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Messages - Matthew Keller

1
MS-DIAL / Exporting Error
I was trying to export alignment to an msp and got an error I wasn't sure what to make of (see below). Can anyone tell me what causes this?
2
MS-DIAL / InChIKey Generation
Developers,

There seems to be a bug in the InChiKey generation. I'm getting a few InChiKeys that don't seem to match their corresponding metabolite. At least, they pull up 0 results on Pubchem. It looks like they should have a S instead of an N in the third position from the end. I listed a few examples below.

Name                             MS-DIAL Generated InChIKey                    Correct(?) InChIKey
3-Hydroxyvaleric acid   REKYPYSUBKSCAT-UHFFFAOYNA-N          REKYPYSUBKSCAT-UHFFFAOYSA-N
Leucine                         ROHFNLRQFUQHCH-UHFFFAOYNA-N      ROHFNLRQFUQHCH-UHFFFAOYSA-N
Pyroglutamic acid        ODHCTXKNWHHXJC-UHFFFAOYNA-N      ODHCTXKNWHHXJC-UHFFFAOYSA-N
Threonine                     AYFVYJQAPQTCCC-UHFFFAOYNA-N          AYFVYJQAPQTCCC-UHFFFAOYSA-N

Could this be easily patched, or is there a workaround? I guess I could use the SMILES instead of the InChIKeys.
Thanks!
3
Vendor specific software / Compound Discoverer Bug
I'm getting a weird error in CD, I'm trying to run a standard ID workflow using mzcloud but it says, "Execution of analysis failed: Cannot create a workflowjob from an invalid WorkflowTree: Missing value for parameter 'Identity Search'" Identity search is one of the parameters for mzcloud, but I've tried selecting each different search method and it still give the same error. If I delete the mzcloud node it works fine. Anyone had this happen to them?
4
MS-DIAL / Re: Few MS Annotations
Hey Hiroshi,

Thanks for the advice, opening up the MS2 accuracy helped a lot. A separate issue I had is that MS-DIAL seemed to be picking some shoulders and dropping the rest of the peak. Do you have any suggestions for that? For some of these, it looked like MS-DIAL was expecting the peak widths to be shorter than they were, is there a way to change that?

Also, I would have uploaded an .abf in case that would be helpful, but I wasn't sure how to do that.

Thanks,
Matthew
5
MS-DIAL / Re: Few issues about MSDIAL and MSFINDER
Hey Sukis,

I think I can answer C and D for you. C, If you want to annotate a feature by hand, you can click the spot and then "show ion table," from here you can type whatever you like into the comment box. If I understand you're asking, that should help. D, if you're doing SWATH or something similar, the deconvolution works by matching EICs of fragment ions with that of parent features. Fragments that have similar EICs are displayed as the deconvoluted MS2 of that feature. The MS-DIAL paper has more details.

~Matthew
6
MS-DIAL / Re: Few MS Annotations
Hi Hiroshi,

Thanks for the advice. We do have the LTQ scanning the MS2 and the Orbi for MS1. However, in our setup, both the LTQ and Orbitrap are in centroid mode. I've tried various values for the MS2 accuracy and identification parameters, but haven't improved things. Is there a guide or something regarding how to optimize parameters for MS2 level annotation?

Thanks,
Matthew
7
MS-DIAL / Few MS Annotations
Hello all,

I'm trying to process a DDA lipidomics sample set I have and after running identification, I'm getting a lot a MS1 annotations (without MS2), but very few assignments that use the MS2s (164 vs 8). Looking at the data by hand, the MS2 look to be of at least moderate quality, so I'm not sure why there would be so few MS2 annotations.
Has this happened to anyone else? Do you know what parameters might need to be adjusted? I'm using an LTQ-Orbitrap in case that's relevant.

Thanks,
~Matthew