biostudies-literatureEriksson JOFru Berta Kamprads StiftelseDutch Research Council (NWO)16138-16148https://www.ebi.ac.uk/biostudies/studies/S-EPMC7745203biostudies-literatureUnknown92(24)Mass spectrometry imaging (MSI) is a technique that provides comprehensive molecular information with high spatial resolution from tissue. Today, there is a strong push toward sharing data sets through public repositories in many research fields where MSI is commonly applied; yet, there is no standardized protocol for analyzing these data sets in a reproducible manner. Shifts in the mass-to-charge ratio (<i>m</i>/<i>z</i>) of molecular peaks present a major obstacle that can make it impossible to distinguish one compound from another. Here, we present a label-free <i>m</i>/<i>z</i> alignment approach that is compatible with multiple instrument types and makes no assumptions on the sample's molecular composition. Our approach, MSIWarp (https://github.com/horvatovichlab/MSIWarp), finds an <iAnalytical chemistryMSIWarp: A General Approach to Mass Alignment in Mass Spectrometry Imaging.PMC7745203184.034.019Marko-Varga GSuits FEriksson JOHorvatovich PSanchez Brotons ARezeli MfalseMSIWarp: A General Approach to Mass Alignment in Mass Spectrometry Imaging.Mass spectrometry imaging (MSI) is a technique that provides comprehensive molecular information with high spatial resolution from tissue. Today, there is a strong push toward sharing data sets through public repositories in many research fields where MSI is commonly applied; yet, there is no standardized protocol for analyzing these data sets in a reproducible manner. Shifts in the mass-to-charge ratio (<i>m</i>/<i>z</i>) of molecular peaks present a major obstacle that can make it impossible to distinguish one compound from another. Here, we present a label-free <i>m</i>/<i>z</i> alignment approach that is compatible with multiple instrument types and makes no assumptions on the sample's molecular composition. Our approach, MSIWarp (https://github.com/horvatovichlab/MSIWarp), finds an <i2020-01-01T00:00:00Z2020 Dec2025-04-26T09:09:06.641Z2025-04-06T12:56:16.218ZS-EPMC77452033331727210.1021/acs.analchem.0c03833