Skip to main content
Topic: Two-Dimensional RT Alignment (Read 871 times) previous topic - next topic

Two-Dimensional RT Alignment

Hiya,

I'm interested in analysing some data from a Shimadzu GC/GC-MS (i.e. two dimensional of gas chromatography) with XCMS.  As far as I can tell, 2D alignment is not something currently covered by XCMS, but it doesn't seem to be a million miles beyond current capability (although far from a simple tweak!).  I wondered if anyone had any experience in approaching this issue.

The raw data (both vendor binary and when converted to open formats, e.g. mzXML) is stored as one-dimensional, i.e.:

Code: [Select]
                      Second Dimension GC -->

First Dimension GC    1  2  3  4  5  6
        |              7  8  9  10  11  12
        V            13  14  15  16  17  18
becomes
Code: [Select]
 <scan num="1" 
      [other spectrum metadata]>
  [spectrum]
 </scan>
 <scan num="2"
      [other spectrum metadata]>
  [spectrum]
 </scan>
 ...
 <scan num="18"
      [other spectrum metadata]>
  [spectrum]
 </scan>
in the mzXML.
 
The dataspace is therefore comprised of the scan list and a parameter for the number of scans in each second dimension elution.

Best wishes, and thanks in advance for any advice!

Phil