Empower 2 processing multiple channels

[sebascuenta]

Hello,
I am new in using Empower 2, I am performing analysis with an LC-MS for 7 compounds.
I made a method set for 7 channels, one for each compound.

I would like to make a final table with all the peaks from each channel for each injection, something like a summary of each of the peaks for each injection.

How is the simplest way to do it? Thank you!

(Nobody around here knows how to make processing methods, they all copy by hand the peak areas from the review window)

[Hollow]

(Nobody around here knows how to make processing methods, they all copy by hand the peak areas from the review window)

1) use "F1" aka Help
2) use the Wizard to create Processing methods

3) maybe you can use the same proc-method for all of the channels? Maybe you want to fill in the "channel information" in the component table, so as the peak is only labeled in its dedicated channel
4) create a report method as "summarized per injection", this should make it possible to use summary tables, where the results of all processed channels are taken into account

[Kristof]

Yes, depending on your results (e.g. peak size) you could use single processing method and one component table for all channels.

If not, it's not a problem - just attach separate processing method to channels in method set and "process using aqusition method".

As for result table - that would be in reporting method and actually default option for most of the tables is to show all results for all channels. It's in "Tables" - "All Peaks Table", "Amount Component Summary", "Area Component Summary" etc. Play around and you'll find what you need.

[sebascuenta]

Thank you, guys.
I managed to integrate each of the components in each channel.

I am now trying to create the report through the report/publisher tool.
I left in the template only the Table with all Peaks, however, when I try to apply to the sample set, the resulting report has the message "Unable to make report because information doesnt match the required data" or something like that.
Where is the error? In the report method or in the process method?
Hope you can give me a hand.
Thanks!

[benW]

Hello sebascuenta,
The processing method and report method are probably good, you just need to use the result set instead of the sample set to bring into report publisher.

This is because you must have processed data to report the peak data as peaks are found and matched during processing. The results and result set contain the processed data, whereas a sampleset contains the unprocessed data.

Hope this helps,
Ben

[sebascuenta]

I found that the problem is the "results".
I created the appropriate Processing Method and fixed the Components Table.
When I want to apply "MEthod Set" and save. The obtained "Results" are only the selected injection at that time. Meaning that for reading all the peaks I would need to apply one by one the method set, selecting each of the injections. I would like to know what is what I don't know for making it one single step.
Thanks!

Thanks BenW. My question is how to make the "Results" set? I don't see any there. I tried to report the single peaks and single injections, and it works, but they are all scattered.

[benW]

No problem.
You can batch or background process your sample set in one as follows:
Right click your sample set > select process...

In the window "process" should be checked, then choose where to find the processing method - for now simply check the radio button to use a specific processing method, then choose your processing method form the drop down box. Choose if you want to clear calibration from the processing method and whether to calibrate and quantitate (select these options until you decide otherwise). Then click OK.

This will create a result set. Go to the Results set tab to see your newly created result set (you may need to click the update button (or ctrl + U) to update the display).

Now take this into report publisher...

[sebascuenta]

Thank you again, benW
I did as you said, but just found that the resulting "Result Set" is not created correctly.
The file appears briefly in the Results Set table, and disappears after a while. In one chance I had to open one of this, it was completely empty.

I am using the same "Processing Method", and also tried using as "Method Set" in the Process Window.
Both of them proved to work when used in the "Review" interface.
I also tried different combinations of the Clear Calibration and the Calibration/Quantitation options.
Is there anything wrong in what I'm doing?
Thanks!

[benW]

This looks like 3D data and you have extracted 2D channels in review and processed them successfully in review.

When you take the raw data channel (sample set) you need to extract the 2D channel.
Assuming this is the case, you will need to extract the same channel in the method set that you extracted in review.
To do this, open the method set and right click data channels in the left window; then select new>derived channel. For channel 1 select a channel from the drop down and fill in the values below.

Now when you process using this method set, via batch/background processing described above, Empower will extract your 2D channel and process in one hit - and your results set should appear..

[sebascuenta]

Thank you again.

I checked whether the channels in the set are 3D, however in the review window bottom part I could see that the all the channels are (8 in total) and when I checked in the Method Set window, the left side with the Data Channel and Derived Channel already had the 8 of them in Data Channel. I did add them in Derived Channel, and linked each of them to the original channels (original channel name is something like W3100 SR1 Channel1 .... ) to see if something changed. I saw that now there were sixteen 2D channels in the bottom list in the Review window.

After that I did try again to process but the same thing happened.
I wonder if some configuration is wrong...
Thanks for your time.

[benW]

take a look at the message center (the blue box with the E in the middle in the windows system icons bottom right of the screen).
Check what messages appeared with the same time stamp as when you processed (and failed) your sample set. You should have a processing category message, possibly data missmatch.

If you need, please contact me directly (via the website link>contacts) in my signature, I can take a quick call to get you on the right track.

[sebascuenta]

Hello!!
Thanks for your help.
I checked the Message Center window and figured that the assigned space for the project in Empower was less than needed. I had to open the Configuration Manager and assigned 50 MB more to the project and then the processing went smoothly.
I already worked making the report and am figuring how to optimize the final report.
I also tried to use the Apex Integrator to compare results in the smoothing of the peaks. Now it all seems to be working right.
Thank you very much for your help, it saved me lots of time.