Converting Agilent Chemstation LC data to .cdf format

[Cynthia]

Hi all,

Does anyone know of a converter program that I can use to convert Agilent Chemstation .d files (LC) to NETcdf format? We are currently using AMDIS software with MET-IDEA for data processing of GC-MS data, but we want to try something similar with MassHunter and MET-IDEA. Unfortunately, MET-IDEA only accepts files NETcdf format.

Thank you!

[lmh]

Doesn't chemstation already do this?

[mardexis]

Try 'export' and choose 'AIA'. This should be net/cdf format it was just an earlier name for it.

[Cynthia]

Oh crud, I'm such an idiot! I meant exporting from MassHunter/Mass Profiler software to net/cdf format...

[ddycus]

Chemstation would do the trick. However, I've been using VMware to emulate XP on OSX Lion. I'm doing so because I'm also trying to model with Wolfram, Matlab, and running the statistics with JMP on the same machine. I've played with some of the R packages and chemometrics as well as some of the C++ source but I'm not the worlds greatest programmer. What I need is .NetCDF or .mzxml conversion from raw .D data from an Agilent machine. I've converted to CSV in many cases when modeling. However direct loading of .NetCDF or .mzxml would improve functionality of the tandem system so metablomics exploration could begin nearly simultaneously with the acquisition of the .D files.

Do you think exporting within Chemstation is still the right choice?
What about losses from file extension?
Any ideas on third party open source conversion software for OSX?

Data Formats:
Comma Separated Values (.csv) format datasets, including :
Compound concentration data - cow, four groups (download)
Compound concentration data - human, two groups (download)
Binned NMR/MS spectra data (download)
Processed peak intensity table (download)
Time-series peak intensity data (download)

Zipped files (.zip) format datasets, including :
NMR peak lists (2 columns - chemical shift and intensity) (download)
MS peak lists (2 columns - mass and intensity) (download)
MS peak lists (3 columns - mass, retention time, and intensity) (download)
LC/GC - MS spectra (NetCDF, mzDATA, or mzXML) (download)

Here is the bioinformatics protocol for metabolic predictions using outliers in conjunction with NMR, LC/GC/MS, and HPLC.
http://onlinelibrary.wiley.com/doi/10.1 ... 234.d02t04

Any help is always a great help.
Dan