Both PEAKS de novo and PEAKS DB search were finished successfully on the 3.4 million MS2 dataset. The computer has two Xeon hex-core CPUs and 32GB RAM running Windows 7 Pro 64 bit OS. The search completed in a little over a week.
PEAKS de novo reported over 2 million de novo peptides that have their ALC score greater than or equal to 50%.
PEAKS DB reported over 1 million PSMs at 1% FDR.
Be sure to check out the protein coverage view of one of the top score proteins. It can help demonstrate that a protein is pretty much fully covered.
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