is lc/ms output data normally in proprietary format?

[matthew]

Hi,

I've purchased a triple quad from Agilent (6410) and I'm happy with it, for the most part.

One thing that I'd like to do (and the software is young and doesn't seem to include this option) is to shoot a matrix blank and then my samples and then subtract the sample's (TIC) chromatogram from the matrix blank. So far, I've been unable to get any feedback from Agilent on this; their answer seems to be: buy our Q-TOF. mmm kay, I'm not so lucky.

Anyway, I'm a recovering programmer, and I'm willing to write this software myself if I absolutely have to... but the output data is encrypted. Is this typical? The data are mine, and nothing annoys me more than having someone restrict your access... to something that you pay for.

Is this an issue with ABI instruments? Thermo? When I do sequencing runs (sequenom), I get lovely spectra in my files, complete with TOF info for the probes and the chromatograms themselves in xml format. This should be standard for every vendor, and if it isn't then the community should move to the vendors that 'open it up'.

[Kostas Petritis]

There is some effort from the scientific community to create a new data format (latest one called mzML and the previous versions being mzdata and mzXML) that all different manufacturers output data could be converted and analyzed.

I know that the Agilent Q-TOF has a converter to mzdata, an already outdated format but hopefully they will release something that can convert to mzML. If you have programming skills maybe that could be an option for you. Probably such a tool will be a welcome addition for a lot of other people out there.

Back to the Agilent response, sometimes is just a question of coming in contact with the adequate person. I would expect an answer like that (i.e. buy our Q-TOF) either from a sales person or a low level support person (I would actually ask them to put their answer in writing for evident reasons).

Your best bet to get a more professional answer is to ask someone in informatics in Agilent Santa Clara life science division... Maybe they won't be able to help at the end, but at least they won't suggest you to buy a Q-TOF...

[matthew]

Thanks Kostras.

I hadn't looked carefully enough (obviously) at Agilent's supporting software (quant/qual tools), but there is an export to mzdata option. I'll have to spend more time with this (as well as the xtd for the output xml file); I had expected a data dump of abundances per time per m/z, but this output tool isn't doing this (yet).

I just noticed that I switched the order of subtraction, oops. I meant to write that I'd subtract the matrix blank from my samples.

Thanks again,
Matt

[lmh]

All manufacturers have their own format. The two general, common-access formats are mzXML, which is new, and netcdf which has been around for ages. Agilent Chemstation definitely supports netcdf but calls it AIA. In some versions of chemstation, the batch exporting tool cannot handle filenames with more than 8 digits, even though the same versions cannot, with the prefix-number file naming system, generate filenames with less than 9 digits. Go figure. If you go to conferences, all manufacturers claim to support mzXML. When you get home, you find they only support it in their latest instrument. This isn't specific to any particular manufacturer; they are all as bad as each other. Bosses think that it's OK to export things as ascii. Generally, ascii exports provided by manufacturers will only output a chromatogram, or a spectrum, not the full data set. Bosses don't understand the difference.
Fortunately some 3rd party packages, including AMDIS, can open the manufacturer's own formats.
Good luck.

[apanag]

We had exactly the same problem with the Agilent QTOF (cannot export to mzXML)

For this reason I wrote an Java application that converters mzData to mzXML. Then, I thought, it would be nice to have an application to be able to convert to mzML as well.

This is what I did too. Then it was quite easy to go towards all directions: mzXML -> mzXML etc.

If you would like to have your data converter, contact me.
The application I made works runs from a windows environment, so, no need to run command line arguments, weird installation etc...

Andreas Panagiotidis

http://www.icecoffee.ch

[Kostas Petritis]

This is an interesting application... I was looking for a converter in the past and couldn't find anything...