title: Sequence protein identification by randomized sequence database and transcriptome mass spectrometry (SPIDER-TMS): from manual to automatic application of a 'de novo sequencing' approach.
abstract: Sequence protein identification by a randomized sequence database and transcriptome mass spectrometry software package has been developed at the University of Basilicata in Potenza (Italy) and designed to facilitate the determination of the amino acid sequence of a peptide as well as an unequivocal identification of proteins in a high-throughput manner with enormous advantages of time, economical resource and expertise. The software package is a valid tool for the automation of a de novo sequencing approach, overcoming the main limits and a versatile platform useful in the proteomic field for an unequivocal identification of proteins, starting from tandem mass spectrometry data. The strength of this software is that it is a user-friendly and non-statistical approach, so protein identification can be considered unambiguous.
authors.affiliation: Scuola di Ingegneria, Università degli Studi della Basilicata, Via dell'Ateneo Lucano, 10-85100 Potenza, Italy.
authors.forename: Raffaella
authors.initials: R
authors.lastname: Pascale
authors.affiliation: Dipartimento di Scienze, Università degli Studi della Basilicata, Via dell'Ateneo Lucano, 10-85100 Potenza, Italy.
authors.forename: Gerarda
authors.initials: G
authors.lastname: Grossi
authors.affiliation: Dipartimento di Chimica, Università di Perugia, via Elce di Sotto, 8-06123 Perugia, Italy.
authors.forename: Gabriele
authors.initials: G
authors.lastname: Cruciani
authors.affiliation: Dipartimento di Matematica, Informatica ed Economia, Via dell'Ateneo Lucano, 10-85100 Potenza, Italy.
authors.forename: Giansalvatore
authors.initials: G
authors.lastname: Mecca
authors.affiliation: Dipartimento di Matematica, Informatica ed Economia, Via dell'Ateneo Lucano, 10-85100 Potenza, Italy.
authors.forename: Donatello
authors.initials: D
authors.lastname: Santoro
authors.affiliation: Studio di Ingegneria, via Aldo Moro, 52-85010 Pignola (Pz), Italy.
authors.forename: Renzo
authors.initials: R
authors.lastname: Sarli Calace
authors.affiliation: Dipartimento di Scienze, Università degli Studi della Basilicata, Via dell'Ateneo Lucano, 10-85100 Potenza, Italy. patrizia.falabella@unibas.it.
authors.forename: Patrizia
authors.initials: P
authors.lastname: Falabella
authors.affiliation: Dipartimento di Scienze, Università degli Studi della Basilicata, Via dell'Ateneo Lucano, 10-85100 Potenza, Italy. giuliana.bianco@unibas.it.
authors.forename: Giuliana
authors.initials: G
authors.lastname: Bianco
mesh_terms: D000595:Amino Acid Sequence; D057225:Data Mining / Q000379:methods; D030562:Databases, Protein; D057166:High-Throughput Screening Assays / Q000379:methods*; D008969:Molecular Sequence Data; D010449:Peptide Mapping / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods*; D059467:Transcriptome