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Strategy for protein isoform identification from expressed sequence tags and its application to peptide mass fingerprinting
Author(s) -
Lisacek Frédérique C.,
Traini Mathew D.,
Sexton Diane,
Harry Jenny L.,
Wilkins Marc R.
Publication year - 2001
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/1615-9861(200102)1:2<186::aid-prot186>3.0.co;2-g
Subject(s) - protein isoform , peptide mass fingerprinting , proteomics , gene isoform , biology , expressed sequence tag , computational biology , identification (biology) , contig , protein sequencing , genome , genetics , redundancy (engineering) , peptide sequence , alternative splicing , gene , computer science , botany , operating system
Expressed Sequence Tags (ESTs) are an invaluable resource for protein identification and characterisation in proteomics. They allow proteins to be identified in the absence of genome sequence data. When EST sequences are used for protein identification, they are usually first processed into contigs to reduce redundancy and generate longer sequences from the overlapping ESTs. However, the process of generating contigs may accidentally group biologically meaningful isoforms together. Here we report means of discovering isoforms in EST sequences and how to use this information in the framework of protein identification and characterisation with peptide mass fingerprinting. We illustrate our strategies with examples from the dbEST database as well as protein isoforms from two‐dimensional polyacrylamide gels.