Chromatography Forum

I was detecting compound A in urine with LC/MS/MS under MRM from 501 to 179. Because A is conjugated in urine, I used enzyme to hydrolyzed it. After hydrolysis, the urine sample was extracted with dichloromethane (7ml for 0.5 mL urine) and dried under N2 and derivatized and analyzed with LC/MS/MS. Without enzyme hydrolysis (blank), the junk peaks were quite small, but after enzyme hydrolysis, the junk peaks were huge. I run the LC/MS/MS with product ion scan to check these junk peaks, all I got was 501 but no 179 in product ion spectrum.

My question is if there is no 179 showed in the product scan, how come I can detect these junk peaks with MRM?

Thanks anyway!

MRM is going to be more sensitive than Product Ion Scan. Also, could it be that there is so much other background in masses adjacent to 179 (plausible if the 501 precursor is actually many compounds), that the 179 daughter signal looks like "grass" or noise in your product ion spectrum?

No, there is no any other product ion but the 501, not even noise. I am so confused by this! The enzyme must play a role in this problem because the junk peaks increased so much after hydrolysis. I really could not figure it out!

If you have another precursor with product 179 in that MRM run, you could be experiencing crosstalk if using an older brand of triple-quad. Otherwise, I can't think of a good explanation at the moment for what you're experiencing.