Tune the MS manually (LC/MS)

The Autotune program adjusts the MS for good performance over the entire mass range. For many applications, you do not need to use anything else. You might consider manually tuning the MS in the following situations:

To achieve maximum sensitivity by sacrificing some resolution
To tune specifically for the very low end of the mass range (< 150 amu)
To tune with a compound other than the standard calibrants

You can only manually tune if your instrument is an Agilent 61xxC. (for example, 6125C, 6135C)

Ionization modes

Separate tuning is not required for electrospray, APCI/APPI, and MMI-ESI+APCI. Tuning involves adjusting the parameters that control the transmission of ions. These parts neither know nor care how those ions are generated. A tune file created in electrospray mode often provides good results for APCI/APPI samples. The reverse is also true.

Polarity

Separate tuning is required for positive and negative ionization. The MS must, at some time, be tuned twice, once with positive ions and once with negative ions. The two tunes can be stored under the same tune file name; the software keeps separate the positive and negative ion settings. Positive ion and negative ion settings can be updated separately.

Mass range

Tuning is almost always done over the entire mass range. The exception is if all the ions of interest are smaller than approximately 150 amu. Correct manual tuning over a reduced mass range can improve transmission and detection of these very low mass ions.

Frequency

Frequent tuning is not required. The MS is very stable and may go weeks or months before it needs to be tuned again.

Ion Source

You can run the manual tune with any source. If you have an MMI source, Agilent recommends that you tune in MMI-APCI mode with the APCI tune calibrant. The APCI tune calibrant does not contain 118 m/z which is needed to tune in ESI mode.

Steps

This section includes step-by-step instructions for manually tuning the MS. The instructions assume the use of one of the standard calibrants and tuning over the entire mass range, but they can be altered for non-standard calibrants or narrower mass ranges. Multiple, often mass-dependent, interactions between multiple parameters make manual tuning a complicated and iterative process. These instructions provide a good starting point but are not a substitute for experience and familiarity with the effects of the various parameters and their interactions.

The main steps of manual tuning are

Prepare for manual tuning (LC/MS).
Set acquisition parameters and adjust mass axis
Ramp the Fragmentor dynamically (LC/MS)
Ramp the lenses during manual tune (LC/MS)
Optimize the Octopole (LC/MS)
Adjust peak widths and mass axis (LC/MS)
Optimize Lens2 RF parameters (LC/MS)
Click to unlock the instrument. You need to unlock the instrument after you finish tuning.