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2007 Proteomics Research Group
Quantitative Proteomics Study

To report your data, we have provided an anonymized protein database containing the sequences of the added and background proteins as well as a number of decoy protein entries. This database is also available on the Protein Prospector, Mascot and X!Tandem web sites.  Your results must be submitted using the accession numbers supplied in the database.



This database is in fasta format and follows the general format:
 
>PRG_seq_5 ABRF_PRG2007_Protein_5
MKTLIRKFSRTAITVVLVILAFIAIFNAWVYYTESPWTRDARFSADVVAIAPDVSGLITQVNVHDNQLVKKGQILFTIDQ
PRYQKALEEAQADVAYYQVLAQEKRQEAGRRNRLGVQAMSREEIDQANNVLQTVLHQLAKAQATRDLAKLDLERTVIRAP
ADGWVTNLNVYTGEFITRGSTAVALVKQNSFYVLAYMEETKLEGVRPGYRAEITPLGSNKVLKGTVDSVAAGVTNASSTR
DDKGMATIDSNLEWVRLAQRVPVRIRLDNQQENIWPAGTTATVVVTGKQDRDESQDSFFRKMAHRLREFG


The file contains 4,346 protein sequences and a number of common contaminants (e.g. keratins, trypsin, etc...).   In addition, an equal number of decoy sequences have been concatenated to the end of the file. The decoys are generated by creating a shuffled sequence for every sequence within the FASTA file.  The decoy sequences can be identified by the accession numbers with the format:
 
>random_seq_524
DIVNLLLLALISHWGSQLESWPHRYSQPREPTLDVPEWESPHYFIALAASQTMSAKWVKVRLQGLWGAYRWPFQAWPFAT
TCLLTAPGPLDFFAQFQRKLFQLFESHAAEAGQAEARGTGGQLEVASLTMTQEALVRLLVFTHTEVFCRLQDALEELPPL
WASELFRADAWSLPFVDNVWEEFSKAAVMQEWPNQELLGAREP

To download the database please click the image below:

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NOTE: for users of the ProteinPilot database searching software. The ABI ProteinPilot software has some specific formating requirments that makes the above fasta format file incompatible with their software.  If you are using ProteinPilot please use this database instead: ABRF_PRG2007-ProteinPilot.fasta.

NOTE: for users of the Spectrum Mill database searching software. There are some specific formating requirments that makes the above fasta format file incompatible with Agilent's software.  If you are using Spectrum Mill please use this database instead: ABRF_PRG2007-SpectrumMill.fasta.