In order to improve the identification frequency and efficiency for protein identification using mass spectrometry we attempted to create an annotated protein search library that is specific for maize. This library eliminates the need to conduct blast searches on at least 50% of hits.

The starting point for this library was release 15.0 of the TIGR Maize Gene Index (ZmGI) which consists of 58,582 unique sequences. Specifics of the TIGR Maize Gene Index can be found at:
TIGR Maize Gene Index (ZmGI)

All hypothetical protein sequences encoded by these nucleic acid sequences were then extracted for annotation. This process involved the use of the EMBOSS (http://emboss.sourceforge.net/) software tools, particularly the 'getorf' command. Translated protein sequences were generated from all six reading frames that yielded proteins of at least 25 amino acid residues in size.

The hypothetical protein sequences were compared to the UniRef90 (http://www.uniprot.org) database using BLAST to determine the best hits and their corresponding UniProt annotations.

The final result is a FASTA formatted sequence file containing the protein sequences and the UniProt annotations which is suitable for use with search tools such as Mascot (http://www.matrixscience.com/).

This library is free to download and use for maize proteomics.

Download the library of 40,473 sequences here (11 Mb)