In "Error_Build_Spectral_Library_Fragpipe_pepXML.txt" the error is:

While searching for spectrum file for the search results file 'C240501_C_elegans_Lib_100ng_17min_dda_141.pepXML', could not find matches for the following basename with any of the supported file extensions (_uncalibrated.mzML, _uncalibrated.mgf, _calibrated.mzML, _calibrated.mgf, .mz5, .mzML, .mzXML, .raw, .wiff, .wiff2, .d, .lcd, .ms2, .cms2, .bms2, .pms2):
D:/C_elegans_lib_3/split_peptide_index_tempdir/C240501_C_elegans_Lib_100ng_17min_dda_141
In any of the following directories:
(a few directories are listed)

What that error is saying is that it was trying to find a file whose name might have been any of the following:
C240501_C_elegans_Lib_100ng_17min_dda_141_uncalibrated.mzML
C240501_C_elegans_Lib_100ng_17min_dda_141_uncalibrated.mgf
C240501_C_elegans_Lib_100ng_17min_dda_141_calibrated.mzML
C240501_C_elegans_Lib_100ng_17min_dda_141_calibrated.mgf
C240501_C_elegans_Lib_100ng_17min_dda_141.mzML
(plus a bunch more filename extensions that are not likely to be a file that you have).

Do you have a file somewhere with any of those names?
If you have a .mgf file somewhere with a similar name to that which you could try renaming it to "C240501_C_elegans_Lib_100ng_17min_dda_141_uncalibrated.mgf" and see if that works.

In "Error_Build_Spectral_Library_PEAKS_pepXML_Converted.mgf.txt" the error was:

While searching for spectrum file for the search results file 'db.pep.xml', could not find matches for the following basename with any of the supported file extensions (.mz5, .mzML, .mzXML, .raw, .wiff, .wiff2, .d, .lcd, .ms2, .cms2, .bms2, .pms2):
C240501_C.elegans_Lib_100ng_17min_dda_141.d

That error seems to be saying that it's looking for a file whose name might be, among other things "C240501_C.elegans_Lib_100ng_17min_dda_141.d.mzML"
I am not sure why, in this case, it's not considering that the file might have the extension ".mgf" because that's what I think we recommend that you use with this type of data.
If you have a .mzML file around somewhere you could try renaming it to "C240501_C.elegans_Lib_100ng_17min_dda_141.d.mzML" and see if this works.

-- Nick

Hey Julian,

Maybe this post can give you some insight: https://skyline.ms/announcements/home/support/thread.view?rowId=56180

If your aim is to make a DDA library my preferred workflow is:

• Process raw dda files with Bruker DataAnalysis to generate .mgf files. This is usually done by default with tunable Bruker Processing methods where the following occurs: precursor m/z has been corrected, precursor charge has been determined, determination of the ion mobility of the precursor ion, summation and peak picking of TOF scans within (user defined) m/z, 1/K0 and retention time boundaries. Optional: If calibrant signal was still observable in your LC-MS run then mass re-calibration is possible
• Take the .mgf stored within the .d folders and use that as input for PEAKS
• Export the PEAKS results (i.e., .pepXML or .mzID)
• Use the PEAKS results and the .mgf files you took from the .d folder to create the spectral library

You can get away with working with the .mgf and .mzID results from PEAKS if you use the raw data as input for PEAKS, but keep in mind the MS/MS spectra will be charge deconvoluted (I have not found a way of turning this feature off) which might not be representative for subsequent DIA data analysis.

Bruker DataAnalysis has an extensive manual, but in the tutorial of this publication (first section; ignore the XL-MS part) you can find some insight about the user defined settings mentioned earlier: https://pubs.acs.org/doi/10.1021/acs.analchem.4c00829

Keep in mind the outlined workflow discards all the MS1 information so PEAKS will not be able to do any quant. But since you are using Skyline I am assuming will rely on the quant output of Skyline instead :p Once you have the DDA library you can import the raw .d files into your Skyline project.

The one thing you will be missing is the IMS library though. Recent updates have changed the IMS library creation from raw data (however, I have not had the time to test it yet). However, 1/K0 of each precursor is encoded by most Bruker default processing scripts and is written in the title of each MS/MS scan of the .mgf files which could be mined out with a parsing python/R script.

Hope the information helps and hit me up if I can be of further assistance!
Sincerely,
Juan C.