Hi,

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.

Darren 

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.