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Messages - sneumann

32
XCMS / Re: CentWave feature detection with LC-MS/MS (tandem) data
Hi Tom,

I had a look at what the data looks like:

Code: [Select]
xr <- xcmsRaw(file, includeMSn=TRUE)

## detect MS1 peaks
p1 <- findPeaks(xr, method="centWave", ppm=10)

precursors <- findPeaks(xr, method="MS1")

## Plot precursor distribution
plotRaw(xr, log=TRUE)
points(p1@.Data[, c("rt","mz")], pch="x")
points(precursors@.Data[, c("rt","mz")], pch=".")

So you have data-dependent MS2 acquisition, and there are potentially
many MS2 spectra acquired could match an MS1 peak. Similarly, several MS1 peaks
could be "isolated" and fragmented for an MS2 spectrum.

So the default xcmsFragments() tries to find these matches, and was written
for a nominal mass ion trap. So for your Orbitrap data there should be
some debugging and double-checking of the results.

Yours,
Steffen
33
Job opportunities / Job Vacancy: Bioinformatician (Metabolomics) at IPB Halle
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.

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 research assistant. You will work on methods for metabolomics data analyses and data fusion, to discover relationships between metabolites and their biomedical effects.

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 in Java. 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.

Further information is available from the institute's homepage http://www.ipb-halle.de/en/, for inquires please contact Dr. Steffen Neumann, telephone: +49 345 5582-1470, e-Mail: bewerbungen@ipb-halle.de
34
Other / Announcement: Computational mass spectrometry initiative
Dear all,

The task group “Computational Mass Spectrometry” [1] represents the CompMS [2] initiative in the Metabolomics society.
The CompMS initiative promotes the efficient, high quality analysis of mass spectrometry data
with state-of-the art computational tools and algorithms through dissemination and training in existing,
and coordination of new, innovative approaches. The CompMS initiative aims to exploit synergies
between different application domains, in particular proteomics and metabolomics.
The scientific remit of the group will include all aspects of computational method development
from signal processing, feature alignment and grouping, to development of metabolite identification algorithms
and metabolic network reconstruction.

The mission is to 1) build a community of scientists working in computational mass spectrometry,
2) integrate experimental and theoretical research, and 3) educate a new generation of computational scientists
via training and dissemination of results. The CompMS is a joint initiative between
the International Society for Computational Biology (ISCB CoSI CompMS), the Human Proteome Organization
and its Computational Mass Spectrometry Initiative (HUPO CompMS), and the Metabolomics Society.

If you want to be involved in the task group, please contact Sebastian Böcker <sebastian.boecker (at) uni-jena (dot) de>
or Steffen Neumann <sneumann (at) ipb-halle (dot) de>, and/or subscribe to the CompMS mailing list at [3]
or subscribe by sending an e-mail to http://metabolomicssociety.org/
[2] http://metabolomicssociety.org/board/sc ... task-group
[3] https://groups.google.com/forum/#!forum/compms
[4] http://metabolomics2015.org/
35
XCMS / Re: QQQ MRM data
Hi,

there are several ways how MRM can be encoded in the mzML,
1) as "degraded" MS2 spectra with single-point spectra (==intensity of the product ion)
2) as <chromatogram>, which was one of the extensions of mzML over mzXML/mzData.
pwiz has for some vendors an "--srmAsSpectra : write selected reaction monitoring as spectra,
not chromatograms" option (http://proteowizard.sourceforge.net/too ... nvert.html)
So 1) might work if you msn2xcmsRaw() the data beforehand.
XCMS currently can't handle <chromatogram>s, but since last your it should
have become easier to extract them from mzR using the new pwiz backend.

Yours,
Steffen
36
CAMERA / Re: CAMERA question
Hi,

you can generate ruleSets based on (modified) ion lists,
check out ?generateRules

Yours,
Steffen
38
XCMS / Re: At which steps are the sample classes used?
Hi,

the quote you found on fillPeaks() only refers to the fact
that peaks are filled if they were found in a previous group() step,
and you're correct there the sample class matters (unless the processing
is done the way you described it).

Of course diffreport() uses sample classes, but you knew that :-)

Yours,
Steffen
42
Other / Re: Metabolite PLS-DA analysis bad p-value
Hi august,

I don't have the first hand knowledge on PLS-DA to comment on your question,
but I remember the excellent keynote by Rasmus Bro at Metabolomics 2012
( http://www.metabolomics2012.org/keynote-speakers/ ) where he used
Matlab (his favourite tool, but can probably done in R as well) to draw
a fully RANDOM dataset, a fully RANDOM Y and got a (visually) nice separation
of the classes.

Maybe this Metabolomics journal article can also help ?
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337399/

Yours,
Steffen

P.S. : If you succeed to reproduce Rasmus' PLS-DA on random data in R,
I'd love to see a code example posted here...
44
CAMERA / Re: CAMERA for peptide isotopic distributions?
Hi Peter,

CAMERA has not been written with peptides in mind, so at least the defaults need to be modified:

1)  maxcharge=3, maxiso=4 in findIsotopes() need to be increased. Maybe it would help to
disable  filter: Should C12/C13 filter be applied which makes an intensity check between M and M+1.
also, make sure the mass accuracy is stringent enough, the default  mzabs=0.01 is too relaxed for e.g. an Orbitrap.

Having said that, I'd expect an isotope detection with a peptide intensity model
to be better suited for proteomics data. If you still want to use (and possibly improve)
CAMERA, I'd be happy to help, time permitting.

Yours,
Steffen