My chromatograms using 6545 LC MS runs above zero.

Question

My chromatograms using 6545 LC MS runs above zero on x-axis. What can be the potential reason?

andyg · Accepted Answer

AHAS- 
 
 You can select the chromatogram by left-clicking on it. You can then right click and select "Adjust". It will adjust the selected chromatogram to the specified percent of full scale. The specified percent is set by right click in the Real Time Chromatogram window and selecting Change. The Y scale is also set there.

ross · Answer

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.

My chromatograms using 6545 LC MS runs above zero.

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