Chromatography Forum

Hi there,

I am at the early beginnings of the LC/MS knowledge pathway - but am also doing LC/MS for my PhD, so need to learn pretty quickly. I have quite a large quantity of LC/MS spectra of blood serum ready to analyse.

I was wondering somebody with experience can give me a bit of guidance as to where to start with this data......?

I have downloaded mzmine2.7, and the xcms package for R, but am struggling a little with these so far. Is there any early basics that I can work through with my data first i.e. to get a better understanding of the data and begin analysing?

cheers

Zoe

Hello,

I've never heard of Mzmine. And how come you can't use the software package that the data was acquired with? What is you're looking for in this data?

If you were to provide some additional information somebody may be able to assist you.

You need to know what you intend to do with the data (what question you'd like to answer). Are you looking for some target compounds, or are you doing a metabolomic experiment?

If you're doing untargeted metabolomics, there are loads of papers and things you can follow, but your best starting point is to get the files converted from whatever format the instrument created, into something that packages such as xcms can open. That means mzXML preferably, or cdf if not. Every piece of instrument software has some sort of exporter with it, and there are lots of freebie ones if you google. You'll get more help here if you can give a few details of the instrument and what you're trying to do. Once you've got a set of files in a common format, the Scripps site that hosts xcms also has references to some of their papers, the early ones of which do give a walk-through of basic metabolomic peak-finding.

If you're looking for target compounds, ideally you should have planned this before running the samples...

Hi,

Yes I am doing untargeted metabolomics, the aim is to look for a biomarker in serum which can be used to diagnose this disease at an early stage, and/or to learn more about the biochemical pathways involved.

For a number of reasons we don't have the software package that the data was acquired with (money also plays a part), so I'm using these open source programmes instead. The problem is I have no experience with mass spectrometry, the programmes I can find information for no problem... but when I have 3000 spectra to work through, it can get overwhelming (especially for someone with no experience)