Not recognition of SILAC labels

[martacouceiglesias]

I am trying to analyse some SILAC data labelled with heavy and medium lysine and arginine. I used the following lines in the additional options: --fixed-mod SILAC,0,0,KR,label --lib-fixed-mod SILAC --channels SILAC,L,KR,0:0; SILAC,H,KR,8.014199:10.008269; SILAC,M,KR,4.025108:6.02013 --peak-translation --original-mods --relaxed-prot-inf But when the analysis starts some WARNINGS appear and the labels are not set (as far as I understood from the message of "unrecognised option")

Did I miss something crucial to put in the Additional options?

[vdemichev]

Strange, looks like some problems with commands being passed. Is the keyboard set to English? Try to re-type them? Also, M channel should be specified between L and H.

Best, Vadim

[martacouceiglesias]

I change the channel and retype it and it worked! thanks!

[martacouceiglesias]

Hi again! I reopen the issue as the actual problem is regarding the same analysis. The analysis runs perfectly now but when I open the report.tsv not any of the peptides is label as SILAC. I am reusing one dataset that we already analyse and that has labeled peptides for sure. How is this possible? The spectral library is not done with SILAC peptides but with the full genome of mus musculus. Do I need to create a specific spectral library with SILAC peptides? Thanks for the help! Best, Marta

[martacouceiglesias]

Here it is the log report report.log.txt

[vdemichev]

How was Mus_musculus v8 3_2021.predicted.speclib generated?

[vdemichev]

No 'SILAC' in Precursor.Id column?

[martacouceiglesias]

The Mus_musculus v8 3_2021.predicted.speclib was generated by the previous bioinformatician (I guess from the mice genome (Mus_musculus v8 3_2021_validated.fasta) FASTA file with the following parameters, but could not confirm it 100%)

Yes, there is no SILAC in the Precursor.Id column but, interestingly, in the file report.pr_matrix_channels_translated.tsv the columns for heavy and medium are created but they are empty. I created the spectral library as I describe before and I am currently reanalysing to see if that was the error.

[martacouceiglesias]

It has finished but the problem still is there. No SILAC labelling nowhere

[martacouceiglesias]

I tried the same data but just looking for Medium SILAC and it worked (I have SILAC peptides). So the problem is to try to find both analogues at the same time. Do you have any tip on what do I need to add to proceed with the analysis of both analogues at the same time?