compatibility Functions: Provides functions to re-format and make data compatible with SAINTq, SAINTexpress, Phosfate, and PHOTON.

Scientific Applications:

• Label-Free Proteomics Analysis: Supports analysis of proteomics label-free datasets through quality control, quantification, and integration workflows.
• Affinity Purification-Mass Spectrometry Data Integration: Enables compatibility with SAINTq and SAINTexpress for interaction proteomics analysis.
• Phosphoproteomics Data Analysis: Supports compatibility with Phosfate and PHOTON for phosphorylation site analysis.

Methodology:

artMS takes the MaxQuant search result output (evidence.txt file) as input and performs quality control, relative quantification using MSstats, downstream analysis and integration.