Recently, I have been trying to use ProteoWizard to convert the data dependant acquisition (DDA) data obtained from Waters QTOF to .mgf format. However, I found that m/z values in the converted file are off by around 0.002 Da. In addtion, the peak intensity is much lower. For example, the precursor ion displayed in Masslynx has a m/z value of 279.0934 and an intensity of 20,000. However, this precursor ion in the converted file shifted to 279.0922 with an intensity of only 2500 (It's still the most intense peak though).
Lockmass correction was automatically applied during data acquistion. I have also tried the lockmassRefiner in msconvert, but it doesn't help. Does anyone have any idea?
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Recently, I have been trying to use ProteoWizard to convert the data dependant acquisition (DDA) data obtained from Waters QTOF to .mgf format. However, I found that m/z values in the converted file are off by around 0.002 Da. In addtion, the peak intensity is much lower. For example, the precursor ion displayed in Masslynx has a m/z value of 279.0934 and an intensity of 20,000. However, this precursor ion in the converted file shifted to 279.0922 with an intensity of only 2500 (It's still the most intense peak though).
Lockmass correction was automatically applied during data acquistion. I have also tried the lockmassRefiner in msconvert, but it doesn't help. Does anyone have any idea?