I downloaded MSPepSearch and am looking at my first result set. Since I haven yet done an FDR analysis, what is a reasonable Score threshold?
While the absolute Score threshold is subject to change based on the size and quality of your dataset, a Score of 450 is a reasonable starting point. This value will frequently approximate a false discovery rate of ~1% for a routine shotgun analysis of tryptic peptides on an ion trap mass spectrometer.
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