msPurity

msPurity calculates precursor purity in tandem mass spectrometry (MS/MS) data to quantify the contribution of targeted precursor ions within isolation windows for LC-MS/MS and direct infusion (DI) MS/MS experiments.

Key Features:

• Precursor Purity Metric: Computes precursor purity as the intensity of the selected precursor divided by the summed intensity of all ions within the isolation window.
• Data Processing: Applies averaging, filtering, and blank subtraction to DI and LC-MS/MS datasets prior to purity calculation.
• Interpolation of MS² Acquisition Points: Interpolates the precursor purity metric at recorded MS² acquisition points using bordering full-scan spectra.
• Isotopic and Low-Abundance Peak Removal: Removes isotopic peaks of the selected precursor and low-abundance peaks unlikely to impact MS² spectra.
• Isolation Efficiency Consideration: Accounts for the instrument's isolation efficiency when estimating precursor contribution.
• Implementation: Provided as a vendor-independent implementation (R package) for processing mass spectrometry data.
• Data Support: Supports analysis of Data-Dependent Acquisition (DDA) MS² datasets and assessment of theoretical isolation windows.

Scientific Applications:

• Quality assessment of DDA metabolomics data: Applied to DDA-based MS² metabolomics datasets from multiple repositories to evaluate precursor contribution and data reliability.
• LC-MS/MS isolation window evaluation: Used on LC-MS/MS datasets with isolation windows >±1 Da, yielding median precursor purity scores from 0.67 to 0.96 across datasets.
• Theoretical isolation window analysis: Assessed theoretical ±0.5 Da isolation windows on LC-MS datasets, reporting a median purity of 0.46 for 64,498 features in the most complex samples and 0.66 for 5,071 features in less complex samples.
• Informing spectral matching and annotation: Identifies low-purity (<0.5) spectra that may produce unreliable spectral matching and metabolite annotation, analogous to observations in proteomics.

Methodology:

Calculates the ratio of selected precursor intensity to total ion intensity in the isolation window, with preprocessing via averaging, filtering, and blank subtraction; interpolates purity at MS² acquisition points using bordering full-scan spectra; removes isotopic and low-abundance peaks; and accounts for instrument isolation efficiency.