how to extract acquisition time/date stamp from .mzXML files?

[trl1]

Hello,
I generate .mzXML files from thermo .raw files using ReAdW. Is there
any tool available to extract a date and time stamp from the .mzXML
file that indicates when the original .raw file was acquired (not the
creation date of the .mzXML file)? Is this information even stored in
the .mzXML schema?

thanks
Tony

[hill...@verizon.net]

Tony,

To my knowledge the date stamp for the acquisition is not captured in
mzXML from ReAdW-converted Thermo .RAW files. In principle the mzXML
<msRun> element start time and end time attributes might hold such
information but AFAIK for ReAdW 4.3.0 these attributes hold relative
start and stop times, typically in seconds. Not a datestamp.

Andrew.

[trl1]

OK, thanks, it's as much as I assumed. What about extracting the
acquistion time and date from the original thermo .raw files? The
info is in there, but I'm nort sure how to get at it, especially in a
script that doesn't require running xcalibur-type report genmeration
in xcalibur (where the only option seems to involve generating
document reports during sequence reprocessing).

thnaks
Tony


On Jul 9, 7:09 pm, "hillan...@verizon.net" <hillan...@verizon.net>
wrote:

[Eric Deutsch]

If you convert the RAW files to the *mzML* format using msconvert, then
the date will be there in the form:

<run id="OR20100622_uk_06_1825_1a_34_1"
defaultInstrumentConfigurationRef="IC1"
startTimeStamp="2010-06-23T01:30:33Z"
defaultSourceFileRef="RAW1">

Eric

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[trl1]

Thanks for the pointer! Unfortunately, I am using xcms (1.21.7 under
R 2.11.1/bioconductor 2.6) to read the .mzXML files, which does not
currently support reading .mzML files in the release version - I think
it is possible with a custom development build (http://
metlinwiki.scripps.edu/mediawiki/index.php/EnableMzMLSupport) , but
not (easily) under Windows, which is what I will be using.....

[Matt Chambers]

What is the purpose of the msRun startTime attribute? It's an
xsd:duration type so using it to store a point in time seems odd. But
the documentation "The time at which the run was started." clearly seems
to refer to a point in time.

Andrew, a straightforward compromise here is to use msconvert to write
out just the file header and the first spectrum in mzML. Something like
'msconvert data.RAW --filter "index 0"' should do the trick. Then a
simple grep/regex over the file should get you the startTimeStamp.

Hope this helps,
-Matt

[trl1]

OK, this works well. However, it would be nice to not write the .mzML
file, but just hold it temporarily in memory for stripping the
appropraite info out. If I try the following in R, trying to coerce
any output to an R object:

test <- shell(paste("msconvert ", "file.RAW"," --filter ", "\"","index
0","\"",sep=""),intern=T)

msconvert runs ok, but I still get file.mzML saved in the appropriate
directory - it is not held in the R object. Any idea on how I might
do this (other than reading the .mzML file into R, stripping out the
timestamp info, then deleting the file = very messy!)

thnaks
Tony





On Jul 13, 2:56 pm, Matt Chambers <matthew.chamb...@vanderbilt.edu>
wrote: