Getting the full LCMS data in text format

Which software/version are you using, the answer will likely vary based on that. In CDS 2.7 (what I'm using), I know you can report out peak height, which would be the same as the intensity for the DAD. If by m/z intensity you mean height of the TIC at the peak for a compound, then this can similarly be done. If you mean percent intensity of the base peak, I don't think you can directly call that, but you may be able to work something out in custom calculations.

What I would do is make a very simple custom report in IR with a couple columns reporting the peak heights for DAD and TIC, test how well it exports to CSV and adjust until it gives me what I want, then go into the processing method, link that report, and tell it to print to file as CSV. If you have CDS, this would probably get you what you're looking for. If you have some other software, I can't say much.

Hello,

If you are asking about exporting the raw data points as a CSV file that is possible for the chromatograms both collected and extracted but not the spectra. If by time point you mean RT of a peak, then as the other reply states you would need to build an IR report and create a CSV from it. This is for OpenLab CDS 2.x, the answer would be different for Chemstation as the process is manual in that software. 

Marty

Hi Cole! Thanks for the answer. I'm also with 2.7. I need to report the raw data points for the DAD chromatograms and the full MS(+&-) spectra data at each time point of aquisition. I though it might work that way but I could find a way to include the MS spectra data. Thanks!

Hi Martin, thanks for the answer! Unfortunatelly, I also need the full MS(+&-) spectra data for all the chromatogram. I've tried it with the CSV pluging but as you mention is not possible for the spectra data and then I got stuck.

Hello,

I am not sure what you are doing with the data but the closest thing to a universal format that can be exported with the spectral data is AIA(netCDF) format. 

Marty

If what Martin said isn't quite what you are looking for, I know you can put spectra in as objects in reports and you can export reports as text or csv. I wonder how it would look when it converts a spectra object to csv. Maybe something you can parse to get what you need. If I may ask, why are you doing this? CDS IR has just about everything you would need in order to report data with the added benefit that the data can't be tampered with (reasonably). If you need the spectra and chromatograms, there are plenty of default reports that do that. You don't get the granularity of exact intensities at every point, but generally, you only need the intensity at the highest point of a peak. CDS takes away most of the data handling that you would need to set up with raw data.