ProtMAX

ProtMAX performs high-throughput protein quantification from mass spectrometry (MS) data for shotgun proteomics.

Key Features:

• Mass Accuracy Precursor Alignment (MAPA): Implements the Mass Accuracy Precursor Alignment (MAPA) strategy for relative protein quantification with high resolution and sensitivity.
• Automated Precursor Alignment: Automates alignment of precursors across hundreds of MS runs to enable rapid cross-run comparison and reduce computational demands.
• Ion Intensity Count and Target Search: Provides ion intensity count and target search functionalities to focus quantification on specific peptides within datasets.

Scientific Applications:

• Shotgun proteomics quantification: Quantitative analysis of proteins in shotgun proteomics experiments.
• Large-scale comparative proteomics: Protein quantification across numerous samples for large-scale proteomic investigations.

Methodology:

Uses the MAPA strategy with precursor mass-to-charge precision of approximately 1 p.p.m.; performs automated precursor alignment across runs; employs ion intensity counting and target search; provides recommended MS settings.