This is normal on this type of instrument. The chromatogram you have displayed is a TIC Total ion chromatogram or Total ion count. It is the sum of all the ions of all m/z that are detected. In LCMS there will always be ions detected, these come from sample, solvent background and your reference ions. Because of this, and unlike a UV detector for example, we cannot zero or balance the MS at the start of a run. You won’t really analyze the TIC, typically you will extract chromatograms for the m/z of interest EICs Extracted ion chromatograms) or the use one of the algorithms to mine compounds from the data eg Find by formula for targeted analysis or find by molecular feature for untargeted analysis.
What you see in qual is the ion count or abundance with Scale Chromatogram Off. The Scale to Largest in All Chromatograms plots everything as a % of the highest abundance in all your data.
If you extract a BPC, base peak chromatogram it might be more informative.
If you know what compounds you are looking for use Find By Formula or extract EIC Ion extracted chromtograms of the exact mass of the ion to 4 places.
Hi, Ross, thanks for your useful information. but I still confused about the TIC. I am working with PFAS based on LC/MS Aglient 1260, I also got a high peak at the 1 min in TIC chromatrograms for the balnk sample (pure methanol). I used the new column, purged the LC/MS, mobile phase is Water 10 mM Am-Ac and 80:20 MeOH:ACN10 mM Am-Ac. I ran ubder SIM mode.
so I wonder is the peak are led by those ions come out from the comlumn in 0-2 min also have the m/z value I set in the SIM acqusition method? The ions with its m/z not in the SIM acqusition method will not detected, right?
Hi, Ross, thanks for your useful information. but I still confused about the TIC. I am working with PFAS based on LC/MS Aglient 1260, I also got a high peak at the 1 min in TIC chromatrograms for the balnk sample (pure methanol). I used the new column, purged the LC/MS, mobile phase is Water 10 mM Am-Ac and 80:20 MeOH:ACN10 mM Am-Ac. I ran ubder SIM mode.
so I wonder is the peak are led by those ions come out from the comlumn in 0-2 min also have the m/z value I set in the SIM acqusition method? The ions with its m/z not in the SIM acqusition method will not detected, right?
The QTOF doesn't really work like that. There is no SIM mode like in quadrupole instrument. It collects full spectral data all the time. The only slight advantage to collecting data over a narrower range is that data files are smaller. However, you need to ensure that at a minimum your mass range also includes your reference correction ions (usually 121 and 922). What you see early in the TIC is probably unretained material from your injection solvents or may just be as your divert valve switches from waste to MS at the time segment. (You can experiment doing no injection run or no switching to see which. (The divert to waste time segment at the start of a run can be useful for keeping unretained junk out of your MS). Its not likely something trapped on the column usually things that are trapped don't elute so early as they require the stronger mobile phase to lute them.
You don't really want to analyze your TIC. Unless this is interfering with compounds of interest I wouldn't be concerned by it. Collect the full data and then extract out chromatograms, Extracted Ion Chromatograms (EICs)of the m/z of interest (to 4 decimal places) or run find by formula algorithm (Targeted workflow) to find the compounds of interest. On a QTOF you effectively filter out the ions of interest in the data analysis stage. On a single or triple quad, you filter them out when you run the sample. Apart from the high resolution and mass accuracy, this is the other big advantage of the QTOF, you have the full spectral data so you can ask more questions from it later if you suspect maybe there was another compound of interest, for example.
If you want to see what ions are making up the early peak (Or any peak for that matter)
Walk the chromatogram
Look at the spectra in the preview pane
Any ions that are of interest you can highlight that range or (multiple ranges)
Right click> Extract EIC> At maxima in ranges
This will extract an EIC of the tallest ion in the selected range. I wouldn't do analysis like this, but it is a quick convenient way to see the profile of any ion over the course of your run.
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