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Hi,
when I submitted my search results to XiView, I was asked to enter the masses of the modifications (btw, which one: average or monoisotopic?) which are were all set in Xi01 and are kind of stan…
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When parsing example file https://github.com/HUPO-PSI/mzIdentML/blob/master/examples/1_2examples/crosslinking/xiFDR-CrossLinkExample.mzid, I find these 2 protein entries as DBSequence elements:
```
…
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I think it’s unclear what the current correct cv terms to be used for the ion series searched for (including losses) are. See pg 28 of the spec.
There are multiple deprecated / obselete terms, the …
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```
We should have a way to represent Protein Ambiguity Groups in mzTab. My
suggestions is that we can add an optional columns with the CVterm MS:1001591
which is the anchor protein. If we use this …
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Since #6 needs an update to the specification from my side I would like some things to be specified a bit clearer in text in the specification. For these there does not have to be any changes in the f…
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I'm trying to run samifier but I'm getting this error (CGI_10000004 is a protein ID) - please let me know what I'm doing wrong. Thank you!
Start of sequence in gene CGI_10000004 overflows gene
at au.…
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how to get MGF and mzId
And, how to get the fasta too (is there a web service?)
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```
What steps will reproduce the problem?
1. Import .dat file
2. Look at PTM section of converter
What is the expected output? What do you see instead?
MonoDelta values are incorrectly rounded value…
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in file the https://storage.jpostdb.org/JPST001851/membrane_5pc_1200IDs.mzid (xiFDR output I believe) there is inconsistency as to whether the "crosslink donor" CV term is accompanied by another CV te…
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Some of the parameters are not actual parameters of the specified engines, e.g.:
```
{
"default_value": 1000,
"description": "m/z value that is used as basis for the conversion from ppm …