Different intensity values from mzML and ScanHeadsman

[sgibb]

Unfortunately we got different values for TIC and BasePeakIntensity from mzML and ScanHeadsman:

colData(myo)[, c("TotIonCurrent", "TIc", 
                 "BasePeakIntensity.SpectraInformation", "BasePeakIntensity.HeaderInformation")]
DataFrame with 5882 rows and 4 columns
                                        TotIonCurrent       TIc
                                            <numeric> <numeric>                                                   
C0707.30_1.0e+05_0.0e+00_00.00_00_07_01      16904906 355247712
C0707.30_1.0e+05_0.0e+00_00.00_00_07_02      17520226 361759808
C0707.30_1.0e+05_0.0e+00_00.00_00_07_03      19653865 348177760
C0707.30_1.0e+05_0.0e+00_00.00_00_07_04      20301836 368366784
C0707.30_1.0e+05_0.0e+00_00.00_00_07_05      17174796 399923680
...                                               ...       ...
C1211.70_1.0e+06_1.0e+07_50.00_28_00_1        4618113  15510952
C1211.70_1.0e+06_1.0e+07_50.00_28_00_2        2603466   7625062
C1211.70_1.0e+06_1.0e+07_50.00_28_00_3        2104302   6140932
C1211.70_1.0e+06_1.0e+07_50.00_35_00_1        3725114  11805720
C1211.70_1.0e+06_1.0e+07_50.00_35_00_2        1786274   4843912
                                        BasePeakIntensity.SpectraInformation
                                                                   <numeric>
C0707.30_1.0e+05_0.0e+00_00.00_00_07_01                              5496660
C0707.30_1.0e+05_0.0e+00_00.00_00_07_02                              5499596
C0707.30_1.0e+05_0.0e+00_00.00_00_07_03                              4979749
C0707.30_1.0e+05_0.0e+00_00.00_00_07_04                              4935137
C0707.30_1.0e+05_0.0e+00_00.00_00_07_05                              4635775
...                                                                      ...
C1211.70_1.0e+06_1.0e+07_50.00_28_00_1                              240546.9
C1211.70_1.0e+06_1.0e+07_50.00_28_00_2                              176790.7
C1211.70_1.0e+06_1.0e+07_50.00_28_00_3                              141276.0
C1211.70_1.0e+06_1.0e+07_50.00_35_00_1                              217099.5
C1211.70_1.0e+06_1.0e+07_50.00_35_00_2                              124652.3
                                        BasePeakIntensity.HeaderInformation
                                                                  <numeric>
C0707.30_1.0e+05_0.0e+00_00.00_00_07_01                            13194801
C0707.30_1.0e+05_0.0e+00_00.00_00_07_02                            14144109
C0707.30_1.0e+05_0.0e+00_00.00_00_07_03                             9578171
C0707.30_1.0e+05_0.0e+00_00.00_00_07_04                            11655850
C0707.30_1.0e+05_0.0e+00_00.00_00_07_05                            18542674
...                                                                     ...
C1211.70_1.0e+06_1.0e+07_50.00_28_00_1                             213727.3
C1211.70_1.0e+06_1.0e+07_50.00_28_00_2                             166102.0
C1211.70_1.0e+06_1.0e+07_50.00_28_00_3                             142550.4
C1211.70_1.0e+06_1.0e+07_50.00_35_00_1                             196772.0
C1211.70_1.0e+06_1.0e+07_50.00_35_00_2                             111784.1

Any idea why this happens?

[sgibb]

After reading the code again, I could easily answer the "TIC" question. We throw away the information from the mzML files and calculate our own TIC:

topdownr/R/import.R

Lines 203 to 206 in 3ded14b

	## depending on the used processing software the header column totIonCurrent
	## doesn't take deisotoping and charge state reduction into account; so we
	## calculate TIC for our own here
	hd$TotIonCurrent <- .vapply1d(peaks(fh)[i], function(ii)sum(ii))

But I have no idea why the BasePeakIntensity differs.