A system for maintaining the precision of mass measurement, comprising: a mass spectrometer; and a processor in communication with the mass spectrometer, wherein (a) the mass spectrometer is configured to perform a plurality of background scans producing a plurality of background measurements, (b) the processor is configured to obtain the plurality of background measurements from the mass spectrometer, (c) the processor is configured to calculate reference features from the plurality of background measurements and calculate a reference feature confidence value for each reference feature of the reference features without knowing an identity of reference ions represented by the reference features, (d) the mass spectrometer is configured to perform a scan of a sample, (e) the processor is configured to obtain a plurality of sample measurements from the mass spectrometer for the scan, (f) the processor is configured to calculate sample features from the plurality of sample measurements and calculate a sample feature confidence value for each sample feature of the sample features without knowing an identity of sample ions represented by the sample features, (g) the processor is configured to determine common features that are common to the reference features and the sample features by aligning the reference features and the sample features, (h) the processor is configured to calculate constants for an equation of mass for the mass spectrometer using a confidence weighted regression of the common features, (i) the processor is configured to calculate new masses for the sample features from the equation of mass and the constants, (j) the processor is configured to update the reference features using the sample features and recalculate the reference feature confidence values, and (k) steps (d)-(k) are repeated until no more scans are performed on the sample. a mass spectrometer; and a processor in communication with the mass spectrometer, wherein (a) the mass spectrometer is configured to perform a plurality of background scans producing a plurality of background measurements, (b) the processor is configured to obtain the plurality of background measurements from the mass spectrometer, (c) the processor is configured to calculate reference features from the plurality of background measurements and calculate a reference feature confidence value for each reference feature of the reference features without knowing an identity of reference ions represented by the reference features, (d) the mass spectrometer is configured to perform a scan of a sample, (e) the processor is configured to obtain a plurality of sample measurements from the mass spectrometer for the scan, (f) the processor is configured to calculate sample features from the plurality of sample measurements and calculate a sample feature confidence value for each sample feature of the sample features without knowing an identity of sample ions represented by the sample features, (g) the processor is configured to determine common features that are common to the reference features and the sample features by aligning the reference features and the sample features, (h) the processor is configured to calculate constants for an equation of mass for the mass spectrometer using a confidence weighted regression of the common features, (i) the processor is configured to calculate new masses for the sample features from the equation of mass and the constants, (j) the processor is configured to update the reference features using the sample features and recalculate the reference feature confidence values, and (k) steps (d)-(k) are repeated until no more scans are performed on the sample. (a) the mass spectrometer is configured to perform a plurality of background scans producing a plurality of background measurements, (b) the processor is configured to obtain the plurality of background measurements from the mass spectrometer, (c) the processor is configured to calculate reference features from the plurality of background measurements and calculate a reference feature confidence value for each reference feature of the reference features without knowing an identity of reference ions represented by the reference features, (d) the mass spectrometer is configured to perform a scan of a sample, (e) the processor is configured to obtain a plurality of sample measurements from the mass spectrometer for the scan, (f) the processor is configured to calculate sample features from the plurality of sample measurements and calculate a sample feature confidence value for each sample feature of the sample features without knowing an identity of sample ions represented by the sample features, (g) the processor is configured to determine common features that are common to the reference features and the sample features by aligning the reference features and the sample features, (h) the processor is configured to calculate constants for an equation of mass for the mass spectrometer using a confidence weighted regression of the common features, (i) the processor is configured to calculate new masses for the sample features from the equation of mass and the constants, (j) the processor is configured to update the reference features using the sample features and recalculate the reference feature confidence values, and (k) steps (d)-(k) are repeated until no more scans are performed on the sample.