Question: quantify() method for MSnExp to MSnSet for MS1 level data only
gravatar for dgemoets
8 weeks ago by
dgemoets0 wrote:


This is probably a poorly phrased question as I am a novice with LC-MS/MS data.  I have Agilent Masshunter data that I converted to mzML format via Proteowizard.  The data was suppose to be MS/MS but only has (with confirmation from the Proteowizard wizards) MS1 data.  I want to use the quantify() method to convert MSnExp to MSnSet, but quantify only uses MS2. 

Any ideas?  I'm following a tutorial using msmsEDA and msmsTests to create a simple volcano plot.

Thanks.  And apologies if this is a dumb question.






ADD COMMENTlink modified 8 weeks ago by Laurent Gatto1.0k • written 8 weeks ago by dgemoets0
gravatar for Laurent Gatto
8 weeks ago by
Laurent Gatto1.0k
United Kingdom
Laurent Gatto1.0k wrote:

In your question, you mention that the data was supposed to be MS/MS - does that mean to you were supposed to quantify in MS2, or only that the MS2 for identification is missing? Assuming it the latter, quantify() doesn't work (yet) for MS1 quantitation. You could look at the rawDiag package or xcms (from Bioconductor) - the latter is generally used for metabolomics, where they don't reply on MS2 data either.

But that you'll need to MS2 data at some point, as you'll want to know what peptides the MS1 features you quantify correspond to.

ADD COMMENTlink written 8 weeks ago by Laurent Gatto1.0k

I should have added: these are metabolomics data.  And all I have from the (now out of business) company that ran analysis is a report and the Agilent files.  The report has significant metolites identified, but lacks clarity.  So I'm trying to "recreate" (within reason) the report as a first step.

I'll look into xcms. Thanks. 

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by dgemoets0
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