Discriminating Facts from Artefacts in the Secreted Ly-6 Protein Family

1. Discriminating Facts from Artefacts in the Secreted Ly-6 Protein Family Christopher Southan Department of Molecular Pharmacology AstraZeneca R&D, M�lndal, Sweden

2. Outline Introduction Proteomic identification of novel secreted rat Ly6 proteins in EST data Discovery of unknown homologues Bioinformatic analysis of chimeric mRNAs Database errors propagated by the chimeras Delineating a large secreted Ly6 family on the rat genome Discovery of mouse homologues but no clear orthologues Equivocal biochemical results for homologues Summary of bioinformatic pitfalls

3. Introduction: Quirks that Lurk in Databases The sequence deluge into the primary databases necessitates automated pipelines to produce 'value added' secondary databases But, however sophisticated the data parsing or curation, anomalies will get through Most things that could have gone wrong, have Although the overall quirk frequency is low, they present pitfalls for the unwary Responsibility for primary annotation and sequence quality lies solely with submitting authors Few originating authors correct, update or withdraw their primary sequence entries It is difficult to discriminate between in vitro artifacts or rare in vivo events

4. Rat Urine ? HPLC ? Intact MALDI ? N-Terminal Sequence