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On the Risk of False Positive Identification Using Multiple Ion Monitoring in Qualitative Mass Spectrometry: Large-Scale Intercomparisons With a Comprehensive Mass Spectral Library



Stephen E. Stein, David N. Heller


Analysts involved in qualitative mass spectrometry have long debated the minimum data requirements for demonstrating that signals from an unknown sample are identical to those from a known compound. Often this process is carried out by comparing a few selected ions acquired by multiple ion monitoring (MIM), with due allowance for expected variability in response. In a few past experiments with electron-ionization mass spectrometry (EI-MS), the number of ions selected and the allowable variability in relative abundance were tested by comparing one spectrum against a library of mass spectra, where library spectra served to represent potential false positive signals in an analysis. Such experiments supported the selection of three or more diagnostic ions for maximum identification confidence. These peak constraints are known as confirmation criteria. We have extended these experiments by carrying out large-scale intercomparisons between thousands of spectra and a library of one hundred thousand EI mass spectra. The results were analyzed to gain insights into the identification confidence associated with various numbers of selected ions. A new parameter was investigated for the first time, to take into account that a library spectrum with a different base peak than the search spectrum may still cause a false positive identificationThe influence of peak correlation among the specific ions in all the library mass spectra was also studied. These analyses showed that false positive probability decreases roughly one order of magnitude for each additional ion selected. Our computations also showed that false positive identifications can result from low-abundance peaks in unrelated compounds, if the method calls for detection at very low levels. The results establish that standardized confirmation criteria do not result in the same identification confidence when applied to compounds with different structures. In other words, standardized confirmation criteria cannot be configured to act with the same degree of confidence in all cases. There are implications for residue chemists who would rely on standardized confirmation criteria to assess the validity of a given confirmatory method: (1) Standardized confirmation criteria should not be used in the absence of interference testing, rational selection of diagnostic ions, and an evaluation of the existence of similar compounds; (2) A MIM method s identification confidence improves in a roughly continuous manner as more ions are monitored; (3) full scan spectra still represent the best alternative, if instrument sensitivity is adequate. The use of large scale intercomparisons with a comprehensive library is the only way to provide direct evidence in support of these conclusions, which otherwise depend on the judgment and experience of individual analysts.
Journal of the American Society for Mass Spectrometry
No. 6


El-MS, electron-ionization mass spectrometry, identification, mass spectral library, multiple ion monitoring (MIM), qualitative mass spectrometry


Stein, S. and Heller, D. (2006), On the Risk of False Positive Identification Using Multiple Ion Monitoring in Qualitative Mass Spectrometry: Large-Scale Intercomparisons With a Comprehensive Mass Spectral Library, Journal of the American Society for Mass Spectrometry (Accessed April 14, 2024)
Created June 1, 2006, Updated February 17, 2017