Manual integration in Chemstation for LC 3d Rev B.04.03[16]

[ender6574]

I'm using Chemstation for LC 3d Systems Rev B.04.03[16] with unique folder creation turned on. After an impurities run, I have gone through and done all necessary manual integration through the navigation pane and saved it with the data file each time. I'd like to see a batch file that included my manual integration but this doesn't seem possible since I didn't do the manual integration within the batch. Alternately, I'd like to be able to output a summary report similar to the batch report without using a batch. Preferably the summary report would be in Excel format, or in a format that is easy to copy into Excel. All I need in the report is the Compound name, area, retention time and height, laid out horizontally like it would be in a batch report. Any suggestions?

I should note the following:

I'm in a research environment, manual integration is definitely acceptable

The method is looking for drug impurities and potential leachables from a medical device. The sample injection volume is high so that the imputies peaks show up, the two main compounds in the samples are not of interest.

Manual integration is necessary because the chromatograms are often so entirely different among samples that a single set of integration parameters cannot be made to work for all samples.

The reason I'd like to know this: this is my first time using this version of chemstation where manual integration changes done in the navigation pane and stored with the data file are completely seperate from manual integration done when reviewing the batch. I did not know this, I thought that if I did all my manual integration in the navigation pane and saved it to the each data file then when I opened the core batch file it would contain the manual adjustments. This is not the case. Even if I reprocess the data with the manual integration saved to each data file, which re-creates the core .b batch file, the batch will not contain the manual integration.

The problem is that I've already done 16 runs over 10 weeks of a 26 week stability study and I don't want to have to go back and open each run as a batch and then re-do the manual integration for all ~6000 samples when I already have the integration done and saved with the data file.

But I can't see any way to get anything equivalent to the batch report based on the modified data files. I'm not able to get sequence summary reporting to do it right, even as a text file (sequence summary reports won't print as Excel files). And I don't even know where to begin with macros.

Any help would be greatly appreciated, I'm looking at having to re-do about 3 weeks of work here.

Thanks!

[ender6574]

The macro that is being discussed in this thread:

viewtopic.php?f=4&t=22429

looks like it might be just what I need. Could someone please send it to me at cg6574@gmail.com, or please let me know were to find it online.

Thanks!

[lmh]

This is actually quite easy to do within Chemstation. A suitable procedure is as follows:

Create a method with peaks in the right places, named as appropriate, and with calibration levels if you are doing proper calibration rather than just trying to get the peak areas. At this point you don't need to worry about integration at all, just make sure the windows for each compound you will eventually identify are wide enough to contain the peak properly in all the samples you wish to work with. If your peaks move around and you can't specify a window, then you are probably doomed (but by this stage you're also probably so far off the scale of reputability that you shouldn't be proceeding anyway!).

Open your sequence in batch review mode, specifying that your method should be used.

Make the manual integrations on the first file

When you're happy, click the "Mark changes for current run done up to now" button, which is the small picture of two peaks next to a floppy disk, to the right of the "Start" button in the batch part of the screen (below the chromatograms).

Repeat the last two steps for all files you wish to integrate manually.

Click on "Start" and go off for a cup of tea.

When it's finished, export your batch data as normal. The peak areas will be those of your manual integrations, and not anything that might have happened automatically from the method.

(Personal note: I do not condone manual integration in particular, and can't remember the last time I was reduced to doing it, so I'm not recommending the process above, but on the other hand I do believe in using manufacturer's software to do what it's written to do, and turning to third parties and macros only when absolutely necessary. I have some suspicions about that other thread because it seems to be attracting a very high percentage of extremely low-posting individuals asking for a macro whose actual function, beyond "exporting data", has never appeared)

[ender6574]

I'm going back and doing it over again within the batch as you describe. This has the disadvantage of lost functionality (no undo button) and according to all Agilent sources this is NOT the way Chemstation is meant to be used. Batch analysis is meant to be used for a first look at a run, or for processing simple, routine runs.

If you don't have need for manual integration ever, then let's suffice to say that you haven't done any raw research into unknown impurities and unknown leachables in quite a while. It is acceptable in this research environment and very necessary.

It boggles my mind that processing from the Navigatioin Pane in Data Analysis view, which is intended by Agilent to be the primary way of processing, doesn't have any native export to Excel functionality for entire sequence results. But it doesn't, so yes, I am going back through each batch and re-doing things as you describe.

[lmh]

I don't envy you the task of doing manual integration on 6000 samples... good luck. Maybe there's a way to get the ones you've already done, but I'm afraid I don't know it.

Just a note: if, while you're doing your integrations in batch mode, you save a batch file, I'd strongly recommend saving it with a new name. The dialogue that pops up when you open a batch file, asking whether you wish to open it with a different method, will never reappear again if you save a batch file that you've opened with a different method, so you're stuffed if you later decide you want to process the same set of samples differently. This is a very annoying feature.

I'm sure you're right that Agilent really had simple automatic processing in mind when they provided the batch mode (i.e. no bracketing or clever stuff going on, just apply one calibration to a whole set of samples and tabulate the results). Perhaps I shouldn't have said "quite easy to do", because with one or two peaks in a handful of samples it's quite easy, but with larger numbers in 6000... well, like I said, I don't envy you... I hope all goes well and you get the data you need.

[ender6574]

Yeah, you definitely make a good point about saving the batch file with a new name, that's the first thing I do after I open one. I actually have been analyzing the same set of samples using 3 different methods (two are isocratic assays and the third is gradient for leachables/impurities, with appropriate equilibration injections between each) in a single multi-day run. This works but it's essential when processing, for each method, to open the core .B file with that method (or the processing version of that method) and select the samples to be processed with that method. Then immediately save the the batch file with a new name indicating the method. Do this for each method.

Just thought I'd share how I'm using it, and to emphasize your very good point about saving the batch file with a new name

And you're right that batch processing is great for a one or two peak assay. We don't even use the calibration functions within Chemstation because our raw and processed data is stored electronically (in compliance) and we just export the batch report and do the necessary calculations in Excel.

It really does boggle my mind though that the great export functionality is built into the 'first pass' batch process, but nowhere to be found in the core processing functionality

FWIW, I did get a hold of the macro to export to Excel, first from Agilent and then from someone from this forum (I was hoping that they would be different). It really looks like it works but I can't use it because my IT department won't let me install the necessary VBA converters that would allow me to open up the resulting Excel file.

[Yama001]

IT departments, more and more they are just an obstacle to getting useful work done.

[koenvanderdrift]

Stumbled upon this thread while looking for information on manual integration.

Is there any way to automatically mark in the report whether an integration was done manually ?

[kvirkler]

Stumbled upon this thread while looking for information on manual integration.

Is there any way to automatically mark in the report whether an integration was done manually ?

I came across this thread today looking for help for another integration issue and saw your question. I have recently created a report that will flag manual integration. It involves a custom macro. I have not explored a more user friendly way to do it...if you are interested in this solution I can share more details of the code I used.