Probability based matching system using a large collection of reference mass spectra

Pesyna, Gail M.; Venkataraghavan, R.; Dayringer, Henry E.; McLafferty, Fred W.

doi:10.1021/ac50003a026

Cited by 146 publications

(93 citation statements)

References 12 publications

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“…Matching against the database should be used first, but its suggested identification(s) can and should always be checked manually (a step termed interpretation). For the first approach, I recommend (not surprisingly) the probability-based matching system (PBM) developed by my research group (48,49) because it is clearly superior for general (e.g., GC/MS) unknowns (50). PBM calculates the statistical reliability of its predictions by weighting the structural importance of its matching to mass, abundance, and other data.…”

Section: Databases Of Mass Spectra: Collecting and Searching 1950-2009mentioning

confidence: 99%

A Century of Progress in Molecular Mass Spectrometry

McLafferty

2011

Annual Rev. Anal. Chem.

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The first mass spectrum of a molecule was measured by J.J. Thomson in 1910. Mass spectrometry (MS) soon became crucial to the study of isotopes and atomic weights and to the development of atomic weapons for World War II. Its notable applications to molecules began with the quantitative analysis of light hydrocarbons during World War II. When I joined the Dow Chemical Company in 1950, MS was not favored by organic chemists. This situation improved only with an increased understanding of gaseous ion chemistry, which was obtained through the use of extensive reference data. Gas chromatography–MS was developed in 1956, and tandem MS was first used a decade later. In neutralization-reionization MS, an unusual, unstable species is prepared by ion-beam neutralization and characterized by reionization. Electrospray ionization of a protein mixture produces its corresponding ionized molecules. In top-down proteomics, ions from an individual component can be mass separated and subjected to collision-activated and electron-capture dissociation to provide extensive sequence information.

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Section: Databases Of Mass Spectra: Collecting and Searching 1950-2009mentioning

confidence: 99%

A Century of Progress in Molecular Mass Spectrometry

McLafferty

2011

Annual Rev. Anal. Chem.

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“…These can be viewed as independent peak occurrence probabilities. Related quantities have been used as weighting factors in library searching [18]. However, probabilities of finding more than one peak in a spectrum are far more complex.…”

Section: Peak Occurrence Probabilities and Correlationmentioning

confidence: 99%

On the risk of false positive identification using multiple ion monitoring in qualitative mass spectrometry: Large-scale intercomparisons with a comprehensive mass spectral library

Stein¹,

Heller

2006

J. Am. Soc. Mass Spectrom.

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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. We 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 identification. The influence of peak correlation among the specific ions in all the library mass spectra was also studied. Our computations showed that (1) false positive identifications can result from similar compounds, or low-abundance peaks in unrelated compounds if the method calls for detection at very low levels; (2) a MIM method's identification confidence improves in a roughly continuous manner as more ions are monitored, about one order of magnitude for each additional ion selected; (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. There are implications for residue chemists who would rely on standardized confirmation criteria to assess the validity of a given confirmatory method. For example, standardized confirmation criteria should not be used in the absence of interference testing and rational selection of diagnostic ions. (J Am Soc Mass Spectrom 2006, 17, 823-835)

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“…Of the several algorithms proposed for assigning structure to electron ionization [EI] spectra [7c, 13], the probability based matching (PBM) system [14] has the special features of "data weighting," shown to be critical for document retrieval from libraries [15], and "reverse searching" [14,16]. Demanding that all the mass values of the unknown spectrum be in the reference makes difficult the matching of mixture spectra; "reverse searching" instead only demands that the reference masses be in the unknown.…”

Section: Computer Data Acquisition Reduction and Interpretationmentioning

confidence: 99%

Billionfold data increase from mass spectrometry instrumentation

McLafferty

1997

J. Am. Soc. Mass Spectrom.

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Probability based matching system using a large collection of reference mass spectra

Cited by 146 publications

References 12 publications

A Century of Progress in Molecular Mass Spectrometry

A Century of Progress in Molecular Mass Spectrometry

On the risk of false positive identification using multiple ion monitoring in qualitative mass spectrometry: Large-scale intercomparisons with a comprehensive mass spectral library

Billionfold data increase from mass spectrometry instrumentation

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