Vitek-Lab
`PDtoMSstatsTMTFormat` Fails with CHIMERYS Data from Proteome Discoverer
Description
When using PDtoMSstatsTMTFormat to process TMT data preprocessed in Proteome Discoverer with the CHIMERYS identification node, the function produces numerous warnings and takes an extremely long time to process before eventually crashing the Jupyter Notebook kernel.
This issue does not occur when using the Sequest HT identification node in Proteome Discoverer.
The warnings (there are hundreds of them) all say the same thing:
Warning message in
[.data.table(input_duplicates, ,:=(keep, .summarizeMultiplePSMs(.SD, : “Coercing 'character' RHS to 'logical' to match the type of target vector.”
Additional Information
MSstatsConvert version: 1.16.1 MSstats version: 4.14.2 MSstatsTMT version: 2.14.2
R version: 4.4.2 (2024-10-31) Platform: aarch64-unknown-linux-gnu Running under: Ubuntu 24.04.1 LTS
Proteome Discoverer version: 3.0.1.27 CHIMERYS version: 1.7.3.10
