Why Don't I get Hits when the Precursor Mass Tolerance Is Set to 0.01 Da when Searching SCIEX Libraries?

For research use only. Not for use in diagnostic procedures.

Issue Description

Searches of SCIEX libraries with the precursor mass tolerance set to 0.01 Da may not yield any hits. This is due to the fact that some of SCIEX libraries contain spectra that were acquired with inaccurate precursor m/z (e.g., looped MS/MS where the precursor m/z was entered using only one decimal place). If the user set too small of a precursor mass tolerance setting for library search, some spectra will not be identified correctly.

 

Resolution

When searching large libraries, processing speed can be slightly improved by decreasing the Precursor Mass Tolerance for library searching. This will filter out any spectra that come from a precursor with a different m/z than the acquired spectra being searched.

It is important to search with a wide enough tolerance to ensure all relevant spectra in the library will be scored against the acquired spectra. When searching SCIEX libraries, keep the default setting of 0.4 Da for Precursor Mass Tolerance. Do not go below 0.1 Da. In the future, SCIEX libraries will be corrected to exact mass for precursors.