Automated extraction of EIC

Hi,

I'm using OpenLab CDS 2.2, build 2.20.484.

I'd like to ask about processing LC-MS runs - some of our methods are processed that EIC is extracted automatically when the run/sequence is opened according to compound list in the processing method. However, when I create a new processing method with similar parameters, I'm unable to make the extraction of EICs automated and it requires manually extracting them for each run individually, which becomes inconvenient for longer sequences. I'm unable to find any option in the processing sequence.

 

Also I'd like to ask regarding reporting, if there's any easy way how add on a report a sum of compounds quantified separately? 

 

Thank you.

Top Replies

  • Hello,

     

    See below for relevant section from the OpenLab Help and Learning:

     

     

    For your reporting question I will need more details. Screenshots can also be very useful when describing what you want to be performed on a report. 

  • In addition of what is saying, 

     

    To sum up different compounds quantified individually, the easiest and straight forward way is to use a named group. You can add a named group in the compound identification table, right-clicking, and selecting add named group. You'll then need to select the compounds which should be part of the group, the amounts will be summed. You can use the MS Quantitative Short/Long report which will report your individual quantified peaks, as well as the groups in a separated table (timed or named groups).

    There is also a table in reporting items on the left which reports peaks,missing peaks or groups together in the same table.

     

    Regarding the EIC extraction:

    There would be EICs extracted automatically when there is a compound identification/quantification in the processing method compound identification list.

    In the revision CDS v2.4, there is an additional way to automatically extract the EICs. With generic MS method (not sample purity), when there is a target mass in the target fields mentioned above, there will be an EIC extracted for each target (but in this case at target mass. Example: if target mass is 311, the EIC will be extracted at 310.7-311.7 with default EIC extraction setting).

  • Oh, I understand where is the issue. Thank you for taking the time describing this. 

    Would you mind sharing your template that I can do a modification on it? 

     

    I will try something which I suspect is the problem you see on that summary table.  I will also give you another option, which would be another way to do it.

     

     

    Thank you!

  • Thank you for your responses. I tried to get the sum of different compounds through custom calculations, however, I ended with different tables in the report showing different values and averages for 3 injections, which is what I need.

    Using named groups it seems easier, however, I still struggle with reporting - I have total of 6 compounds in the method, not all of them are present in the sample. When I create a table with all compounds listed, it shows the named group (named 'total') 6x per injection. When I check field for 'Remove duplicate peak(s)' in table properties, it shows detected compounds correct but only 1 injection of 3 for the total.

     

     

    I'd prefer to show only 1 line of total per injection, but I'm not sure if there's any additional settings to look at.

    Also I'd like to have the unit diplayed next to the average number for each compound and total, however, the field for average seems to be only available for numerical values, so it doesn't apply to 'Unit'. Is there any workaround for that?

    Thank you.

  • What would be the best way to send the template? I'd prefer to not disclose it publicly if possible.

  • Sounds a good plan. , If this solution works for you, I added you on my following list.

    To keep more confidentiality, ou can also extract only that particular table, as following:

     

    1. Select the table you have, and right-click, then select "Group".

     

     

    2. Once you have a group, around your table (if that was already the case, you can skip the step 1), select this surrounding frame representing the group, and select "Save Composite Group".

     

     

    3. Give a name, and you will see this custom report item in the reporting item list:

     

     

     

     

     

    But also as a file in Content Management under report templates (for Workstation Plus or Client Server systems), or in windows explorer for file based systems:

     

     

    This type of report items are designer tools to help saving custom reporting sections you may want to reuse in other templates.

     

     

    4. You can send me that *.ircg file. 

  • It is possible to send direct messages to users in the Community if both users are following each other. That might be a good way to coordinate a way to send the template.

     

  • Hi ,

     

    I modified your report template. 

    In OpenLab CDS v2.2, the "Remove duplicate peak(s)" was not fully compatible with missing compounds or group reporting. We enhanced this from CDS v2.4.

    As this is not out of the box in your CDS v2.2, I have modified your report template to be able to report the group or missing compounds.

     

    Just be aware that with the change I did, you shall not modify the "Remove duplicate peak(s)" as if so, the change I did would be reverted to the default.

    If you need to do this for other tables, you could modify your template just as I did in a text editor, looking for the keyword "distinct". You will see the below expression in your table :

     

     

    Which you should change to the following:

     

     

    I hope this solves your issue.

  • ,

    Good to hear it worked.

    I'm sorry, I forgot to answer this question. When you use an internal table grouping as you do, there would not be a way to display the unit for the summary calculation.

     

    You could add the units for the summary values using a table which is grouped and repeated per compound name. The layout would be slightly different (the summary values will not be part of the table)... An example:

     

  • Thanks a lot, this helped!

    I'm still curious if there's a possibility how to add a unit to the field next to average as indicated on the screenshot:

     

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