MSMS Chooser FAILED JOBS

[Luis Manuel Quiros guerrero]

After selecting the files from a MassIVE repository (uploaded by me), and uploading the MSMS-Chooser Submission File.tsv, i've got the following message error: 

https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=165f3914c6564f5f9491fdc50152872b

https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=ffbf1103529c4b9f90fd44050e38ba4a

i'm not clear what is the problem.

Some comments:

1) Before creating the Massive repositories, i've got an error, but after some emails, it was kindly solved and i could create them. 

    I don't know if it's related to this new error somehow, however here the elaborated answered i got for the problem. 

    (This file is indeed legal mzML, but is unusual in a way that our software is not prepared to deal with at the moment. Specifically, the file contains many spectra having an unusual "controllerType=4" value in their Thermo identifiers, e.g.:

File [quirosgu/PF_Stds/Converted/PF076_pos/181109_PMA_LQG_PF076_B02.mzML] (Line 239,451):

----------

<spectrum index="4270" id="controllerType=4 controllerNumber=1 scan=1" defaultArrayLength="390">

----------

Almost all Thermo spectra have a standard controllerType=0. The fact that your file contains mixed controllerType values means that scan numbers will overlap, which complicates things but isn't the real problem here. The real problem is that all of your file's controllerType=4 spectra have no standard "ms level" parameter, so our peak list parser is unable to accurately identify them. For instance, all of the normal controllerType=0 spectra do have this parameter:

File [quirosgu/PF_Stds/Converted/PF076_pos/181109_PMA_LQG_PF076_B02.mzML] (Lines 112 - 114):

----------

<spectrum index="1" id="controllerType=0 controllerNumber=1 scan=2" defaultArrayLength="4">
  ...
  <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2"/>

----------

At the moment our peak list file parser requires each mzML spectrum to have a parameter of this type so that we can identify each spectrum individually. We are currently looking into this to find a solution, since presumably the semantics of controllerType=4 spectra justify the omission of this ms level parameter.)  

Jeremy Carver

CCMS/MassIVE Software Developer

2)The MassIVE repositories are still private. This could cause problems?

 

Thank you in advance for your help

[Chrissy Aceves]

Yes so basically the xml parser will open the file, but it will fail to retrieve the information from your files. It could be related to what you mention in (1), but not (2). I can't tell the exact point at which the exception is raised, however we all look for 'ms level' so it is likely related.

Best,

Chrissy

[Chrissy Aceves]

Just to clarify, the data will need to be public, but that's not what's causing the immediate error.

[Luis Manuel Quiros guerrero]

Is there a way to solve this? some feed back form the developers maybe.

Best, 

Luis

[Chrissy Aceves]

Please email me a file to test at cmac...@health.ucsd.edu and I'll get back to you!

- Chrissy

[Chrissy Aceves]

Hi! 

So it would appear that ms-ms chooser workflow doesn't support .mzML files  - however thank you for calling this to our attention. We'll provide support for this in the upcoming weeks.

- Chrissy

[Luis Manuel Quiros guerrero]

Hello Chrissy, thank you so much for the answer and concerns! 

Kind regards.