spectral library formats

[GeorgWa]

Discussed in #375

^{Originally posted by rednaSander November 15, 2024}
Hi,

Issue:
The software crashes when attempting to load a .spectronaut.tsv spectral library file.

CopyEnvironment:

• Data format: TIMS diaPASEF (.d)
• Library format: .spectronaut.tsv

Questions:

1. Is the .spectronaut.tsv format currently supported?
2. For the 'generic' .tsv library format mentioned in the documentation, could you please specify the required column headers and their expected contents?

Additional Information:

• The crash occurs during the library loading step
• No error message is displayed before the crash

log.txt

[GeorgWa]

Hi,

Thanks for reporting the bug. I moved this to an issue so we can track it.

In the log you attached the library was loaded correctly (see log) and the crash happened during the search.

0:09:28.922740 INFO: ============ Library Stats ============
0:09:28.922777 INFO: Number of precursors: 7,949,947
0:09:30.066559 INFO: 	thereof targets:3,976,150
0:09:30.066689 INFO: 	thereof decoys: 3,973,797
0:09:30.130564 INFO: Number of elution groups: 3,976,150
0:09:30.130678 INFO: 	average size: 2.00
0:09:30.358665 INFO: Number of proteins: 36,330
0:09:30.377999 INFO: Number of channels: 1 ([0])
0:09:30.378151 INFO: Isotopes Distribution for 4 isotopes
0:09:30.378175 INFO: =======================================

The crash in the log might have been due to hitting memory limitations. Is this a separate issue or the one you are referring to with the library.

[GeorgWa]

If you have a spectronaut library which is failing to load it would be great if you could send a minimal example. We will add it to our test suite.

[rednaSander]

The crash of the search was a due to a memory issue which is now fixed.

While the Spectronaut library loads successfully, I notice that all entries containing phosphorylation modifications (defined as [Phospho]) are being removed during import because it is seen as an unkown modification. Is there a way to define "Phospho" as a custom modification in the YAML configuration to prevent this removal and ensure these modifications are properly recognized?

from log:
"0:00:00.050188 INFO: Loading .tsv library from /home/sander/apps/slim/experiment_1/human_pasef_phospho-enriched/speclibs/Human_PhophoE_005_speclib.spectronaut.tsv
425921518 Entries with unknown modifications are removed"

AlphaDia_log.txt

Current configuration yaml (as a txt file)
config_yaml.txt

a section of my spectral libarary spectronaut.tsv
speclib_section.spectronaut.tsv.csv

[rednaSander]

Changed modification definitions from "[Phospho]" to "[UniMod:21]" and it is now successfully recognized. But Now I am still running into the 'No objects to Concatenate' error

[mschwoer]

Hallo,
Please check if the issue still persists with v.1.11.0

best,
Magnus