michaelsteidel86

A potential solution to avoid any ambiguity in case of quantification at both peptide-level and protein-level could be to propagate this information in the TMT-integrator ouput (i.e. concatenated string pointing...

Thanks. So I assume one really needs to specify RAW data here (which is actually a spectral library? Which of the options needs to be selected? ( as 'speclib_tsv' is...

- Are you refering to MS instrument method settings or DIA-NN parameters? - Would you mind providing more details on sample type? - Please share the a relevant log file.

There various published ones, i.e. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7124470/ Optimal settings mainly depend on sample type and gradient length. Would you mind sharing details on your MS settings?

 Any further details on your MS/MS? How many windows, which mass range?

Hi Fengchao, has situation changed in the meantime? Does current version (Fragpipe / Ionquant) support MBR for SILAC samples? Thanks Michael

LysC does not require any changes of default settings as it specifically cuts C-terminal of Lysines, which also Trypsin does.

Is this still considered as an open issue? To my understanding the re-analysis step based on the empirical library actually is an MBR -analysis. Please correct me if I am...