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@jpfeuffer are UNASSIGNEDPEPTIDE entries in this output format all PSMs?
Follow-up question: If I have a tsv output from TextExporter(idXML) I get a "flat" tsv table with only the peptide informati…
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not really an "issue" per se, but a question worth asking for the benefit of all: let's say that for many very good reasons, the proteomics lab team is running many separate batches of multiplexed sam…
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There are 400 SRC proteins in the IEDB `source` table that are not in ONTIE. Of these, 189 are inactive or related, so they don't appear anywhere in the protein tree. Of the remaining 211, 73 of them …
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Hello! Great tool you have developed.
I was curious as to the specific preprocessing steps for the proteomic data. For instance, CPTAC LUAD seems to contain 11485 proteins, where the original was …
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I'm trying to cluster a set of ~500 conformations of the same protein but no matter what I try I only get 1 cluster.
Do I need to do something to the set of structures before clustering them?
I'…
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Hi,
A couple of questions as a new user:
I'd like to run this from the command line non-interactively, when using the docker version is there any way to run it without it pausing on this expect…
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Hello,
How do you decide whether you want to work with one unique peptide or multiple peptides? I searched the DIA-NN output matrices and found the "proteotypic" column, which provides information…
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Dear Vadim,
I am struggling a bit with the cleaning of my data.
I do plasma proteomics on a TIMS-TOF and DIA-NN 1.8.1 found many low abundant proteins with an intensity under 1000. I even obtained…
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Drug product is defined in DRON as the following: a material entity (1) containing at least one scattered molecular aggregate as part that is the bearer of an active ingredient role and (2) that is it…
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See [here](https://github.com/personalcancertoolkit/openmrs-module-healthybehaviors/blob/master/omod/src/main/webapp/resources/defined_behaviors/nutrition/advice/view.html#:~:text=over%2Dindulging%20o…