PAAS 3: A computer program to determine probable sequence of peptides from mass spectrometric data

Sakurai, Toru; Matsuo, T.; Matsuda, Hisashi; Katakuse, Itsuo

doi:10.1002/bms.1200110806

Cited by 64 publications

(36 citation statements)

References 3 publications

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“…Over the years, there have been a number of algorithms described for the computer-aided interpretation of peptide mass spectra. One method 13,14 involves the generation of all amino acid combinations that account for the molecular mass of the peptide. From these amino acid compositions, all possible sequences are calculated and compared with the actual mass spectrum to determine which one best matches the data.…”

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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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“…One approach has involved the generation of all amino acid combinations that account for the peptide mass, and then compare predicted fragment ions with observed (26). However, this becomes computationally prohibitive for peptides beyond a length of about eight amino acids.…”

Section: Historical Backgroundmentioning

confidence: 99%

De Novo Sequencing and Homology Searching

Johnson

2012

Molecular & Cellular Proteomics

143

118

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In proteomics, de novo sequencing is the process of deriving peptide sequences from tandem mass spectra without the assistance of a sequence database. Such analyses have traditionally been performed manually by human experts, and more recently by computer programs that have been developed because of the need for higher throughput. Although powerful, de novo sequencing often can only determine partially correct sequence tags because of imperfect tandem mass spectra. However, these sequence tags can then be searched in a sequence database to identify the exact or a homologous peptide. Homology searches are particularly useful for the study of organisms whose genomes have not been sequenced. This tutorial will present background important to understanding de novo sequencing, suggestions on how to do this manually, plus descriptions of computer algorithms used to automate this process and to subsequently carryout homology-based database searches.

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PAAS 3: A computer program to determine probable sequence of peptides from mass spectrometric data

Abstract: The computer program PAAS 3 is developed to determine the probable amino acid sequences of a peptide from sequence ion peaks experimentally obtained by mass spectrometry.

Cited by 64 publications

References 3 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 and Homology Searching

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