Selected spots from 2-DE were excised, destained, and processed by proteolysis with trypsin, as described before
11 and analyzed by MALDI-TOF peptide mass fingerprinting and MS/MS on a MALDI-TOF/TOF tandem mass spectrometer (ABI 4700 Proteomics Analyzer; Applied Biosystems, Inc. [ABI], Foster City, CA). For positive-ion reflector mode spectra 2500 laser shots were averaged and processed with external calibration. PMF spectra were not smoothed, and background was not subtracted. Monoisotopic peak masses were automatically determined within the mass range 800 to 4000 kDa with a signal-to-noise ratio minimum set to 5 and the local noise window width
m/
z 200. Up to seven of the most intense ion signals with signal-to-noise ratio above 30 were selected as precursors for MS/MS acquisition excluding common trypsin autolysis peaks and matrix ion signals. In MS/MS positive ion mode 4000 spectra were averaged with 1 kV collision energy, collision gas air at a pressure of 1.6 × 10 to 6 torr and default calibration. Monoisotopic peak masses were automatically determined with a signal-to-noise ratio minimum set to 10 and the local noise window width
m/
z 200. Combined PMF and MS/MS queries were performed (Mascot Database search engine v1.9; Matrix Science Ltd., UK,
http://www.matrixscience.com, embedded in GPS-Explorer Software; ABI) on the SWISS-PROT database (version 20070531; 270778 sequences; 99412397 residues;
http://expasy.hcuge.ch/tools/scnpsite.html/ provided in the public domain by the Swiss Institute of Bioinformatics, Geneva, Switzerland), the MSDB metadatabase (version 20061115; 3239079 sequences; 1079594700 residues;
http://proteomics.leeds.ac.uk/bioinf/msdb_simple.html), or the horse genome database (retrieved from UCSC, version 20070101; 39612 sequences; 252365 residues; provided in the public domain by the University of Santa Cruz, CA;
http://genome.ucsc.edu/cgi-bin/hgGateway) with the following parameter settings (if applicable): entries restricted to mammalian, 65 ppm mass accuracy, 0.3-Da fragment mass tolerance, trypsin cleavage, one missed cleavage allowed, carbamidomethylation was set as fixed modification and oxidation of methionines was allowed as variable modification. A protein was regarded as identified, if the probability-based MOWSE score was significant for the respective database (protein scores >58 were significant for SwissProt, scores >67 for MSDB, and scores >54 for the horse genome database;
P < 0.05), if the matched peptide masses were abundant in the spectrum and if the theoretical masses of the significant hit fit the experimentally observed values.