Saving config file

[algirdasvelyvis]

Dear Michael,

First of all, thank you for creating Unidec and releasing it under a very permissive license.

I'm using UPP (UD v. 8.0.1) to process a set of intact mass Waters spectra. It seems to me a convenient workflow is to open a representative chromatogram in UniChrom, work out a good set of processing and peak picking parameters, save that set of parameters into a config file, and pass it to the batch processor. However, saving a config file seems cumbersome. Perhaps I'm missing something, but I could not find a menu command to export processing params from UniChrom. There is File -> Save Default Config File , but it seems to me imprudent to overwrite the default. I'd much rather save a current set of params somewhere in a working directory.

As a workaround, after establishing a good set of params I tried generating an HTML report, which includes processing params at the bottom, then pasting the parameters into a config file. It seems to me that the parameter set from the HTML report is incomplete or incompatible with UD v. 8 E.g. for the upper bound of the charge range, HTML report provides variable 'endz' but not 'numz'. Loading parameters into UD it seems to me 'endz' is ignored, but 'numz' is read correctly - it populates the correct box in the GUI.

At a moment the only method I can find to access the UD config parameters while processing a chromatogram with UniChrom is to:

1. extract m/z as a manual selection in UniChrom;
2. click "Open Selection in UniDec GUI";
3. perform processing of the mass spectrum in the UD GUI, which autosaves the correct and complete config file;
4. copy and use this config file.

I wonder if there is a less convoluted method to export a config file?

Cheers,
Algirdas
p.s. apologies if this post turns out to be duplicated, I tried posting it yesterday, but was defeated by github.

[michaelmarty]

Hi Aldirdas,
Good to hear from you. You've done well to work around on these things. I think there wasn't a more straightforward way to do it. It might be possible to put in the HDF5 file as the conf file, but I'm not sure.

In any case, it was easy to add this feature in. I just committed it to the v3 branch.

Try this version and let me know if it does the trick. Basically, I've added "Save External Config File" as an option on the File menu. My suggestion is to add _conf.dat at the end, but it's not strictly necessary to use in UPP.

https://www.dropbox.com/scl/fi/frcdukqbl59pp1vnj3riw/UniDec_Windows_250325.zip?rlkey=d7579gfs5c7eoyusee08uspi0&dl=0

Thanks!
MTM

[algirdasvelyvis]

Hi Michael,

Thanks for a quick update. The new menu command works like a charm.

My suggestion is to add _conf.dat at the end, but it's not strictly necessary to use in UPP.

I understand that UPP can run with the default settings for all processing and deconvolution parameters, even if no config file is provided and no individual parameters are set in the input table. But I'm not sure what you mean by "at the end". Do you mean that I should save my *_conf.dat at the end of UniChrom workflow when all parameters have been tweaked to my satisfaction? For sure! Or are you saying that the order of the columns matters in the input table, and "Config File" column should go last? Based on the help file, where you write "Note, any settings specified in the batch file will override the config file." I thought that the geometric order of the columns within the input table is irrelevant. As an example, I've been using the attached input table, and it seems to be doing what I want.

(All the nans must be coming from pandas conversion of absent values in the input csv, the columns with individual parameter values I have mostly empty in my spreadsheet and only add values on line 7 where I want to overwrite the config file.)

Again, this seems to work, but if you see any potential problems - please let me know!

Best,
Algirdas

[michaelmarty]

Glad it seems to be working! Good question. What I meant was to add it to the end of the file name, like you've done with mab_conf.dat. In practice, with UPP, any file that you put in the Config File column will work as long as it's a readable text format. However, adding _conf.dat at the end of the file name is recognized in other parts of the programs, mostly with the drag and drop feature. If you drag and drop test.txt it will attempt to open it as a data file, but it will recognize anything as *_conf.dat as a config file. Again, totally optional for the UPP workflow (which is why your SV_4122.dat works fine), but makes drag and drop more convenient.

[algirdasvelyvis]

Ah, it's the file name. Got it! [facepalm]

[michaelmarty]

No worries. Glad this worked for you. We'll include this in the next release. Thanks!