crux spectral-counts input formats not including mzML and mzXML.

Malcolm Cook

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Sep 19, 2023, 3:35:13 PM9/19/23

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The help for `crux spectral-counts` reads

<input PSMs> A PSM file in either tab delimited text format (as produced by
percolator), or pepXML format.

However File formats documentation seems to suggest that othr formats would be accepted as well, including mzML and mzXML.

Am I misunderstanding the documentation?

Thanks,

~Malcolm

lin...@uw.edu

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Sep 19, 2023, 4:21:00 PM9/19/23

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Hi Malcolm,

I think that there is a mistake in the documentation need to be updated. To my knowledge mzML/mzXML files do not contain any PSMs (please correct me if I am wrong). As a result, these files can not be used as input into spectral counts.

Thanks for catching this,

Andy

lin...@uw.edu

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Sep 19, 2023, 5:00:32 PM9/19/23

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Hi again - sorry I just realized that I missed something in my explanation above.

The input into spectral-counts is a list of PSMs. As I noted mzML and mzXML are scan files, not PSM files. However, the Normalized Spectral Index score does require the corresponding PSM file. That file is given to spectral counts using the --input-ms2 parameter.