creating and matching library to unknown compouds

[sindibad]

Dear sir
can you please show me the steps to create a PDA library in clarity.
I could understand that with standard I must construct calibration curve for each, is it necessary? second should also I create a method for peak purity before to construct library
can you please show me what should I do
kind regards

[Daniel Mentlik]

Dear Samira,
the creation of the PDA spectral library in Clarity is pretty simple. Open the PDA Chromatogram window by using the Window - PDA Window menu command from Chromatogram window (Instrument type must be LC - PDA or GPC - PDA for the option to be there). Then, use the Library - New command to create new library (it becomes active, but is not saved yet), and use the Library - Save As command to save it under custom name. The library is then ready to be used with the other commands.

You can add spectra to the library by selecting the desired retention time, then adding the spectrum to the active library by using Add to Library... function from the local menu (invoked by right-click on the spectrum).

I could understand that with standard I must construct calibration curve for each, is it necessary? second should also I create a method for peak purity before to construct library

Please elaborate further, I do not understand what you are trying to achieve, so any answer on those would be probably misunderstood.

Best Regards,
Daniel

[sindibad]

many thanks,
to add spectra in the library, should I must before construct the calibration of standard, meaning UV spectra and absorbance depend also in concentration, so each UV standard to be put in the library must have their uv spectra depending also on their concentration
Please if Im not clear, I can try to explain more
kind regards

[Daniel Mentlik]

Dear Samira,
the spectra are normalized for operations regarding spectral libraries, meaning you do not need to make calibrations etc for each peak, and you do not have to use all compounds whose spectra will be put into library at the same concentration. Of course using as pure compounds as possible and as much concentrated samples as possible (in the linear range of the detector) when putting compounds into library is beneficial.

Best Regards,
Daniel

[sindibad]

Dear daniel
I come accros on the net of this file recommanding the standards curves of standards before creating library.
is it correct? as you do not recommend me to make these standards curves if we need to create library
my second question is related to adding signal which I could not understand in which case should we work on it:
the following sentences is taken from manuel ''Add or replaces the chromatogram signal with a new
signal taken as a cut from the PDA data.'' what does it mean, and when should I work with add signal in PDA extension
many thanks
best regards

[Daniel Mentlik]

Dear Samira,
I have to admit I have never seen the file you linked before. Obviously it was created by someone in Korea, possibly from YoungLin, and most probably it describes the settings made in Clarity used with their particular PDA detector. I haven't checked it thoroughly so cannot confirm every letter written in there, but using different PDA detector most probably for different analytical purposes may make the manual slightly off.

I am not discouraging you from running the calibration standards you mentioned before, just thought that for the purpose of creating the library, it would be fully satisfactory to run each standard compound to be added to the library once, or use a mixture of these standards where the compounds are well resolved. After that, you can add spectra of the compounds to the library under the situation where each compound is "clean", as opposed to adding spectra found in real samples (which will be modified by matrix, possibly other co-eluents etc...)

The sentence Add or replaces the chromatogram signal with a new signal taken as a cut from the PDA data. means what it says - under normal conditions, Clarity works with "standard signals", something a simple UV detector would provide. These signals in the PDF represent the absorbances measured on a single wavelength. It strongly depends on the PDA detector control module used how many (if any) such signals can produce.
Aside from such normal signals, PDA detectors create so called matrix data, which is a field of data points for each wavelength and each time point. As opposed to standard signals, which are one-dimensional, the PDA signal is two-dimensional. From such field you can get information on the spectra at any time of the analysis, or create artificial signals by selecting any single wavelength and showing all data points for that wavelength over the whole course of the analysis. The function debated simply allows the creation and display of such secondary one-dimensional signals.
You might want to use such functionality for example in cases you want to make sure some compound is or is not in the sample, when you know that it should demonstrate on particular wavelength. This way you can extract the particular wavelength signal and inspect it, which is much more transparent then inspecting whole matrix.

Best Regards,
Daniel

[sindibad]

Dear daniel
I m creating a new library for PDA UV compounds, I create the UV spectra and add spectra to the new file of library, but how can I visulize the content of the library of such compound and see the number of PDA UV I have construct
any suggestion please because I could not see what I have added to the library
best regards

[Ivan Vins]

Dear Samira,

in the PDA window set the Spectral View and Spectral Library View.

In Spectral Library view you will see the table with spectra in currently opened library (Use Library, Open), the spectra could be displayed in the Spectral view by the Show checkbox