Computer-aided peptide sequencing by fast atom bombardment mass spectrometry

Ishikawa, Keiichiro; Niwa, Yoshio

doi:10.1002/bms.1200130709

Cited by 47 publications

(24 citation statements)

References 23 publications

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“…An alternative algorithm, that was first demonstrated on data obtained from electron ionization (EI) mass spectra of peptide derivatives, 15 and was subsequently used on fast-atom bombardment (FAB), 16,17 highenergy CID 18 and low-energy CID 19,20 data is sometimes referred to as 'subsequencing'. In this approach, small sequences that represent only a portion of the total sequence are tested against the mass spectrum.…”

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confidence: 99%

Sequence database searches viade novo peptide sequencing by tandem mass spectrometry

Taylor

Johnson

1997

Rapid Commun. Mass Spectrom.

382

279

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A method is described for searching protein sequence databases using tandem mass spectra of tryptic peptides. The approach uses a de novo sequencing algorithm to derive a short list of possible sequence candidates which serve as query sequences in a subsequent homology-based database search routine. The sequencing algorithm employs a graph theory approach similar to previously described sequencing programs. In addition, amino acid composition, peptide sequence tags and incomplete or ambiguous Edman sequence data can be used to aid in the sequence determinations. Although sequencing of peptides from tandem mass spectra is possible, one of the frequently encountered difficulties is that several alternative sequences can be deduced from one spectrum. Most of the alternative sequences, however, are sufficiently similar for a homology-based sequence database search to be possible. Unfortunately, the available protein sequence database search algorithms (e.g. Blast or FASTA) require a single unambiguous sequence as input. Here we describe how the publicly available FASTA computer program was modified in order to search protein databases more effectively in spite of the ambiguities intrinsic in de novo peptide sequencing algorithms.

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confidence: 99%

Sequence database searches viade novo peptide sequencing by tandem mass spectrometry

Taylor

Johnson

1997

Rapid Commun. Mass Spectrom.

382

279

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“…De novo sequencing [17][18][19][20][21][22] has become a method of prominent importance in the field of functional proteomics. De novo sequencing is necessary because database search procedures [23,24] often fail if the proteins are modified, unknown, mutated, artificially created via, e.g., combinatorial techniques, are from unknown species or cancerous cells [25].…”

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confidence: 99%

“…Basic residues (as strong proton acceptors) in the middle of a peptide sequence almost regularly lead to highly complicated fragmentation spectra which can be very difficult to interpret unequivocally. Several algorithms for de novo sequencing were reported [17][18][19][20][21][22], but none of them has been shown to be absolutely reliable and efficient if MS-MS data were obtained from non-ideal fragmentation processes. They use experience based or learned information about fragmentation behavior of peptides.…”

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confidence: 99%

De novo sequencing, peptide composition analysis, and composition-based sequencing: A new strategy employing accurate mass determination by fourier transform ion cyclotron resonance mass spectrometry

Spengler

2004

J. Am. Soc. Mass Spectrom.

133

104

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A new strategy is described for the determination of amino acid sequences of unknown peptides. Different from the well-known but often inefficient de novo sequencing approach, the new method is based on a two-step process. In the first step the amino acid composition of an unknown peptide is determined on the basis of accurate mass values of the peptide precursor ion and a small number of accurate fragment ion mass values, and, as in de novo sequencing, without employing protein database information or other pre-information. In the second step the sequence of the found amino acids of the peptide is determined by scoring the agreement between expected and observed fragment ion signals of the permuted sequences. It was found that the new approach is highly efficient if accurate mass values are available and that it easily outstrips common approaches of de novo sequencing being based on lower accuracies and detailed knowledge of fragmentation behavior. Simple permutation and calculation of all possible amino acid sequences, however, is only efficient if the composition is known or if possible compositions are at least reduced to a small list. The latter requires the highest possible instrumental mass accuracy, which is currently provided only by fourier transform ion cyclotron resonance mass spectrometry. The connection between mass accuracy and peptide composition variability is described and an example of peptide compositioning and composition-based sequencing is presented. (J Am Soc Mass Spectrom 2004, 15, 703-714)

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“…To assist in the sequencing of peptides by MS/MS, another computer program called LUTEFISK was written in-house, which uses only the MS/MS data from low-energy collision-induced dissociations of multiply-charged precursors to derive a list of possible sequences (Johnson et al, 1991). This program is conceptually similar to that used by others (Ishikawa & Niwa, 1986;Johnson & Biemann, 1989;Yates et al, 1991). As with MADMAE, the LUTEFISK output scores correspond to the fraction of product ion current that can be accounted for according to the fragmentations shown in Scheme 1.…”

Section: Resultsmentioning

confidence: 94%

Sequence analysis of peptide mixtures by automated integration of Edman and mass spectrometric data

Johnson

Walsh

1992

Protein Science

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A computer algorithm is described that utilizes both Edman and mass spectrometric data for simultaneous determination of the amino acid sequences of several peptides in a mixture. Gas phase sequencing of a peptide mixture results in a list of observed amino acids for each cycle of Edman degradation, which by itself may not be informative and typically requires reanalysis following additional chromatographic steps. Tandem mass spectrometry, on the other hand, has a proven ability to analyze sequences of peptides present in mixtures. However, mass spectrometric data may lack a complete set of sequence-defining fragment ions, so that more than one possible sequence may account for the observed fragment ions. A combination of the two types of data reduces the ambiguity inherent in each. The algorithm first utilizes the Edman data to determine all hypothetical sequences with a calculated mass equal to the observed mass of one of the peptides present in the mixture. These sequences are then assigned figures of merit according to how well each of them accounts for the fragment ions in the tandem mass spectrum of that peptide. The program was tested on tryptic and chymotryptic peptides from hen lysozyme, and the results are compared with those of another computer program that uses only mass spectral data for peptide sequencing. In order to assess the utility of this method the program is tested using simulated mixtures of varying complexity and tandem mass spectra of varying quality.

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Computer-aided peptide sequencing by fast atom bombardment mass spectrometry

Cited by 47 publications

References 23 publications

Sequence database searches viade novo peptide sequencing by tandem mass spectrometry

Sequence database searches viade novo peptide sequencing by tandem mass spectrometry

De novo sequencing, peptide composition analysis, and composition-based sequencing: A new strategy employing accurate mass determination by fourier transform ion cyclotron resonance mass spectrometry

Sequence analysis of peptide mixtures by automated integration of Edman and mass spectrometric data

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