smith-chem-wisc / mzcal Goto Github PK

In ASL file, scan 8928 spans MS1 range 8894-9070. This is too wide.

Try using a separate tolerance for MS1 vs MS2, or even individualized, evolving tolerances

calibrating:
a) decide scan parameters
b) calibrate taking m/z and intensity (possibly relative) values

not sure if this is related to using two dictionaries. mzid files had unimod and psi-mod listed, which seems fine.

        else
        {
            myMsDataFile = new ThermoRawFile(origDataFile);
            myMsDataFile.Open();
            if (((ThermoRawFile)myMsDataFile).monoisotopicPrecursorSelectionEnabled)
                deconvolute = false;
        }

followed by

       }
        else
            throw new Exception("Not familiar with modification dictionary " + dictionary);

Have a file with two sets of identifications. Use one to calibrate with, use the other to assess the quality of calibration before and after.
Check quality by computing MSE of IDENTICAL points recognized by the software.