In the earlier Select the processing workflow topic, you selected the Core GC PCI - Before Reprocessing workflow for this tutorial.

TIP

You can select the processing workflow for an analysis on the first page of the New Study and Analysis Wizard or on the Workflows page of a created study.

On the Workflows page, select a default processing workflow template for GC EI data by selecting Open Common and then browsing to the following folder: Workflow Templates > GC > GC PCI.

The GC PCI folder contains a variety of default processing workflow templates optimized for different types studies.

Before submitting the analysis to the job queue, review the processing workflow on the Workflows page and make changes as needed.

To review the processing workflow for this tutorial, do the following:

Procedure

  1. In the study, open the Workflows page of the analysis by selecting the Workflows tab or by selecting Edit in the Analysis view.
  2. The Workflows page opens, displaying the graphical Workflow Tree (center) and the Workflow Nodes pane (left).
  3. In this tutorial, the Core GC PCI - Before Reprocessing workflow contains three nodes.
  4. Workflows page displaying the default Core GC PCI - Before Reprocessing workflow
    Figure Workflows page displaying the default Core GC PCI - Before Reprocessing workflow
  5. In the graphical Workflow Tree, select the GC CI Deconvolution node.
  6. The Parameters of 'GC CI Deconvolution' pane appears (left).
  7. The Workflows page also includes the Current Workflow Issues pane, which opens when the processing workflow contains missing parameter settings or missing connections between the workflow nodes and closes after you fix all the issues.

  8. NOTE

    For this tutorial, do NOT modify any of the settings in the processing workflow template.

  9. Parameters of GC CI Deconvolution node
    Figure Parameters of GC CI Deconvolution node
  10. Refer to Submit the analysis to the job queue to continue the tutorial.

For your own analysis, consider modifying the GC PCI workflow template as appropriate, using the following information as a guide:

Peak Detection Settings area

Select the CI gas type for your GC/MS system:

  • Methane: Produce [M+H]+, [M+C2H5]+, and [M+C3H5]+ ions.
  • Ammonia: Produce [M+H]+, [M+NH4]+ ions.

Take care when modifying any of the other parameter settings for peak detection. Decreasing the Ion Overlap Window [%] from the default value of 98% increases the probability of grouping co-eluting ions together as one compound.

RI Settings area

When you have the retention indexing information for your GC/MS system, enable the Calculate RIs feature and enter the n-alkane reference items.

To limit the library hits for compounds with RI data to those with matching RI values within a user-specified tolerance, enable the Use RI Delta Filter or the Use RI Diff [%] filter.

Group Compounds Settings area

Keep True as the setting for the Group Compounds Across Samples By Retention Time and Spectrum Dot Product parameter even when the analysis includes only one input file, as this parameter must be set to True to send data about the detected compounds to the downstream nodes. When you reprocess and analysis, adding downstream nodes does not trigger full processing, but resetting any parameter in the deconvolution node does trigger full reprocessing.

Consider increasing the Composition Threshold. For example, if the analysis includes multiple input files and you want the application to ignore compounds unless they are present in more than one of the input files or all the input files, increase this percentage.

Library Search Settings

The default library search setting is false. If a custom PCI library in NIST format is available, it can be selected for use. Additionally, database search nodes such as Search ChemSpider, Search mzCloud, and Search Mass List can be used in the workflow for searching to enhance compound identification.