Ours is a SCIEX 5600 Qtof machine. We are standardizing the methods. We are always getting very high ppm error and therefore no matching in library. I have attached my data file for reference.
I also need some suggestions on the method standardization part.
I can share additional details when needed.
Thankyou
Higher ppm error can in some cases be attributed to concentration, try to keep your sample concentration around 0.1 mg/ml only.
Hi
How often are you doing an Autocal or a tune and optimisation?
The file appears to show the last mass calibration back in November. Run the Tune and Optimise before reinjecting your standards. Most labs would do a mass calibration on this instrument at intervals measured in minutes or hours.
If using an internal standard it _may_ be possible to reprocess the data to correct the mass error on samples already run, so you may be able to still use the data you have collected.
Thanks Richard Evers, no its not like that, we do calibration on daily basis, or twice a day if in case the machine runs for more than 5-6 hours. So the present data set was generated the same day evening when the calibration was performed. In addition I have not run any internal standard in this case.
Thanks Amjad Alkhdhairawi I t could be a concentration issue u may be right, but I have used low concentration only in this case.
If u have any other suggestions pls share
I can't think of anything to give higher ppm other than concentration of the sample and calibration of the instrument. However, what i would like to know is what kind of sample are you running? how sure are you of the expected mass of the sample? and did you try running both negative and positive mode?
mine are plasma samples done with chloroform methanol method for protein purification. This is an untargeted procedure. I have done this only with positive polarity not negative polarity yet.
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