GNPS bug and waters raw data

[thomas...@unice.fr]

Dear all

When I try to run GNPS molecular networking from MS data obtained from Waters instrument (Xevo G2 GTOF), I have got this kind of message:

DEBUG: convert2.cpp : 129: Loading data using pwiz 
ERROR: main_specnets.cpp : 245: Input spectra set is empty for file inputspectra/spec-00000.mzML 
DEBUG: convert2.cpp : 129: Loading data using pwiz 
ERROR: main_specnets.cpp : 245: Input spectra set is empty for file inputspectra/spectwo-00000.mzML 
DEBUG: convert2.cpp : 129: Loading data using pwiz 
ERROR: main_specnets.cpp : 245: Input spectra set is empty for file inputspectra/specthree-00000.mzML 
ERROR: main_specnets.cpp : 263: Input spectra set is empty 
ERROR: main_specnets.cpp : 264: Please make sure input files are 32-bit uncompressed mzXML files that contain MS/MS spectra 
ERROR: main_specnets.cpp : 908: Failed loading initial data. 
Tool execution terminates abnormally with exit code [1] 

Is someone knows how to debug my data and run again with GNPS? Could be from the fact that data obtained from Xevo G2 QTOF instrument contain 4 acquisitions: sample base peak, UV, lockmass and MS/MS???

Here is the link https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=8b9d1894dfcc42698e26650742cfacb9

Best regards

Thomas 

[Pieter Dorrestein]

Thomas, 

Waters data has been challenging. They have provided some solutions. See some discussion on this forum on this very topic. If they do not work contact your Waters Rep. Jimmy Yuk at Waters has been really responsive.

P

[Laura Sanchez]

Thomas, 

Ming or Vanessa can probably comment more, but the error would suggest that the data didn't convert correctly. Is the data centroid and a 32- bit mzXML file with both MS1 and MS2 data in the file? We recommend that everyone try to open their data after it's been converted in another viewer, such as InSilicos, if the data does not open it isn't converted properly to be compatible with molecular networking. 

Also you might want to look back to the post I made to Genia last week about Waters data conversion. 

Here is a link for a dropbox folder for Insilicos: https://www.dropbox.com/sh/ckegaqcdjzeo2dr/AACXw22GxDAZrDaHe0nD6Pgia?dl=0

Best, 

Laura

[Vanessa Phelan]

Here is an infographic slide for converting Waters data.

Best wishes,

Vanessa

[Rafael de Felício]

Hi Vanessa, 

Could you give more details about how shoud I set up MS convert for Waters DDA data? Specifically in Filters: Which should I use? MS Level or Peak Picking? In Levels: 1 - 2 is correct?

TPP compability box must be checked?

I attached a print of how I've been converting Waters data, but I'm not sure if it is the right or best way to do it. 

Best wishes

Rafael

[Rafael de Felício]

Now it is attached

[Laura Sanchez]

Rafael, 

We usually use peak peaking level one to help convert profile data to centroid, and I usually uncheck the TPP box, but you might have to try a few different conversions with Waters and open the resulting file in InSilicos to see how the conversion worked. A link to a download for InSilicos is in a previous thread. You might also want to contact Waters directly. Neither Vanessa, Pieter, or I's lab have a Waters instrument. Jimmy Yuk from Waters can speak more directly about the conversion unless someone else wants to weigh in on their successes or workflows. 

Best, 

Laura