title: High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for MS/MS de novo sequencing results.
abstract: With the increasing availability of de novo sequencing algorithms for interpreting high-mass accuracy tandem mass spectrometry (MS/MS) data, there is a growing need for programs that accurately identify proteins from de novo sequencing results. De novo sequences derived from tandem mass spectra of peptides often contain ambiguous regions where the exact amino acid order cannot be determined. One problem this poses for sequence alignment algorithms is the difficulty in distinguishing discrepancies due to de novo sequencing errors from actual genomic sequence variation and posttranslational modifications. We present a novel, mass-based approach to sequence alignment, implemented as a program called OpenSea, to resolve these problems. In this approach, de novo and database sequences are interpreted as masses of residues, and the masses, rather than the amino acid codes, are compared. To provide further flexibility, the masses can be aligned in groups, which can resolve many de novo sequencing errors. The performance of OpenSea was tested with three types of data: a mixture of known proteins, a mixture of unknown proteins that commonly contain sequence variations, and a mixture of posttranslationally modified known proteins. In all three cases, we demonstrate that OpenSea can identify more peptides and proteins than commonly used database-searching programs (SEQUEST and ProteinLynx) while accurately locating sequence variation sites and unanticipated posttranslational modifications in a high-throughput environment.
authors.affiliation: Department of Pediatrics, School of Dentistry, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239-3098, USA.
authors.forename: Brian C
authors.initials: BC
authors.lastname: Searle
authors.forename: Surendra
authors.initials: S
authors.lastname: Dasari
authors.forename: Mark
authors.initials: M
authors.lastname: Turner
authors.forename: Ashok P
authors.initials: AP
authors.lastname: Reddy
authors.forename: Dongseok
authors.initials: D
authors.lastname: Choi
authors.forename: Phillip A
authors.initials: PA
authors.lastname: Wilmarth
authors.forename: Ashley L
authors.initials: AL
authors.lastname: McCormack
authors.forename: Larry L
authors.initials: LL
authors.lastname: David
authors.forename: Srinivasa R
authors.initials: SR
authors.lastname: Nagalla
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D016208:Databases, Factual; D006801:Humans; D007908:Lens, Crystalline / Q000737:chemistry; D013058:Mass Spectrometry / Q000379:methods; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis / Q000737:chemistry; D011506:Proteins / Q000032:analysis* / Q000737:chemistry*; D012984:Software; D013997:Time Factors
chemical_list: D010455:Peptides; D011506:Proteins