Open louisebuur opened 10 months ago
This indeed sounds like a problem! I've just requested access to the files so I can take a look. My guess is that perhaps the peptide strings are formatted in a way that isn't accounted for in mokapot, but I'll have to take a closer look.
Would it be alright to post examples from the pin file here as future documentation for the issue?
Hi Will, I should have given you access to the file now. And yes of course, feel free to post examples :)
The file I analysed with MS Amanda is not mine, but obtained from this data set
Thanks!
Hi!
I am having an issue with getting protein level confidence.
I have an MS Amanda output file that I am reading using the
psm_utils
package, and then converting that file to aLinearPsmDataset
This is the file that I am using https://drive.google.com/file/d/1PiztK5BY4byAR2Loup6kTf7j9Q4QMgGQ/view?usp=drive_link
I used the
make_decoys
function to add decoy sequences to my FASTA fileAnd then I use the
add_proteins
function and put in the parameters that correspond to the ones I used in the searchThen I want to assign confidence and print the results
However I get this error:
25362 out of 46118 peptides could not be mapped. Please check your digest settings.
ValueError: Fewer than 90% of all peptides could be matched to proteins. Please verify that your digest settings are correct.
I realized that I didn't include the
decoy_prefix
, so I tried to do thatRun this again
And then get this error
46118 out of 46118 peptides could not be mapped. Please check your digest settings.
ValueError: Fewer than 90% of all peptides could be matched to proteins. Please verify that your digest settings are correct.
I did double check that the digest settings are correct. And it seems that half of the peptides can be mapped if I do not specify the decoy prefix in the
add_proteins
function. So, to me it seems like there is an issue with the decoy prefix pattern.I also tried to use the default decoy pattern
decoy_
when creating the FASTA file using themake_decoys
function, and then also changed the decoy prefix in the input file. I still got the same errors.I am using version
0.10.0
of MokapotCan you give me a hint of what may be wrong here? And please let me know if I should provide further information.
Thanks in advance!