Conversion of Shimadzu LC-IT-ToF (.lcd) files to "open" format (mzXML, etc)?

[Selenome_Miner]

Hello Folks,

This is my first post here, so please let me know if there is a more
appropriate place to post this question.

We recently acquired an LC-IT-ToF instrument from Shimadzu Scientific,
and aree looking to convert the data files to an "open"format (such as
mzXML and mzDATA) that will enable us to utilize the many fantastic
proteomic tools that are available.

The usual converters I have come across do not address Shimadzu .lcd
files. Can anyone please recommend a solution that will enable us to
convert to an open XML format?

Thank you in advance!

[Natalie Tasman]

Hello Selenome,

You're in the right place :)  However, I've never come across this instrument or format, and I don't know of any existing converters.  Do their tools have export options for converting to a simpler format, like .dta or .mgf, which we could then help you convert to mzXML/mzML/mzData?

I encourage anyone in the community here to share their experiences, too.

Good luck, and please let us know here if you find a solution,

Natalie

[Selenome_Miner]

Hi Natalie,

The instrument is a hybrid quadrupole ion trap-time of flight MS that
would be very similar I believe to the Hitachi model linear ion trap-
time of flight MS, in case you are familiar with that.

Unfortunately, the export options are severely limited it would seem.
I do not see any option for blanket data export of an intact file, the
only spectrum export option seemingly available is one that results in
the construction of a text file containing mz vs intensities for
previously integrated peaks... nothing that indicates the ability to
export into mzXML.

Perhaps fortunately, I do have Shimadzu's "Protein Layer" analysis
software that performs automated peak picking in preparation for
MASCOT searching. This Protein Layer software does indeed off an
option to save the peak list as an .mgf file, but wouldn't that file
result in the loss of much of the raw data, and thus I still couldn't
load my raw data into such tools as mzMine, MetAlign or MSight?

Thank you for the quick reply and the insight so far. This
proprietary data format situation is frustrating to no end... To think
that we invest so much money in acquiring the instrument only to have
our hardwon data locked in some inaccessible format!




On Nov 12, 4:56 pm, "Natalie Tasman" <ntas...@systemsbiology.org>
wrote:

> Hello Selenome,
>
> You're in the right place :)  However, I've never come across this
> instrument or format, and I don't know of any existing converters.  Do their
> tools have export options for converting to a simpler format, like .dta or
> .mgf, which we could then help you convert to mzXML/mzML/mzData?
>
> I encourage anyone in the community here to share their experiences, too.
>
> Good luck, and please let us know here if you find a solution,
>
> Natalie
>
> On Wed, Nov 12, 2008 at 2:51 PM, Selenome_Miner <
>