Acquired raw data as used for the protein identification of differential spots from the quantitative analysis of the response of the barley root proteome to salinity stress

Acquired raw data as used for the protein identification of differential spots from the quantitative analysis of the response of the barley root proteome to
salinity stress. Acquisition of peptide mass fingerprint data was performed on a Reflex III MALDI-TOF device (Bruker Daltonics, Bremen, Germany, www.bruker.com/) operating in reflector mode using
the FlexControl software. Spectra were calibrated using external calibration, with subsequent internal mass correction. Protein identification was performed with the Mascot search engine (Matrix
Science, London, United Kingdom, www.matrixscience.com/home.html), by searching the barley EST (expressed sequence tag) Gene Index in the TIGR database
(compbio.dfci.harvard.edu/cgi-bin/tgi/gimain.pl?gudb=barley) and the HarvEST database (harvest.ucr.edu/). Parameters for the search were: monoisotopic mass accuracy 100 ppm tolerance, missed
cleavages 1, allowed variable modifications: oxidation (Met), propionamide (Cys) and carbamidomethyl (Cys). When this approach failed, the samples were subjected to analysis by nanoLC-ESI-Q-TOF
MS/MS and de novo sequencing (nanoLC ESI-Q-TOF MS/MS, Waters Corporation, Milford, USA, www.waters.com), following Amme et al. (2006) using the MassLynx software. A 10 ppm peptide, 0.1 Da fragment
tolerance, one missed cleavage and variable oxidation (Met), propionamide (Cys) and carbamidomethyl (Cys) were used as the search parameters. Database searches were conducted against the barley EST
Gene Index of the TIGR database and the HarvEST database.