"Use Acquistion Method Set"

Empower2018

I cloned a project recently that had a number of sample sets in it. I noticed that when I reprocessed a sample set that was acquired early on in the project the results were very bad- peaks misidentified, over integration etc (I made no changes to the proc method). But when I checked the result set from the original project, it was fine. Obviously between that run and the final run, there were changes in thresholds, retention time markers etc. 

Am I right in saying that when the project was cloned, it brings with it the most up to date versions of instrument, processing methods and method sets? So that when I picked Use Acquisition method set it used the most recent version and hence accounted for the missing peaks, thresholds etc because its applying the most recent processing integration parameters to the sample set?

If that is true then even if I select "Use specified method set" or "Use specified processing method" then I would get the same result as only the most recent versions are applied? Empower Help states that using acquisition method set is helpful for bracketing set ups etc but wouldn't any processing method still process the sample set in whatever order its set up in in regards to bracketing standards and clear calibration etc lines? Any thoughts much appreciated.

MJS

Based on the wording, I'd presume it is an error in the help file.  I imagine it is supposed to be directed towards "interactive processing" rather than background processing.  When processing interactively (i.e. through the review window and saving results), then those specialized/instructional steps in the sample set are indeed ignored.

DavidHPLC

Check version history to see what changes were made? Methods tab and right click and then view as audit trail.

Setting specific processing method/method set is useful when you want to process specific results (different integration) or when working with multiple wavelengths (difference processing methods for each).

Having one method set/processing method for multiple sample sets can be problematic. I'd argue that adding a date suffix to sample set/method set/processing method (even if the content is the same) is the most organized way and it can save you from some problems along the way.

Empower2018

Hi DavidHPLC, yes that's our policy to use one method set to process all system-specific runs. I checked the differences between the PM used to process the earlier sample set and the later one and there were several which explained why using the recent PM to process an earlier sample set gave such strange results. 
Do you know why using a PM to process a run and using the acquisition method set may be different? Help states that the specific functions and bracketing in a sample set like Clear Calibration etc aren't carried out if only a PM and not method set is used...

MJS

Using a PM vs a method set should only matter if you have PDA/3D data as the method set is required to extract the chromatogram before the PM is applied.  For our simple 2D analyses like content and dissolution, we use PMs only most of the time as it is simply one less thing to create/save/edit whereas we have to use method sets for degs analysis in order to extract the chromatogram.  Using the acquisition method set for processing is just another way to specify which method set would be used.  None of these options should ever affect how bracketing would function if configured correctly.

What is the title on the help article? or can you save that as a pdf and post to the thread?  That seems a bit odd.

I do have one method where I have to use the "Acquisition Method Set" approach for processing.  It was a method that was inherited a long time ago for assay/degs that resulted in three channels.  It used a low-level standard to quantify degs (2 channels), and a high-level standard to quantify assay on the same injections (rather than inject twice or in two separate analyses).  Using the Acquisition Method Set for processing results in a single result set with everything as the processing instructions in the sample set are adjusted accordingly to point to one method set for calibrate/quantitate instructions, then clear the curve and do it again for the other.  On the report, I'm able to filter based on the channel name to report the degs and assay in separate tables with their own calibrations.  I don't see any limitations to specific functions or bracketing and I've had this approach for this old method for years.

In simpler methods like the content/dissolution, we use bracketing functions all the time and use just the processing method rather than a method set.  I can't think of any function or bracketing issue not working properly.

Empower2018

Hi MJS, I cant attach it but its Empower 3 FR2 and the title in the Help Bar is "Background Processing and Reporting dialog box". It describes the options like Use Acquisition Method set, use specified method set and under the use specified processing method section I quote:

"Specifies a processing method other than the one in the acquisition method set. After selection, select a processing method from the list on the right. When background processing a sample set, any specialized processing that was part of the acquisition method set does not occur, including the clear calibration lines in a sample set method. Instead, sample sets are processed as defined by the specified processing method"

I haven't been able to recreate this- I processed a few sample sets with bracketing standards set up within the sample set and, as long as there was a clear calibration line between different standard strengths, I always got the correct standards and points for each set of samples ie the clear calibration line in the sample set worked perfectly. This was the same whether I used a method set or processing method, and even when using processing methods and method sets that were different to that used in the acquisition method set. 

In fact, the ONLY way I could get the clear calibration to not work is if I simply didn't put it into the sample set method- then my standard points were all wrong, including all the strengths in one curve and yielding incorrect quantitation. I understand with the PDA data requiring a method set to process because I have a method with 2 derived channels extracting 2 single wavelengths. 

Maybe its a mistake in the Help because unless im missing something, the clear calibration line always works whether the sample set is processed with a PM or method set and is not affected by selecting the clear calibration tick box in the background processing box either..

Empower2018

HI MJS, yes I suspected as much, there are a few little mistakes or confusing statements in the help of Empower. 

HeatherLongden

In my explanation in my head 'Use Acquistion method Set', means, to me: Use whatever Method Set is used in the SampleSet Method. So, for the case of low and high standards I mentioned before, I can use DIFFERENT processing methods by selecting Use Acquistion Method Set. I used to always advise to use this setting for batch processing bracketed Sample Sets, because there was a couple of in frequent/ odd situations where "use specified Method Set" or "specified Processing Method" might skip bracketing instructions. I have no idea if those edge situation still happen, but it built me a habit.