Wrong mass error displayed on top of the spectrum

[WeiqiangChen]

The error on top of the spectrum is 154 Da, while below in the table, it is -0.95ppm. The settings were 6ppm MS1 and 15ppm MS2

https://xiview.org/network.php?upload=26642-44225-82650-47218-81521

[colin-combe]

Hi,
yes, there is something strange going on.

The numbers along the top of the Spectrum View are returned from the annotator (which provides the annotations of peaks in the spectra).

I can see the calc M/z in the spectrum view and the table are different, and hence the differing mass errors.

It seems like the calc m/z returned by the annotator is different if one of the peptides contains the (-28.006128) modification.

We'll look into it further,
best wishes,
Colin

(@lutzfischer - any ideas? the data is from an mzIdentML file)

[WeiqiangChen]

This mzid file was manually modified in Notepad++ to remove all empty cvParam lines, to be able to load into (XiView Issue #563).

Maybe this somehow changes the behavior of XiView.

[colin-combe]

you may be right - e.g. there is missing modification info because of the missing CV term.
These empty elements were in Peptide/Modification in the mzIdentML file?

[WeiqiangChen]

Yes. .mzid

[colin-combe]

actaully, i think the masses are not in cv params...

[lutzfischer]

@WeiqiangChen could you upload/email me the config. I am trying and failing to get to the correct mass based on the peptide masses and crosslinker mass (-28Da). Looks like somewhere something got lost but I am not sure what got lost where.

[WeiqiangChen]

ID_24036_R498_with_Phospho_STY.zip
The configue file is in the zip

[lutzfischer]

Ok not sure how this actually happened but to me it looks like the modification mentioned in xiVIEW/mzIdentML is not correct. Changing the modification to the configured photo modification (126Da) the masses fit again. Not sure where the -28 comes from here. I guess the crosslinker modification got somehow duplicated and replaced the "photo" (126.something) modification

[lutzfischer]

if you could find the original and edited parts of the mzIdentML that define that peptide pair could be helpful.