error in fun MRM_Ion_Pair_Finder

[stolltho]

Hi there.

Executing fun MRM_Ion_Pair_Finder
data_ms1ms2_final <- MRM_Ion_Pair_Finder(file_MS1 = "C:\R_WorkingDirectory\MRM_Ion_Pair_Finder\LianneL\Delete Iso-Add Result.csv",
filepath_MS2 = "C:\R_WorkingDirectory\MRM_Ion_Pair_Finder\MS2",
tol_mz = 0.01,
tol_tr = 0.2,
diff_MS2MS1 = 13.9,
ms2_intensity = 750,
resultpath = "C:\R_WorkingDirectory\MRM_Ion_Pair_Finder\LianneL")

returns the following error:

MS1 reading is finished.
Read 244910 items
Deleting the data in QC_MP_itMS2pos_CE20_it01.mgf with charge > 1 is finished.
Error in if (mz_ms1 - mz_ms2 <= diff_MS2MS1 | int_ms2 <= ms2_intensity) { :
missing value where TRUE/FALSE needed

Any idea what the problem might be? My r skill level is just basic.

Cheers,
Thomas

[zhengfj1994]

Hi Thomas.

This error is happened when processing the mgf files. If you don't mind, you can send me an example of your mgf file. My e-mail is [email protected]

Cheers,
Fujian Zheng

[zhengfj1994]

Hi Thomas.

This error is happened because of the format of mgf is different from the mgf file I used. I have modified the code to support your mgf files. In addition, please note that the file name of the mgf files need to be modified to a name that only contains the CE value.

Cheers,
Fujian Zheng

[stolltho]

Thanks Fujian. It works now.
Cheers,
Thomas