Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2023 Mar 29;14:1752. doi: 10.1038/s41467-023-37446-4

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Fig. 3 — The same MS2Query model was used for all test sets, for more details about the model used for the case studies, see Supplementary Note 1. A minimal threshold of 0.633 for the random forest score was used to determine if an analogue was selected. The threshold of 0.633 was selected, since this resulted in a recall of 35% for the “analogue test set”. Source data are provided as a Source Data file. a The variation of recall across case studies using the same settings. b The percentage of query spectra with a predicted analogue (precursor m/z > 1 Da) is compared to the percentage of spectra with an exact match predicted (precursor m/z < 1 Da) c Results were manually validated based on the retention time MS1 mass and MS2 spectra, by comparing to online libraries or in-house reference standards. These reference standards were used to judge the quality of the predicted analogues. In the Supplementary Note 6 more details about the validation can be found. For the anammox bacteria sample set, tentative validation was attempted for 50 features. d Three examples of predictions for mass spectra in the case studies. These examples came from the case study test sets LTR Urine, LTR Blood Plasma, and NIST Blood Plasma in that order. For LPC(20:4/0:0) the exact position of the double bonds could not be determined and was therefore guessed for the visualization.