Skip to main content
U.S. flag

An official website of the United States government

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.

Development of a Tool to Determine the Variability of Consensus Mass Spectra



Benjamin Place


The success of non-targeted analysis often depends on libraries containing reference mass spectra of known chemical compounds; the mass spectra of unknown compounds are compared to these reference mass spectra, leading to a probable compound identity. Typical calculations include the mean measured values for each ion m/z and intensity with no estimation of the variability of the measurement. This study presents a novel tool for the calculation of the variability of a measured mass spectrum, including the various data parameters that can impact the measured variability. Using perfluorooctanoic acid (PFOA) as the model compound, the variability of measured data-dependent fragmentation mass spectra (ddMS2) was calculated within replicate measurements of a simple solution of PFOA and a complex mixture (house dust extract) containing PFOA. The variability of the measured ddMS2 for PFOA in the solution and house dust extract were similar, with standard deviations about the measured m/z value ranged from m/z 0.00003 to 0.00015 and the standard deviations about the measured relative intensity ranged from 0.0077 to 0.0211 relative intensity units. In addition, the selected parameters for the extraction of ddMS2 from a single analytical run varied between the sample types due to the increased presence of background ions in the house dust extract. Finally, the variability of the ddMS2 spectra for PFOA in both samples was used to calculate a more robust similarity factor, informing the confidence of the identification of unknown compounds.
Journal of the American Society for Mass Spectrometry


mass spectrometry, uncertainty analysis, PFAS


Place, B. (2021), Development of a Tool to Determine the Variability of Consensus Mass Spectra, Journal of the American Society for Mass Spectrometry, [online],, (Accessed July 23, 2024)


If you have any questions about this publication or are having problems accessing it, please contact

Created March 8, 2021, Updated April 6, 2021