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An assessment of AcquireX and Compound Discoverer software 3.3 for non-targeted metabolomics.

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Title: An assessment of AcquireX and Compound Discoverer software 3.3 for non-targeted metabolomics.
Authors: Cooper, Bret1 (AUTHOR) bret.cooper@ars.usda.gov, Yang, Ronghui1 (AUTHOR)
Source: Scientific Reports. 2/28/2024, Vol. 14 Issue 1, p1-13. 13p.
Subject Terms: *METABOLOMICS, *FALSE discovery rate, *EXPLORERS, *SINGLE parents, *CHEMICAL libraries, *SPECTRAL imaging
Company/Entity: MICROSOFT Corp. 081466849 MSFT
Abstract: We used the Exploris 240 mass spectrometer for non-targeted metabolomics on Saccharomyces cerevisiae strain BY4741 and tested AcquireX software for increasing the number of detectable compounds and Compound Discoverer 3.3 software for identifying compounds by MS2 spectral library matching. AcquireX increased the number of potentially identifiable compounds by 50% through six iterations of MS2 acquisition. On the basis of high-scoring MS2 matches made by Compound Discoverer, there were 483 compounds putatively identified from nearly 8000 candidate spectra. Comparisons to 20 amino acid standards, however, revealed instances whereby compound matches could be incorrect despite strong scores. Situations included the candidate with the top score not being the correct compound, matching the same compound at two different chromatographic peaks, assigning the highest score to a library compound much heavier than the mass for the parent ion, and grouping MS2 isomers to a single parent ion. Because the software does not calculate false positive and false discovery rates at these multiple levels where such errors can propagate, we conclude that manual examination of findings will be required post software analysis. These results will interest scientists who may use this platform for metabolomics research in diverse disciplines including medical science, environmental science, and agriculture. [ABSTRACT FROM AUTHOR]
Copyright of Scientific Reports is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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  Data: An assessment of AcquireX and Compound Discoverer software 3.3 for non-targeted metabolomics.
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  Data: <searchLink fieldCode="JN" term="%22Scientific+Reports%22">Scientific Reports</searchLink>. 2/28/2024, Vol. 14 Issue 1, p1-13. 13p.
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  Data: *<searchLink fieldCode="DE" term="%22METABOLOMICS%22">METABOLOMICS</searchLink><br />*<searchLink fieldCode="DE" term="%22FALSE+discovery+rate%22">FALSE discovery rate</searchLink><br />*<searchLink fieldCode="DE" term="%22EXPLORERS%22">EXPLORERS</searchLink><br />*<searchLink fieldCode="DE" term="%22SINGLE+parents%22">SINGLE parents</searchLink><br />*<searchLink fieldCode="DE" term="%22CHEMICAL+libraries%22">CHEMICAL libraries</searchLink><br />*<searchLink fieldCode="DE" term="%22SPECTRAL+imaging%22">SPECTRAL imaging</searchLink>
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– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: We used the Exploris 240 mass spectrometer for non-targeted metabolomics on Saccharomyces cerevisiae strain BY4741 and tested AcquireX software for increasing the number of detectable compounds and Compound Discoverer 3.3 software for identifying compounds by MS2 spectral library matching. AcquireX increased the number of potentially identifiable compounds by 50% through six iterations of MS2 acquisition. On the basis of high-scoring MS2 matches made by Compound Discoverer, there were 483 compounds putatively identified from nearly 8000 candidate spectra. Comparisons to 20 amino acid standards, however, revealed instances whereby compound matches could be incorrect despite strong scores. Situations included the candidate with the top score not being the correct compound, matching the same compound at two different chromatographic peaks, assigning the highest score to a library compound much heavier than the mass for the parent ion, and grouping MS2 isomers to a single parent ion. Because the software does not calculate false positive and false discovery rates at these multiple levels where such errors can propagate, we conclude that manual examination of findings will be required post software analysis. These results will interest scientists who may use this platform for metabolomics research in diverse disciplines including medical science, environmental science, and agriculture. [ABSTRACT FROM AUTHOR]
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  Data: <i>Copyright of Scientific Reports is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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              Text: 2/28/2024
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