Computer identification of infrared spectra by correlation-based file searching

Powell, Linda A.; Hieftje, Gary M.

doi:10.1016/s0003-2670(01)93327-6

Cited by 45 publications

(26 citation statements)

References 11 publications

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“…The same trend is observed with the Genpept database (data not shown). A related trend was observed when correlation analysis of infrared library spectra [30] was used. Rankings by both scoring procedures are included in Table 2.…”

Section: Database Searching With Tandem Massmentioning

confidence: 67%

“…A cross-correlation analysis is used to compare the top 500 identified ammo acid sequences obtained from the search with the experimental data. This method has been employed to provide a measurement of spectral similarity for infrared library searches [30] and has been reviewed it length by Owen [31] for use in mass spectral analysis. To compare the amino acid sequences obtained from the database search to the acquired tandem mass spectrum by using a correlation analysis, a "spectrum" is reconstructed from the character-based ammo acid sequences.…”

Section: Database Searching With Tandem Massmentioning

confidence: 99%

“…A graphical output of the crosscorrelation of the two "spectra," Figure 2b and c, is shown in Figure 2d. The final score attributed to each candidate peptide sequence is the value of the function when 7 = 0 minus the mean of the cross-correlation function over the range -75 < 7 < 75 [30]. The scores are normalized to 1.0 and termed C,.…”

Section: Database Searching With Tandem Massmentioning

confidence: 99%

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An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

Eng

McCormack

Yates

1994

J. Am. Soc. Mass Spectrom.

6,267

5,480

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A method to correlate the uninterpreted tandem mass spectra of peptides produced under low energy (lo-50 eV) collision conditions with amino acid sequences in the Genpept database has been developed. In this method the protein database is searched to identify linear amino acid sequences within a mass tolerance of * 1 u of the precursor ion molecular weight. A cross-correlation function is then used to provide a measurement of similarity between the mass-to-charge ratios for the fragment ions predicted from amino acid sequences obtained from the database and the fragment ions observed in the tandem mass spectrum. In general, a difference greater than 0.1 between the normalized cross-correlation functions of the first-and second-ranked search results indicates a successfol match between sequence and spectrum. Searches of species-specific protein databases with tandem mass spectra acquired from peptides obtained from the enzymatically digested total proteins of E. coli and S. cerevisiae cells allowed matchmg of the spectra to amino acid sequences within proteins of these organisms. The approach described in this manuscript provides a convenient method to interpret tandem mass spectra with known sequences in a protein database, fJ Am Sot Mass Spectrom 1994, 5, 976-989) A mino acid sequence analysis is often the initial step in characterizing a newly isolated protein.Conventional sequencing strategies employ chemical reagents to remove one amino acid at a time from the amino terminus followed by isolation and analysis of the released amino acid derivative [l, 21. Limitations in the chemical efficiency of the process prevents determination of the complete sequence of a protein from small quantities of sample. Partial sequence information, however, can be used to search a protein or nucleotide database to discover relationships to previously identified proteins or to determine if the protein sequence is novel 13, 41. Although sequence information may have been determined previously, the context in which the protein is identified may be relevant to the biological process under study [51. Another method to identify known protein sequences employs site-specific proteolysis followed by measurement of the mass-to-charge ratios of the pep tides by mass spectrometry. The set of observed peptide mass-to-charge ratios is then used to search a protein database to find a set of peptide masses predicted from enzymatic digestion of each protein in the database [6-101. Both chemical degradation and peptide mapping approaches require the use of fairly homogeneous samples to avoid ambiguity in assigning Address reprint requests to John R.

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Section: Database Searching With Tandem Massmentioning

confidence: 67%

Section: Database Searching With Tandem Massmentioning

confidence: 99%

Section: Database Searching With Tandem Massmentioning

confidence: 99%

See 1 more Smart Citation

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

Eng

McCormack

Yates

1994

J. Am. Soc. Mass Spectrom.

6,267

5,480

View full text Add to dashboard Cite

show abstract

“…In a previous study, Hieftje and Powell 22 used cross-correlation to perform library searching. However, their approach to spectral matching was limited to comparing the midpoint of the cross-correlation of the unknown and each library spectrum using the average value in a 20-point window to normalize the midpoint.…”

Section: Methodsmentioning

confidence: 99%

Pattern Recognition-Assisted Infrared Library Searching of Automotive Clear Coats

et al. 2015

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Pattern recognition techniques have been developed to search the infrared (IR) spectral libraries of the paint data query (PDQ) database to differentiate between similar but nonidentical IR clear coat paint spectra. The library search system consists of two separate but interrelated components: search prefilters to reduce the size of the IR library to a specific assembly plant or plants corresponding to the unknown paint sample and a cross-correlation searching algorithm to identify IR spectra most similar to the unknown in the subset of spectra identified by the prefilters. To develop search prefilters with the necessary degree of accuracy, IR spectra from the PDQ database were preprocessed using wavelets to enhance subtle but significant features in the data. Wavelet coefficients characteristic of the assembly plant of the vehicle were identified using a genetic algorithm for pattern recognition and feature selection. A search algorithm was then used to cross-correlate the unknown with each IR spectrum in the subset of library spectra identified by the search prefilters. Each cross-correlated IR spectrum was simultaneously compared to an autocorrelated IR spectrum of the unknown using several spectral windows that span different regions of the cross-correlated and autocorrelated data from the midpoint. The top five hits identified in each search window are compiled, and a histogram is computed that summarizes the frequency of occurrence for each selected library sample. The five library samples with the highest frequency of occurrence are selected as potential hits. Even in challenging trials where the clear coat paint samples evaluated were all the same make (e.g., General Motors) within a limited production year range, the model of the automobile from which the unknown paint sample was obtained could be identified from its IR spectrum.

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“…[42] DD-WP 237728; Holand, W.; Naumann, K.; Vogel, W. [43] Holand, W.; Naumann, K.; Vogel, W.: Wiss [52], [53] [73], [74]. UnabhLngig davon, ob Interferogramme oder Spektren verglichen werden, liefert eine Kopplung GC/FT-IR eine Zusatzinformation in Form der Retentionszeiten der jeweiligen Peaks.…”

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Stand und Entwicklungstendenzen des computergestützten Vergleichs von Infrarotspektren

Schaarschmidt

1982

Zeitschrift fuer Chemie

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Computer identification of infrared spectra by correlation-based file searching

Cited by 45 publications

References 11 publications

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

Pattern Recognition-Assisted Infrared Library Searching of Automotive Clear Coats

Stand und Entwicklungstendenzen des computergestützten Vergleichs von Infrarotspektren

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