diaPasef: No objects to concatenate

[rednaSander]

Describe the bug
When analyzing phospho-enriched diaPASEF data using a Spectronaut TSV spectral library, AlphaDIA fails with "No objects to concatenate" error during the search. The analysis works for Orbitrap QEHF-X data with similar libraries but fails specifically for diaPASEF data. This is the case on the "main" and "development" branch (v1.8.2.) I've already tried the solutions from previous discussions on this issue, but they haven't resolved the problem.

To Reproduce
AlphaDIA_Log_Tims_diaPasef_NO_OBJ_TO_CONCAT_ERROR.txt
config_yaml.txt
test.spectronaut.csv

system:
Linux thestral 6.1.0-21-amd64 1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux

[GeorgWa]

Thank you for submitting the bug! This should be addressable quickly.

Searching large libraries is currently not a supported use case and it might take some time to search though.

[rednaSander]

@GeorgWa
Thank you for your response.
I have some follow-up questions to better understand the limitations:

1. Could you clarify what constitutes a "large" library in this context? My current library contains approximately 5 million target precursors.

2. I've successfully used larger libraries with non-timsTOF PaSEF data in the past (20M target precursors). Does this mean those results might be unreliable since searching large libraries isn't a supported use case?