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Messages - sneumann

46
Job opportunities / Bioinformatician (Metabolomics) at the IPB Halle
The research group “bioinformatics and mass spectrometry” in the department of Stress- and Developmental Biology at the Leibniz-Institute of Plant Biochemistry (IPB) is seeking applications by highly motivated candidates for a position as Bioinformatician (Metabolomics).

You will work on methods and algorithms for the analysis and interpretation of metabolomics data from state-of-the-art mass spectrometers. You should hold a diploma or masters degree in bioinformatics or computer science, with experience in algorithm- and software engineering and statistics. You are able to program in the statistics framework R, and have worked C/C++. Knowledge in metabolomics or analytical biochemistry would be an advantage.

The position is limited to 3 years and available immediately. Payment is according to local regulations TV-L.

The IPB is an international research institute located on the Weinberg-campus of the Martin-Luther-University Halle-Wittenberg and provides state-of-the-art facilities for research in bioinformatics, metabolomics and plant biochemistry.

Further information is available from the institute's homepage and in particular http://www.ipb-halle.de/en/career/job-v ... abomolics/
48
XCMS / Re: rawEIC return in seconds
Hi Cole,

no, not directly. But you can:

Code: [Select]
library(faahKO)
library(xcms)
xr <- xcmsRaw(filepaths(faahko)[1])
e <- rawEIC(xr, mzrange=c(300.5, 301.5))
xr@scantime[e$scan]

Yours,
Steffen
49
XCMS / Re: Saving an xcmsSet object
Hi,

yes, you can

    xsall <- c(xs1, xs2)

check  "? c.xcmsSet"

Yours,
Steffen

    Combines the samples and peaks from multiple 'xcmsSet' objects
    into a single object. Group and retention time correction data are
    discarded. The 'profinfo' list is set to be equal to the first
    object.
52
XCMS / Re: memory error during fillpeak step
Hi,

how far do you get with nSlaves=1 ? The parallel fillPeaks currently
passes the xcmsSet down to all slaves, and the slaves operate on a subset
of them. The more clever way would be to pass trimmed xcmsSets to the slaves,
so the memory requirement is not mutliplied by the number of slaves.

Steffen
53
Other / Re: Converting LCMS profile data to centroid?
Hi,

you need to convert to *.mzML anyway, so I'd suggest to do the centroiding
as part of the pwiz conversion, although I don't really have hands-on experience there.

Yours,
Steffen
54
XCMS / Re: XCMS error after peak detection
Hi,

this most likely has to do with the raw data conversion,
I guess you have a waters instrument ?
Check the forum for "m/z sort assumption violated"

Yours,
Steffen
55
CAMERA / Re: Downstream analysis after CAMERA
Hi,

one idea would be to ignore all higher isotopes, and "subtract" the mass of the adduct
from the m/z. You could use the Rdisop subMolecule() for that.

Yours,
Steffen
57
Compound identification / CASMI contest continues this year
Hi,

The Critical Assessment of Small Molecule Identification  CASMI 2012 special issue in Metabolites is finally finished! Emma Schymanski and I continue to present the results of CASMI 2012 at different occasions, e.g. the last ASMS conference in Minneapolis (June 2013) and the upcoming Water Forum in Langenau in November this year.

The organisation of the contest and special issue was a lot of work, but also a lot of fun. We'd like to thank all of our participants and our advisory board, but also everyone who expressed interest or engaged us in discussions at meetings.

And CASMI keeps going: CASMI 2013 is currently being organised by a team of Japanese mass spectrometry experts headed by Prof. Nishioka, and the challenge data has already been opened up. Make sure to send your submissions before the deadline in december 2013.

In addition to the CASMI specific mailing lists, the Metabolomics' society is also hosting the Metabolite Identification Interest group.

The small molecule analytical chemistry and computational mass spectrometry world is quite small, we're looking forward to bumping into you at some time in the future!

Yours,
Steffen
58
XCMS / Re: error with "scanrange" variable of xcmsSet
Two things:

before and after the group(), have a look what A is,
and optimize group() parameters so that afterwards
A actually *has* groups.

Second: Use

xr <- xcmsRaw("filename.cdf") and
plotRaw(xr, mzrange=c(200,210), rtrange=c(rtmin,rtmax), log=TRUE)

to have a look at the raw data, zoom into a typical region using the mz and rtrange.
Maybe you can reduce the ppm down to 1000 ?

Yours,
Steffen
59
XCMS / Re: error with "scanrange" variable of xcmsSet
Hi,

Is it possible that you sent the wrong xcmsSet object to retcor(),
i.e. not the one that resulted from the group() ? Can I see the full code snippet ?

Can I have a traceback() information after your last error ?
can I have the sessionInfo() output ?

Yours,
Steffen
60
XCMS / Re: xcmsRaw and obiwarp
Hm, in that case I'd have to check the source myself:
Look out for the retcorr.obiwarp() function
and see where it iterates over the raw files
and applies the obiwarp()ing.

Yours,
Steffen