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Shotgun proteomic analysis of Arabidopsis thaliana leaves
Author(s) -
Lee Joohyun,
Garrett Wesley M.,
Cooper Bret
Publication year - 2007
Publication title -
journal of separation science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.72
H-Index - 102
eISSN - 1615-9314
pISSN - 1615-9306
DOI - 10.1002/jssc.200700151
Subject(s) - arabidopsis thaliana , shotgun , shotgun proteomics , chemistry , chromatography , mass spectrometry , computational biology , botany , proteomics , biology , biochemistry , gene , mutant
Two shotgun tandem MS proteomics approaches, multidimensional protein identification technology (MudPIT) and 1‐D gel‐LC‐MS/MS, were used to identify Arabidopsis thaliana leaf proteins. These methods utilize different protein/peptide separation strategies. Detergents not compatible with MudPIT were used with 1‐D gel‐LC‐MS/MS to help enrich for the detection of membrane‐spanning and hydrophobic proteins. By combining the data from all MudPIT and 1‐D gel‐LC‐MS/MS experiments, 2342 nonredundant proteins spanning a broad range of molecular weights and p I values were detected. With the exception of unknown proteins, the distribution of gene ontology (GO) classifications for the detected proteins was similar to that encoded by the genome, which shows that these extraction and separation procedures are useful for a broad proteomic survey of plant cells. Unknown proteins will likely have to be targeted by using additional methods, some of which should be compatible with separation strategies taken here.