-
```
Email thread copied from list:
Hi Sean,
Good point – this is clearly an error in the specification document,
retention time is certainly allowed to be present in a PSM and is used in this
way…
-
```
> Modifications that cannot be found in UniMod
> -------------------------------------------------------------
> It is not a good idea to allow exporters to have a 'wild card' to
> report 'undeter…
-
```
Minor schema update:
Removed mzIdentML-->DatabaseReference
This is no longer a valid element now that Database has been removed.
(i.e. this gave the ability for a file to reference a correspo…
-
Dear developers,
While exporting results (obtained from searchGUI + PeptideShaker) to MzIdentML I have encountered issues when reading these MzIdentML by third party software (openMS,pyteomics).
In…
-
```
Do we need a PeptideEvidenceList element of type Identifiable (having attribute
"id")? It is not referenced...
It seems, that is only necessary for grouping the
elements together having the s…
-
Overlapping peptides are ignored resulting in coverage potentially higher than > 100%.
-
Hi Marc/Harald
Not really an issue, more of a question. When importing MSGF+ search results to PeptideShaker, do you use the MSGF RawScore or the SpecEValue for calculating the PEP/confidence?
Than…
-
```
When the general case for an mzIdentML element is to use the same value over
and over for an attribute, e.g. searchDatabase_ref, spectraData_ref,
massTable_ref, we should add a "default" version…
-
```
if I get it right, for Modifications as search parameters
()mzIdentML cannot differentiate between peptide or protein
terminus.
In the CV there are "modification specificity C-term" and "modifi…
-
[Uploading peptides_1_1_0.pride.mztab.zip…]()
```
In the case of Identification Complete mzTab files, the numbers of protein
columns grow very fast because of the mandatory fields referencing ms run…