vdemichev
commented
8 months ago Hi Nicolas,
Yes, correct, can reuse quant files. .quant files contain full identification information & integrated fragment & ms1 signals. .quant files are considered only for raw files specified, i.e. if you remove some raw file from the list, DIA-NN will ignore the respective quant file. Normalised intensities are calculated after the second pass.
Best, Vadim
Dear Vadim,
apologies to bother you with such a trivial question, but I didn't find the answer among all the post. I am using DIA-NN V1.8.2 beta 27 with MBR. I had to stop my DIA-NN process because it was stacked in processing the same raw data file for 3 days. It appears this raw data does not contain any peptides. But now I need to continue the processing of my 800 samples cohort. I hope I don't have to redo everything from scratch. If I understood properly, I should be able to restart the processing by removing the samples i want to exclude and by using the .quant files generated at the first pass. Is it correct? Also I don't find what information is saved in the .quant files so I would have another question: I prepared pooled QC for every of my batch. I know the variability of within a batch is neglectable and i would like to remove them from the processing to speed it up. What would happen if I also removed all my QC from the sample list so the .quant files of the already processed QC are not considered after i restart the processing? Are the normalized intensities (cross run normalization) calculated after the second pass of the MBR or does it start already at the first pass?
Many thanks in advance for your answer and for all your hard work :)
Regards, Nicolas