Can we cluster deconvoluted top-down MS/MS mass lists?

[dtabb73]

Hi! I've run into a little problem trying to use spectra-cluster-cli with deconvoluted MS/MS scans. FreeStyle Xtract is handling deconvolution of my top-down experiments, and then I am assigning precursor charges and reformatting to msAlign format (very, very similar to MGF). When I rename my 3 msAligns to MGF and attempt to run spectra-cluster on them, I produce this error:
Converting 3 input files...
Clustering 0 binary files...
java.lang.Exception: No clustering result files found for merging.

I am unsure what format differences are causing the software to be unable to read them. Could you look at the files in https://drive.google.com/file/d/1gvfTcx-O0zsPqTlO8MYWhXq84a9m2wBJ/view?usp=sharing to discern what is blocking the transition to binary format?

Thank you!
Dave

[jgriss]

Hi @dtabb73 ,

When you processed the files, did you keep the .msalign ending or did you rename the files to .mgf?

Unfortunately, we never added an automatic detection of file formats to the code but rely on the filename for that.

Thanks,
Johannes

[dtabb73]

Hi, Johannes. Yes, I renamed all three files to "MGF" before running. Specifically, my command line looked like this:
java -jar "C:\Program Files\spectra-cluster-cli-1.1.2-bin\spectra-cluster-cli-1.1.2.jar" *.mgf -output_path thing.txt

I also attempted running on a single MGF:
java -jar "C:\Program Files\spectra-cluster-cli-1.1.2-bin\spectra-cluster-cli-1.1.2.jar" -output_path thing.txt 20140722_F_EV_Hp1_repl1_Inclusion_HCD25_M_Xtract.mgf

Both result in this error:
Clustering 0 binary files...
java.lang.Exception: No clustering result files found for merging.
at uk.ac.ebi.pride.spectracluster.implementation.SpectraClusterStandalone.mergeClusteringResults(SpectraClusterStandalone.java:584)
at uk.ac.ebi.pride.spectracluster.implementation.SpectraClusterStandalone.clusterBinaryFiles(SpectraClusterStandalone.java:122)
at uk.ac.ebi.pride.spectracluster.implementation.SpectraClusterStandalone.clusterPeaklistFiles(SpectraClusterStandalone.java:103)
at uk.ac.ebi.pride.spectracluster.cli.SpectraClusterCliMain.run(SpectraClusterCliMain.java:344)
at uk.ac.ebi.pride.spectracluster.cli.SpectraClusterCliMain.main(SpectraClusterCliMain.java:43)
Error: No clustering result files found for merging.

Thanks!
DT