Probability-based-matching algorithm with forward searching capabilities for matching unknown mass spectra of mixtures

Stauffer, Douglas B.; McLafferty, Fred W.; Ellis, Robert D.; Peterson, David W.

doi:10.1021/ac00283a021

Cited by 41 publications

(26 citation statements)

References 16 publications

(26 reference statements)

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“…It remains the primary method of analyzing GC-MS data. [14][15][16][17] The use of a library of authentic peptide spectra was impractical when protein identification was initially demonstrated. The main reasons that it was not employed were as follows:…”

Section: Introductionmentioning

confidence: 99%

Using Annotated Peptide Mass Spectrum Libraries for Protein Identification

et al. 2006

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A system for creating a library of tandem mass spectra annotated with corresponding peptide sequences was described. This system was based on the annotated spectra currently available in the Global Proteome Machine Database (GPMDB). The library spectra were created by averaging together spectra that were annotated with the same peptide sequence, sequence modifications, and parent ion charge. The library was constructed so that experimental peptide tandem mass spectra could be compared with those in the library, resulting in a peptide sequence identification based on scoring the similarity of the experimental spectrum with the contents of the library. A software implementation that performs this type of library search was constructed and successfully used to obtain sequence identifications. The annotated tandem mass spectrum libraries for the Homo sapiens, Mus musculus, and Saccharomyces cerevisiae proteomes and search software were made available for download and use by other groups.

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Section: Introductionmentioning

confidence: 99%

Using Annotated Peptide Mass Spectrum Libraries for Protein Identification

et al. 2006

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“…K , confidence index, which is a sum of individual values ( K i ) calculated for each examined mass spectral peak (originally probability that particular library spectrum corresponds to the unknown compound is estimated to be equal to 0.5 K · 100%); ∆Δ K , difference between K and K perfect match ( K perfect match corresponds to hypothetical situation when unknown and reference mass spectra are completely identical); the sum U i + A i corresponds to the probability of finding a mass spectral peak with a particular m / z value and certain intensity; W i corresponds to the probability of random coincidence of peaks in unknown and library spectrum; D is equal to 0 if pure unknown mass spectrum is considered. More detailed information about PBM algorithm can be found in the works of McLafferty's group …”

Section: Methodsmentioning

confidence: 99%

Evaluation of mass spectral library search algorithms implemented in commercial software

Samokhin

Lashin²,

Revelsky

2015

J. Mass Spectrom.

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Performance of several library search algorithms (against EI mass spectral databases) implemented in commercial software products ( acd/specdb, chemstation, gc/ms solution and ms search) was estimated. Test set contained 1000 mass spectra, which were randomly selected from NIST'08 (RepLib) mass spectral database. It was shown that composite (also known as identity) algorithm implemented in ms search (NIST) software gives statistically the best results: the correct compound occupied the first position in the list of possible candidates in 81% of cases; the correct compound was within the list of top ten candidates in 98% of cases. It was found that use of presearch option can lead to rejection of the correct answer from the list of possible candidates (therefore presearch option should not be used, if possible). Overall performance of library search algorithms was estimated using receiver operating characteristic curves.

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“…GC‐MS data files were processed using an original procedure for the automated purification of mass spectra from the total ion chromatogram . Purified mass spectra were submitted to search against the reference library using the probability‐based matching (PBM) algorithm . The method is able to identify over 300 acidic, neutral, and basic drugs of forensic interest at therapeutic and toxic levels.…”

Section: Methodsmentioning

confidence: 99%

“…Purified mass spectra were submitted to search against the reference library using the probability-based matching (PBM) algorithm (9). The method is able to identify over 300 acidic, neutral, and basic drugs of forensic interest at therapeutic and toxic levels.…”

Section: Systematic Toxicological Analysis By Gc-msmentioning

confidence: 99%

Analytical Challenge in Postmortem Toxicology Applied to a Human Body Found into a Lake after Three Years Immersion

Morini

Vignali

Tricomi

et al. 2015

Journal of Forensic Sciences

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The body of a 30-year-old woman was found in Como lake at a depth of about 120 meters in her own car after 3 years of immersion. The aim of this study was to evaluate psychoactive drugs as well as alcohol biomarkers in biological matrices. The following analyses were initially performed: GC-MS systematic toxicological analysis on biological fluids and tissues; GC-MS analysis of drugs of abuse on pubic hair; direct ethanol metabolite determination in pubic hair by LC-MS/MS. After 7 years, the samples, that had been stored at -20°C, were re-analyzed and submitted to an LC-MS/MS targeted screening method, using multiple reaction monitoring mode. These analyses detected citalopram (150-3000 ng/mL), desmethylcitalopram (50-2300 ng/mL), clotiapine (20-65 ng/mL), and ethyl glucuronide (97 pg/mg). The methods showed an acceptable reproducibility, and the concentrations of citalopram and desmethylcitalopram calculated through the two analytical techniques did not significantly differ in biological fluids.

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Probability-based-matching algorithm with forward searching capabilities for matching unknown mass spectra of mixtures

Cited by 41 publications

References 16 publications

Using Annotated Peptide Mass Spectrum Libraries for Protein Identification

Using Annotated Peptide Mass Spectrum Libraries for Protein Identification

Evaluation of mass spectral library search algorithms implemented in commercial software

Analytical Challenge in Postmortem Toxicology Applied to a Human Body Found into a Lake after Three Years Immersion

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