Output question

[Kim03143]

In the output, there are a larger number of entries in the pg column formatted as 'ProteinA; ProteinB.' Does this notation represent the same meaning as in DIA-NN? I analyzed the same dataset using both DIA-NN and AlphaDIA in library-free mode. Such entries in alphaDIA are more than five times those in DIA-NN.

I followed the tutorial and set both MS1 and MS2 mass accuracies to 0, enabling automatic optimization. However, for parameters like collision energy—which aren't specifically mentioned in the tutorial—should this be adjusted based on the instrument (e.g., for a Sciex 6600)?

It would also be helpful if the 'pg' matrix could provide additional information, such as species and gene annotations.

[vbrennsteiner]

Thank you for reaching out, the grouping works as with other search engines, summarizing proteins with shared peptides into one group and avoiding over-reporting proteins.
Using your example, "ProteinA; ProteinB" indicates that there is evidence for both Protein A and B could not be differentiated given the precursors detected. Could you provide the total number of protein groups detected by DIANN and AlphaDIA? Also, consider running AlphaDIA one more time with Inference Strategy = maximum_parsimony, in order to see how the grouping mode affects the outcome.

[Kim03143]

Sorry for the late reply.

The results (hek293) are from the SCIEX 7600, as I don't know how to set the parameters for the 6600.
I will use the maximum_parsimony mode and upload the results later.

diann: default
alphadia: 7600; ms1 15, ms2 15

pg ids as follow:
diann %>% nrow()
[1] 7462
alpha %>% nrow()
[1] 5870
sum(grepl(";", diann[[1]]))
[1] 43
sum(grepl(";", alpha[[1]]))
[1] 621

unique pg overlap:

1. I understand that your current focus is on astral. Will you be optimizing parameters for sciex instruments in the future?

2. Could you provide the ms error parameters for the sciex 6600 and orbitrap exploris 480?