It is a major challenge to develop effective sequence database search algorithms to translate molecular weight and fragment mass information obtained from tandem mass spectrometry into high quality peptide and protein assignments. We investigated the peptide identification performance of Mascot and X!Tandem for mass tolerance settings common for low and high accuracy mass spectrometry. We demonstrate that sensitivity and specificity of peptide identification can vary substantially for different mass tolerance settings, but this effect is more significant for Mascot. We present an Adjusted Mascot Threshold, which allows the user to freely select the best trade-off between sensitivity and specificity. The Adjusted Mascot Threshold was compared with the default Mascot and X!Tandem scoring thresholds and shown to be more sensitive at the same false discovery rates, for both low and high accuracy mass spectrometry data.