1. Email: help@uniprot.org URL: www.uniprot.org European Bioinformatics Institute (EMBL-EBI) Swiss Institute of Bioinformatics (SIB) Protein Information Resource (PIR ) Capturing Protein Sequence Data Paul Browne 1, Ruth Eberhardt 1 and the UniProt Consortium 1,2,3 1 European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK 2 Swiss Institute of Bioinformatics, Geneva, Switzerland 3 Protein Information Resource, Georgetown University, Washington DC, USA Protein submission with SPIN Most of the sequences in UniProtKB are derived from the conceptual translation of nucleotide sequences. The aim of the submission project is to facilitate the incorporation into UniProtKB/Swiss-Prot of peptide sequence, obtained directly using techniques such as Edman degradation and MS/MS. In addition to capturing sequence data that might not otherwise find its way into UniProtKB, for example venom toxin or insect antimicrobial peptide sequence, they can confirm that a protein exists and identify the true N- terminus. They are a valuable source of information concerning the post- translational modification of proteins and are often accompanied by function and expression data. The web based sequence submission tool SPIN was introduced in late 2003. SPIN enables users to submit peptide sequence along with structural and functional annotation, citations, and details about the source organism of the peptide. SPIN can be found at: http://www.ebi.ac.uk/swissprot/Submissions/spin/ Submissions are processed within 7 working days of receipt and the submitter is then sent either notification of which accession numbers have been assigned to their sequences or a request for additional information that we require before we can send the numbers to them. A submitter may request that a sequence be kept confidential until an associated journal article is published, or until a date of their choosing. Acknowledgements UniProt is supported by grants from the National Institutes of Health, European Commission, Swiss Federal Government and PATRIC BRC. European Bioinformatics Institute P. centralis Bulk submission P. granulatus S. lycopersicum We have recently received several submissions of more than a hundred entries. These are currently dealt with on an ad hoc basis, but if the number of such bulk submissions continues to rise we will develop submission tools specifically for them to ensure that we continue to capture this valuable information. Journal scanning Protein submission via SPIN since 2004 In addition to the peptide sequences we receive via SPIN we also regularly check the scientific literature for papers that report peptide sequence, creating about one hundred entries per year. Some very heavily modified proteins enter UniProtKB/Swiss–Prot through this route, for example Amatoxin from the Death cap fungus Amanita phalloides. UniProtKB/Swiss-Prot submission and journal scan entries are a valuable resource that not only add sequence that might otherwise be missed but also provide experimental confirmation of the predictions made by sequence analysis software. Ultimately this information improves the quality of protein sequences derived from the conceptual translation of nucleotide sequences. Amatoxin: UniProtKB P85421Amanita phalloides