Systems and methods for using variable mass selection window widths in tandem mass spectrometry

A method for analyzing a sample using variable precursor mass selection window widths, comprising:

• instructing a tandem mass spectrometer to perform at least two fragmentation scans of at least two variable precursor mass selection window widths with different precursor mass selection window widths across a mass range of a sample in a single scan of the mass range using a processor, wherein the tandem mass spectrometer includes a mass analyzer that allows variable precursor mass selection window widths, wherein the different precursor mass selection window widths are calculated by
• creating a list of molecular weights for known target compounds in the sample;
• generating a molecular weight distribution from a database using the list of molecular weights, and
• selecting narrow mass selection window widths for the known target compounds and selecting wider mass selection window widths for areas in between the known target compounds.

A computer program product, comprising a tangible computer-readable storage medium whose contents include a program with instructions being executed on a processor so as to perform a method for analyzing a sample using variable precursor mass selection window widths, the method comprising:

• providing a system, wherein the system comprises one or more distinct software modules, and wherein the distinct software modules comprise a mass selection window width module;
• and
• instructing a tandem mass spectrometer to perform at least two fragmentation scans of at least two variable precursor mass selection window widths with different precursor mass selection window widths across a mass range of a sample in a single scan of the mass range using the mass selection window width module, wherein the tandem mass spectrometer includes a mass analyzer that allows variable precursor mass selection window widths, wherein the different precursor mass selection window widths are calculated by
• creating a list of molecular weights for known target compounds in the sample;
• generating a molecular weight distribution from a database using the list of molecular weights, and
• selecting narrow mass selection window widths for the known target compounds and selecting wider mass selection window widths for areas in between the known target compounds.