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. 2023 Jul 11;14:4113. doi: 10.1038/s41467-023-39889-1

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a On a dataset of 184 repeated samples analyzed on an Orbitrap ID-X mass spectrometer (HZV029), XCMS generated 10,901 features and MZmine generated 42,099 features (see Supplementary Methods for versions and parameters). Between the two results, 6186 features are uniquely matched. Additional comparisons are reported in Supplementary Tables 1, 2. b Many mismatched features are due to failure to resolve reciprocal best match. This example shows all 3 features in XCMS match to all 5 features in MZmine. Retention time (rtime) is in seconds. c Illustration of mSelectivity as a function of how distinct a m/z value is, regarding to its neighboring features and mass resolution. Each dot represents a m/z feature, and its mSelectivity value (Y axis) depends on the horizontal distance to neighbor features. The error in matching m/z values is modeled as a Gaussian distribution dependent on mass resolution, and mSelectivity is low when a feature has neighbors with close m/z values. d Distribution of mSelectivity in the features produced by three processing tools. Feature m/z values are rounded to the 3rd decimal place, so that minor variations are ignored and split peaks are not taken into account. Rounding has no impact on asari, because asari m/z values are linked to mass tracks. Source data are provided as a Source Data file.