TagGraph

TagGraph identifies and characterizes protein post-translational modifications (PTMs) from large tandem mass spectrometry datasets to expand and validate PTM assignments across proteomes.

Key Features:

• Unrestricted string-based search: Employs an unrestricted string-based search approach that enables comprehensive exploration of vast PTM search spaces across diverse proteomes and is reported up to 350-fold faster than existing methods.
• Probabilistic validation model: Incorporates a probabilistic validation model optimized for PTM assignments to distinguish correct from incorrect spectrum interpretations and increase confidence in identifications.

Scientific Applications:

• Large-scale human proteome analysis: Applied to a human proteomic dataset comprising 25 million mass spectra.
• Improved spectrum identification: Tripled the number of confident spectrum identifications compared to the original analysis of the dataset.
• Broad PTM discovery: Enabled discovery of thousands of modification types across nearly one million sites in the proteome.
• Biological insight into specific PTMs: Revealed alternative contexts for abundant modifications such as proline hydroxylation and uncovered associations between certain PTMs and cancer mutations.

Methodology:

Combines an unrestricted string-based search approach (reported up to 350-fold faster) with a probabilistic validation model specifically optimized for PTM assignment.