Support for Shimadzu LCD mass spectrometry streams

[silasmellor]

Hi, is it possible to add a parser for Shimadzu .lcd files? I have attached a file example for reference.
Best, Silas
Anthocyanin_2_MeOH001.zip

[ethanbass]

I will try to look into it, though I can't really make any promises or give you a timeline. It's a little bit tricky since the format is not documented at all, as far as I know. It would be helpful if you could provide a little more information about your file (e.g. what kind of instrument/software it was produced with and what the detectors are on the machine). Thank you for sharing the file!
Ethan

[silasmellor]

Hey Ethan, that is all i can ask! The file comes from Shimadzu Lab Solutions v 5.71. The instrument is a shimadzu LC-20 with PDA iirc, but i will double check and let you know.

[ethanbass]

Thanks. Also, you may already know this (and I know it's not as convenient as reading the .lcd files directly), but I believe you can export the raw PDA data from LabSolutions by right clicking the sample name and selecting File Conversion:Convert to ASCII. These ascii txt files do have a parser in chromConverter already.

Also, if you can generate the ascii file for the .lcd file you sent it would be helpful to have as a point of comparison.

[silasmellor]

Hey Ethan, i was actually not aware of that, that sounds excellent! I will try it and upload the ascii file for you.
Thanks again,
Silas

[silasmellor]

Hey Ethan, here is the corresponding ASCII from LabSolutions.
Anthocyanin_2_MeOH001.txt

[ethanbass]

Thanks for providing this file! I don't know if you tried to read it yet using chromConverter, but it actually throws an error because it has commas as the decimal separator (european style) rather than periods (american style). I will put up a patch shortly that can read the european-style files.

[ethanbass]

This should be fixed by 725ddff. You should now be able to read in these ascii files at least:

x<-read_chroms(path_to_file_or_files, format_in="shimadzu_dad")

[silasmellor]

Hey Ethan, yep i did try it with the ascii and got an error, but didnt have time to figure out what it was about. Well, you fixed it before i even got that far so thanks once again!

[silasmellor]

edit:fixed the format_in parameter, still get an error...
edit:tried updating from CRAN and github, same thing

Warning in read_chroms(paths = "Anthocyanin_2_MeOH001.txt", format_in = "shimadzu_dad") :
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
scan() expected 'a real', got '0,00000'

I feel i should apologize on behalf of european PCs, for some reason comma is default decimal here even though it means we have to jump through all sorts of hoops with our data files...

[ethanbass]

This is the old error -- it should be fixed in the latest version. Did you refresh your R session after reinstalling the package? Usually the old package is still cached if you install a new version of a package and don't reset your R session. The CRAN version will not be updated for a while, so that one will not work.

I'd suggest:

1. install new version from github: remotes::install_github("ethanbass/chromConverter"
2. Reset R session (In R studio, you can do this by selecting Session:Restart R).
3. Reload the package: library(chromConverter)
4. Try again: read_chroms("Anthocyanin_2_MeOH001.txt", format_in="shimadzu_dad")

[silasmellor]

Yep, you're right, i had restarted the session before reinstalling from github but didn't think to do so after... works now!

[ethanbass]

Excellent! I'm glad to hear it is working now

[captainsailboat]

Fully willing to do what I can to help with adding a .lcd parser, it would make life a lot easier! Let me know if there is anything I can do to help.