[BioC] LC-MS data

[Nicholas Lewin-Koh]

Hi,
To my knowledge there are only 2 packages in R specifically for MS data,
mscalib on CRAN, and PROcess in bioconductor devel. The first is for
MALDI tof spectrometers and assumes you have picked peaks already and
works on the peaks list. The second is for seldi, but the baseline
correction and peak picking are pretty generic. To process LC-MS data you
have to decide how far back in the device internal processing you want to
go. Personally, I have found that the mantra for mass spec data at the
moment is "Don't trust vendor software". It mostly sucks. If you can get
it you want to be grabbing the data stream as it is read of the column by
the sensor, because it helps to warp the chromatagram from each scan so
that the peaks align properly. Then you want to conver to m/z. After that
comes all the signal processing song and dance, to subtract the chemical
noise, make a baseline adjustment, etc. The tools for this in R are here
and there and development for processing this stuff is nacent. There is
much more available in matlab, which though much more expensive is mostly
faster than R. The signal processing community and the chemometrics
people tend to work in matlab.


Note that it has been my experience that automated peak detection is an
art, with more pitfalls than clustering. If you can do anything to avoid
that using prior knowledge it helps. Good luck.

Nicholas
> 
> Message: 2
> Date: 12 Mar 2004 19:12:32 +0100
> From: Stephen Nyangoma <S.Nyangoma at cs.rug.nl>
> Subject: [BioC] LC-MS proteomics data
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <1079115152.10700.12.camel at iwi142>
> Content-Type: text/plain
> 
> Sorry for bothering you with this question.
> 
> Has someone analylsed LC-MS data? How do you read this data into R? Are
> there preprocessing tools in R? What are the crusial preprocessing
> steps? Do the ascii files obtained from Brucker software contain raw
> files? Thanks. Stephen.
> 
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