Update: 3.4 million MS2 spectrum project, PEAKS DB completed!

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. Here is the search parameters I used.

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.

Here is the protein coverage view of one of the top score proteins. The protein is pretty much fully covered.