title: Discovery of neuropeptides in the nematode Ascaris suum by database mining and tandem mass spectrometry.
abstract: Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was used to discover peptides in extracts of the large parasitic nematode Ascaris suum. This required the assembly of a new database of known and predicted peptides. In addition to those already sequenced, peptides were either previously predicted to be processed from precursor proteins identified in an A. suum library of expressed sequence tags (ESTs) or newly predicted from a library of A. suum genome survey sequences (GSSs). The predicted MS/MS fragmentation patterns of this collection of real and putative peptides were compared with the actual fragmentation patterns found in the MS/MS spectra of peptides fractionated by MS; this enabled individual peptides to be sequenced. Many previously identified peptides were found, and 21 novel peptides were discovered. Thus, this approach is very useful, despite the fact that the available GSS database is still preliminary, having only 1× coverage.
authors.affiliation: Neuroscience Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors.forename: Jessica L
authors.initials: JL
authors.lastname: Jarecki
authors.forename: Brian L
authors.initials: BL
authors.lastname: Frey
authors.forename: Lloyd M
authors.initials: LM
authors.lastname: Smith
authors.forename: Antony O
authors.initials: AO
authors.lastname: Stretton
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D017165:Ascaris suum / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D002853:Chromatography, Liquid; D057225:Data Mining / Q000379:methods*; D030562:Databases, Protein; D020224:Expressed Sequence Tags / Q000737:chemistry; D056726:Genetic Association Studies / Q000379:methods*; D049751:Genome, Helminth; D006257:Head; D008969:Molecular Sequence Data; D009479:Neuropeptides / Q000032:analysis* / Q000737:chemistry / Q000235:genetics; D010446:Peptide Fragments / Q000032:analysis* / Q000737:chemistry; D019151:Peptide Library; D040901:Proteomics / Q000379:methods*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013552:Swine; D053719:Tandem Mass Spectrometry; D014357:Trypsin / Q000378:metabolism
chemical_list: D009479:Neuropeptides; D010446:Peptide Fragments; D019151:Peptide Library; D014357:Trypsin