Peak Integration

Peaks should be integrated completely from end to end. Sometimes extremely large peaks will have tailing, which is fine as long as the majority of the peak is integrated. However, over time compounds can shift and peak recovery can be affected as a result of instrument/component wear. Sometimes, this can cause peaks to split and as a result, the program only integrates a portion of a peak instead of the entire peak. This can be remedied using two methods:

1. Adjusting retention time windows
2. Adjusting integration parameters

Retention Time Windows

Sometimes compounds aren't integrating properly because the retention time window is either cutting off the peak or the compound is being misidentified as an adjacent peak (common with isomers). Adjusting the retention time window so it focuses on a specific peak within the time frame usually solves the issue.

WARNING: Doing this will change the update time for your method. Do NOT save method when doing this unless you're processing ICAL.

ICAL

1. Go to InitCal > Edit Compounds > [compound name].
2. Under "Extract signals from" adjust the retention time as needed. Save and close.

3. Requant the affected data to check whether the integration is correct now. Repeat as needed until the integration is correct.

Do this before you replace the compound responses when processing ICAL.

QC

1. Go to InitCal > Edit Compounds > [compound name].
2. Under "Extract signals from" adjust the retention time as needed. Save and close.
3. Requant the affected data to check whether the integration is correct now. Repeat as needed until the integration is correct.
4. Reload the method WITHOUT SAVING.

This will undo the changes made to retention time, but it also resets the update time to the original time.

5. Repeat steps 1-2. Do NOT do step 3.
6. Go to Tools > DOLIST > ``

Go to InitCal > Edit Compounds > [compound name]. 2. Under "Extract signals from" adjust the retention time as needed. Save and close.

3. Requant the affected data to check whether the integration is correct now. Repeat as needed until the integration is correct.

Do this before you replace the compound responses when processing ICAL.

Integration Parameters (ICAL)

This technique works better when the retention time window is correct, but the peak itself is splitting or not integrating completely.

Adjusting the integration parameters won't change the update time for your ICAL method, but if multiple compounds share the same parameter file, the integration for those compounds will also be affected. This is why it's important to try not to reuse the same integration parameters for multiple compounds.

1. Go to InitCal > Edit Compounds > [compound name]. Switch to Page 3.
2. Check if there are any integration parameter files listed (see image). Write down (or memorize) the file name next to "Tgt" and close the window.

3. Go to Int > Integration Parameters.

4. This is the integration parameter settings for the current parameter file. This file should be RTE.P for all instruments. Do not touch this file. Go to Load > [int param name you wrote down before]

5. Write down the Start/Stop threshold values, then you can fiddle with the settings in the red box. Usually I start by toggling Smoothing because that tends to do...something most of the time. If the peak is splitting or not picking up the correct peak, you can try fiddling with the Start/Stop thresholds to see if it helps.

6. Requant the affected data to check if the integration is correct. Repeat as needed.

Do this before you replace the compound responses when processing ICAL.