An efficient algorithm for sequencing peptides using fast atom bombardment mass spectral data

Siegel, Marshall M.; Бауман, Н. А.

doi:10.1002/bms.1200150606

Cited by 42 publications

(18 citation statements)

References 13 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.

379

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.

379

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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“…Additionally, successful de novo sequencing requires full sequence coverage, thus demanding better quality spectra than those typically used for data base searching. Beginning with electron ionization spectra of peptides [11], and applied to FAB spectra [12], a method of developing small peptide sub-sequences that could be extended to progressively larger fragments was developed and later applied to both high and low energy CID spectra [13,14].…”

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confidence: 99%

De novo sequencing of peptides using MALDI/TOF-TOF

Yergey¹,

Coorssen

Backlund³

et al. 2002

J. Am. Soc. Mass Spectrom.

194

145

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The recently developed MALDI TOF-TOF instrument yields relatively complex but interpretable fragmentation spectra. When coupled with a straightforward sequence extension algorithm, it is possible to develop complete peptide sequences de novo from the spectra. This approach has been applied to a set of peptides derived from typtic digestion of electrophoretically separated sea urchin egg membrane proteins. When directed to proteins that have been described previously, the results were in essential agreement with those obtained by conventional data base searching approaches, with certain important exceptions. The present method detected errors in published sequences and was able to develop sequences from peptides differing in mass by one dalton (Da). These results show both the power of the present approach and the need for using de novo methods more frequently than may be otherwise appreciated. (J Am Soc Mass Spectrom 2002, 13, 784 -791)

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An efficient algorithm for sequencing peptides using fast atom bombardment mass spectral data

Cited by 42 publications

References 13 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

De novo sequencing of peptides using MALDI/TOF-TOF

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