Set up a processing method
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Set up a processing method

Preparations

You need the following privileges. Privileges are configured in the Control Panel.

  • Project Management  > Edit content of project

  • Processing Method  > Create processing method

  • Data Processing  > Reprocess data

  • Processing Method  > Edit signal parameters

  • Processing Method  > Edit chromatogram extraction parameters

  • Processing Method  > Edit spectrum extraction parameters

  • Processing Method  > Edit identification parameters

  • Processing Method  > Edit calibration parameters

  • Processing Method  > Save master method

  • Processing Method  > Save result set method

  1. In Data Analysis, load the result set with your acquired oligo data.

  2. Create a new method with method configuration MS, and save it.

  3. Link the new method to the result set.

  4. Set the method parameters as specified below.

  5. Reprocess and save your results.

Method section

Settings

General  > Signals ,

Blank Subtraction tab

Blank subtraction applied on: Select All injections

Use specific blank: Select the third blank in your current result set.

Ensure that the third blank injection baseline closely resembles the baseline of the 25 µL sample

You have to set this parameter individually for each new result set.

Extraction  > Chromatogram ,

MS tab

Single m/z expansion chromatograms: This is typically set to either 0.3, 0.7 asymmetrical, or ±0.5 symmetrical. Determine this parameter empirically.

Extraction  > Spectrum

MS tab

  • Arbitrary spectra: Select Use external time range

  • Peak spectra:

    For spectrum type, select Average peak spectrum. This is needed to identify impurities across the entire TIC.

    For background mode, select External background time range

  • External background time range (recommendation):

    Start time: 0 min

    End time: 3.0 min

  • Automatic spectrum extraction: Select the check box, and choose Identified Peaks.

  • Spectral smoothing: Select the check box. The width is typically 1 or 2, but this is method-specific. Determine this parameter empirically.

Compounds  > Calibration ,

General Table tab

Set Number of levels to 4.

Compounds  > Identification ,

Compound Table tab

Add a compound for your full-length product (FLP). Use exactly the same name and spelling as in the ion list.

  • Set Signal for this compound to the UV signal.

  • Set the expected retention time as appropriate to our analysis.

  • Set Peak match for this compound to Largest area.

Compounds  > Calibration ,

Compound Table tab

  • Set Amount unit for your FLP compound to µg.

  • Keep the Level 1 to Level 4 fields empty. The different amounts are defined by the injection volumes of calibration standards in the sequence (see Set up a Sequence).

  • Set Origin for your FLP compound to Ignore.

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