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Conceptually similar in some ways to what happens in pVACvector. In working with peptide manufacturers, there is sometimes a case where the manufacturer wishes to add a few (e.g. 1-3) amino acids to…
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Hi,
Is it possible to change the filter for peptide length for predictions ?
Although the default (8 to 12 residues) can work well for some allotypes, others may include shorter or larger peptides…
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the default peptide length in DIANN is 7-30.
Clearly, this is an overall suitable r…
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Hello. I am very glad to know about this package.
I am working on a way to represent peptide coverage over a protein sequence (i. e. represent peptides identified by MS over the whole protein). I t…
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https://www.biorxiv.org/content/biorxiv/early/2017/12/24/239236.full.pdf
Very cool work for predicting binding of peptides to MHC-I. Would welcome PRs adding the benchmark datasets featured here or…
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Simple options would be:
a) grouping of shared proteins (this is happening now)
b) only unique peptide
Future options could/will be different versions of the parsimony principle
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For a while, we have been avoiding `Protein Group` modelling in the psm and feature in the format. @jpfeuffer triggered this issue a long time ago. Our main tools DIA-NN, OpenMS TMT, and OpenMS LFQ pi…
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_**Case 1: Inserting the fragment below CHEM structure with R1-R1, R2-R2 bonds**_
**Steps to Reproduce**
1. Open two Ketcher browser tabs – the Macro mode
2. Open this file (first unzip) [CHEM R…
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Hello, firstly thanks so much for this great software!
I have a query regarding data analysis with DIANN v 1.9.1. I analysed two samples together in DIANN and identified 7,260 proteins and 7,246 pr…
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Hello,
My understanding is that the `coord` column contains the coordinates of the _splicing event_ (e.g. the coordinates may be that of a skipped exon) and not the genomic coordinates of the seque…