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Greetings Crux devs,
I'm developing tools to support the output of Tide data generated by Crux and am trying to parse and use the pepxml generated by tide. This is, generally, far preferable to me …
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Hi @mvaudel do you think would be possible to implement phosphoRS without the fragment annotations. That means if I give you a peptide sequence, spectrum, modification, and positions. ?
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Some times the modification a peptide is selected as the "correct" one for a match where the modification site id clearly wrong.
Example:
SearchID: 12828
PSMID: 7684197169
Scan: 27259
The sda m…
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Hello,
With the capabilities in the new version, I am interested in using DIA-NN to search for histone PTMs from extracted histones. The since histone tails are highly decorated with PTMs, the main…
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Ville Koskinen is working on mzIdentML 1.2 export from Mascot and reports this issue:
we're looking at what changes are needed to export mzIdentML 1.2 from Mascot Server. One problem we've encounte…
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Hi, we have a few term requests that are not exactly protein modifications, but we use them in our data in a similar way that we use PSI-MOD terms, so we are hoping that you can help us with them. If …
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Hello, I encountered an error while importing the pepxml file: "RuntimeError: the value 'B' was used but is not valid; Modification '': origin must be a letter from A to Y, excluding B and J."
The …
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Hi, thanks for creating this tool. But recently when I use pepquery2 in web application and stand alone version, there was error about the mgf file in s3 bucket is not exist. I attached the screenshot…
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The `combined_peptides.tsv` that comes from multigroup or multimix experiments does not have information regarding the type of modification assigned.
The information regarding the N-term acetyl/TM…
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Hi all,
It looks as though there may be a bug in Crux reporting masses for some modifications. I am seeing this in the PepXML:
```
```
It's a rare error only happening a f…