Method for automated checking and adjustment of mass spectrometer calibration

A method for automatically checking a calibration of a mass spectrometer including an atmospheric pressure ion source, a first quadrupole device (Q1), a fragmentation cell, and a mass analyzer during a sequence of mass analyses of a plurality of samples introduced into the atmospheric pressure ion source, comprising:

• (a) providing a one of the plurality of samples having therein at least one known chemical entity;
• (b) decreasing a kinetic energy applied to ions entering the fragmentation cell so as to prevent fragmentation therein;
• (c) ionizing the at least one known chemical entity using the ion source so as to generate ions of a known ionic species;
• (d) transmitting a portion of the ions through Q1;
• (e) transmitting the portion of the ions from Q1 to the fragmentation cell so as to be transmitted through the fragmentation cell to the mass analyzer;
• (f) performing a mass analysis of the transmitted ions by the mass analyzer and an ion detector configured to receive ions from the mass analyzer;
• (g) comparing the results of the mass analysis with expected results;
• and
• (h) determining, from the comparison, if any of a peak centroid position, peak intensity, peak width or peak resolution differs from a respective expected value derived from a prior calibration of mass-to-charge ratio or abundance by greater than a respective tolerance.