MSe

[Johanna Villén]

Hello, 

I am new to GNPS and am trying to figure it out. I have MSE files that I would like to upload to GNPS and Cytoscape and am wondering if that is possible or if it needs to be normal MS/MS files. I am also a bit confused about what files I need to upload, in the documentation on how to upload files to massive it says that both peak list files and result files are required, so my question is what is result files and how do I get those? 

I tried doing a job with my MSE files but the job failed, here is a link to that job: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=f089304480a04eb39d27471431ed16c9 

The file was in 32-bit uncompressed mzXML format. 

Do you know anything that I can do to make it work? 

Kind regards 

Johanna 

[Mingxun Wang]

Johanna,

Thank you for your question. 

Molecular networking currently is not designed to work with MSE data. Specifically what is missing is there is no precursor mass for each spectrum that is fragmented and additionally is not recognized as a bonafide MS2 spectrum in mzXML. You have several options:

1. Attempt to transform your MSE data into pseudo MS2 spectra through deconvolution of the MSE spectra. Software such as DIA-Umpire is designed for Data independent acquisition and might work on your data.

2. Convert your MSE mzXML file into an MGF file so that the MSE spectra appear like MS2 spectra and hope that molecular networking will work (though I don't haev super high hopes for this)

Hope this helps. 

-Ming

[Vanessa Phelan]

Following on Ming's response-

Data upload for GNPS and Massive are separate, although data uploaded and made public on Massive can be used in GNPS. GNPS is an analysis platform, while Massive is a data repository.

To run jobs on GNPS, you need to upload your data using an open source format (typically .mzXML or .mgf) into your folder. Follow these directions for molecular networking: https://bix-lab.ucsd.edu/display/Public/Molecular+Networking+Documentation

To create a Massive dataset, peak list files mean your data in an open source format (.mzXML, .mzML or .mgf). Result files are list of compound IDs in tab format. Massive datasets created without results files are considered partial (not complete), but can still be analyzed.

Best wishes,
Vanessa

[Kathleen and Pieter Dorrestein]

Hi Joahanna,

I assume this is a Waters system. If Ming's solutions does not work, contact your Waters rep. Or perhaps Waters reps that subscribe to the forum can respond in this forum or Johanna directly. Recently during a visit in my office I was told they indeed have a solution for this but have not seen it yet. If they do it would be great if they made the solution available with links in this GNPS forum.

In the future GNPS we may accommodate MSe without any need for "prediction" of MS1 but this requires some development, in the meantime you have to use the alternative approach of converting your files with the predicted MS1's as Ming highlighted.

P

[dko...@gmail.com]

I wonder if any progress has been made on the use of MSe files from Waters machines?  Just checking google for old threads and found this.

Currently using a Xevo G2-S Q-TOF.  

I'm wondering what people normally do for acquiring large amounts of MS/MS data on known masses?  It seems tedious to go through each peak on a chromatogram, note the parent mass, and setup subsequent MS/MS experiments for every single one.

A crude extract even run over a 30 minute gradient can have a tremendous amount of masses/peaks to chose for follow-up MS/MS.

Even after bio-assay guided fractionation, one fraction I am looking at has 12 peaks, which happened to be, going through 1 by 1 by hand and entering masses into the GNSP database, alkyl quinolones and some rhamnolipids.

I'd like to use this fraction as a "test" for the full GNPS process which so far I've yet to get all the way through.

My plan for the next step is to create a MS/MS run for each of the 12 parent masses present in the 12 peaks, at their respective retention time windows.

Then, use MS Convert to change the Water's RAW file to an mzXML, 32 bit, and upload to GNPS. 

Before putting in effort with bio-assay guided fractionation, is there a "faster" alternative to setup targeted MS/MS on all the peaks in a fermentation extract without manually going through and noting all parent masses?

I also have access to Progenisis but, have found that only useful for alignment.

Thanks.