Simple data analysis in OpenLab/ChemStation

[tony_sarno]

Please don't laugh at my stupidity...

Background:
I've been using an old Agilent 1100 to fractionate my samples prior to LCMSMS. I measure nucleoside modifications so my samples are comprised of enzymatically hydrolyzed DNA. The final quantification uses both LCMSMS data (for measuring the low abundance modified nucleosides) and LC-UV data (for measuring the high abundance unmodified nucleosides). That is, I measure the fractionated nucleosides an LCMSMS and normalize them to the chromatograms of the four canonical nucleosides from an LC-UV during fractionation.

My problem:
The chromatogram from the LC-UV is a simple four-peak affair with good signal-to-noise and clear baseline separation (using OpenLab software, previously called ChemStation). I almost never have to manually integrate the peaks. However, I cannot figure out how to get the data in an Excel (or CSV) format for all the samples at once. Thus far, I have found the simplest solution to be mass-printing the PDFs (I like to keep hard copies anyway) and manually typing the peak areas into Excel for quantification! I always tell myself I'll figure out a better way but never got around to it.

My question:
How do I obtain a tabularized version of my results that shows the peak areas for all four peaks for all my samples in a given run?

Thanks in advance for your help!

[tkubowicz]

Hello

You have 2 ways to do it:

1.Go to specify report tab and pick format you want to save (there are a lot of formats: .txt, .csv, .pdf etc). Your report in specified format is saved in data folder for specific run. You can have format that fits to Excel

2. You can also save chromatogram (signal vs. time) in .csv value. You will find it in tab "File"- "Export". Than you can integrate in any spreadsheet.

You can also (however it is quite advanced) configured reporting method so you can generate report to Excel file and it looks exactly like report you see on screen in OpenLab Chemstation. You will find it in "help". It requires to load files from Chestation core.

Regards

Tomasz Kubowicz

[tony_sarno]

Hello

You have 2 ways to do it:

1.Go to specify report tab and pick format you want to save (there are a lot of formats: .txt, .csv, .pdf etc). Your report in specified format is saved in data folder for specific run. You can have format that fits to Excel

2. You can also save chromatogram (signal vs. time) in .csv value. You will find it in tab "File"- "Export". Than you can integrate in any spreadsheet.

You can also (however it is quite advanced) configured reporting method so you can generate report to Excel file and it looks exactly like report you see on screen in OpenLab Chemstation. You will find it in "help". It requires to load files from Chestation core.

Regards

Tomasz Kubowicz

Thanks for your reply, Tomasz! I've tried option 1, but it outputs one file per injection. I would then have to individually open each CSV or XLS file (I have tens to hundreds per experiment) and combine the peak areas into another file. Do you know if I can get a file that gives me the results for all the injections in a given sequence? This is very common in LCMSMS analysis, so I just assumed it would be straightforward here too.

[carlo.annaratone]

Joining CSV files sounds like a task where someone with some basic programming skills could easily help you. If you work with nucleotides, I assume you might in contact with bioinformatics: in 15 minutes they will make a PERL or R script for you to merge the files together

[tony_sarno]

Joining CSV files sounds like a task where someone with some basic programming skills could easily help you. If you work with nucleotides, I assume you might in contact with bioinformatics: in 15 minutes they will make a PERL or R script for you to merge the files together

I had been thinking about this as a solution. Guess I'll try it out unless someone knows of a more straightforward approach. Thanks for your help!

[lmh]

Yes, it is very straightforward. Use the batch processing part of Chemstation. It should be possible to add all the integration and smoothing details into a chemstation method, reprocess the batch using that method, and the result will be a table of peak areas for all compounds (you can use multiple signals from different detectors, everything) in Excel. Just a tip though: guard your .b files jealously, and never save over a .b file. They cannot be recreated, and if you save when reprocessing using a different method to that used to collect the data, Chemstation never gives you a chance to change the method again.

(I'm assuming you're using an LC-friendly version of Chemstation. If you're in the GC-versions, which are "C" I think, then it's called a custom database instead of a batch, and it works a little differently, but it's still easy).