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\author{Florian P.\ Breitwieser, Jacques Colinge}

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\begin{document}

\title{Isobar for developers}
\maketitle
\tableofcontents

\section{Introduction}
This documents highlights the structure of the S4 classes and methods in the
\texttt{isobar} pacakge.

<<>>=
  library(isobar)
@

\section{Classes}
\subsection{IBSpectra}
<<>>=
  getClass("IBSpectra")
@ MSMS isobarically tagged proteomics data consists of spectrum
identifications and quantitative values. Spectrums are identified as
stemming from distinct peptides, and quantitative information of each
spectrum are extracted from a certain \texttt{m/z} region.

\Robject{IBSpectra} class holds this qualitative and quantitative
information. It is a virtual class. It extends \Robject{eSet} from
Biobase to store meta-information of spectrum identifications and
quantitative information (\texttt{m/z} and \texttt{intensity}) of
reporter tags. \Robject{eSet} is extended by slots for protein
grouping, tag names, tag masses and isotope impurity correction
matrix.

\Robject{ProteinGroup} objects store the mapping and grouping of
peptide level identifications to protein identifications.

\Robject{IBSpectra} is a virtual class. Currently used isobaric
tagging kits iTRAQ 4plex and 8plex, and TMT 2plex and 6plex are
implemented in the \Robject{iTRAQ4plexSpectra},
\Robject{iTRAQ8plexSpectra}, \Robject{TMT2plexSpectra}, and
\Robject{TMT6plexSpectr}, respectively. These are subclasses of
\Robject{iTRAQSpectra} and \Robject{TMTSpectra}, resp.\, which in turn
are virtual subclasses of \Robject{IBSpectra}.

\subsection{ProteinGroup}
<<>>=
  getClass("ProteinGroup")
@ Bottom-up MSMS proteomics experiments identify peptides which are
mapped back to proteins. This mapping leads to protein groups, which
explain the observed peptides according to the parsimony law.

A \Robject{ProteinGroup} object is generated when a
\Robject{IBSpectra} object is created by
\Rfunction{readIBSpectra}. Protein to peptide to spectrum mapping is
extracted from a suitable identication format\footnote{IBSpectra CSV,
  and MzIdentML format. Mascot DAT and Phenyx pidres.xml format
  converters to IBSpectra format are provided.}

\subsection{NoiseModel}
<<>>=
  getClass("NoiseModel")
@ \Robject{NoiseModel} objects model the technical variance observed
in the spectrum-level ratios of a certain experimental setup.


\section{Session Information}

The version number of R and packages loaded for generating the
vignette were:

<<echo=FALSE,results=tex>>=
  toLatex(sessionInfo())
@ 

\end{document}
