MSI-R

MSI-R performs adaptive pixel mass recalibration of mass spectrometry imaging (MSI) data to correct spectrum-specific mass shifts and improve molecular annotation accuracy.

Key Features:

• Per-pixel spectral recalibration: Recalibrates each spectrum individually by estimating its specific mass shift.
• Data-adaptive internal calibrants: Generates lists of pixel-specific internal calibrating ions automatically in a data-adaptive manner.
• Mass-shift mitigation across image and m/z range: Addresses mass shifts arising from pixel-to-pixel ion count variability across the entire image and m/z range.
• False-positive reduction: Uses adaptive, pixel-specific calibrants rather than global standards to minimize the risk of false positive annotations.
• High-resolution MSI support: Applied to and compatible with high-resolution MSI datasets, including whole-body tissue sections.

Scientific Applications:

• High-resolution zebrafish whole-body MSI: Validated on a high-resolution zebrafish whole-body section MSI dataset to mitigate mass shift impacts.
• Public METASPACE datasets: Recalibrated 31 diverse public MSI datasets from METASPACE spanning various sample types and MSI methods.
• Molecular annotation improvement: Increased the number of annotations in tested datasets by up to 400 additional entries and improved high-confidence annotations with a low false discovery rate.

Methodology:

Recalibration is performed by estimating spectrum-specific mass shifts using automatically generated lists of pixel-specific internal calibrating ions in a data-adaptive manner.