\name{NEWS}
\title{OrgMassSpecR News}

\section{Changes in version 0.5-4 (2026-01-26)}{

  \itemize{
    \item Modified the documentation for FragmentPeptide.
    \item Cleaned up citations for isotopic masses.
  }
}

\section{Changes in version 0.5-2 (2017-08-11)}{

    \itemize{
      \item Added print.alignment and print.graphic arguments to SpectrumSimilarity, providing options to generate these outputs. Added x.threshold argument to SepectrumSimilarity to exclude a lower portion of the spectrum from the similarity score calculation.
      \item Added output.list argument to SpectrumSimilarity, providing the option to return the similarity score, alignment dataframe, and plot in a list (thanks to M. Witting). In this case the plot is a grid graphics object.
      \item Added remove.placeholders argument to ReadMSPFile and ReadMSPDirectory to optionally remove zero intensity peaks from the resulting data frame.
      \item Included iodine in ListFormula and MolecularWeight (thanks to G. Getzinger).
      \item Fixed error in PeptideSpectrum. If only one fragment ion match was made, the function stopped with an error when annotating the spectrum (thanks to H. Kim).
    }
}

\section{Changes in version 0.4-6 (2016-10-18)}{

    \itemize{
      \item Added example to WriteMspFile.Rd.
    }

}

\section{Changes in version 0.4-4 (2014-05-21)}{

    \itemize{
      \item Fixed error in ConvertPeptide. When output = "elements", the resulting element list did not include the additon of water. This caused the mass calculated by, for example, MonoisotopicMass(ConvertPeptide("SEQENCE")) to be incorrect.
    }

}

\section{Changes in version 0.4-2 (2014-03-14)}{

    \itemize{
      \item Vingette changed to R Markdown format and complied using knitr.
    }

}

\section{Changes in version 0.4 (2013-10-04)}{

    \itemize{
      \item Added trypsin.strict option to Digest function (thanks to S. Michalik).
    }

}

\section{Changes in version 0.3-18 (2013-09-04)}{

    \itemize{
      \item Function Digest fixed. It now correctly determines peptide sequences when the number of missed cleavages is > 1 (thanks to S. Michalik).
    }

}

\section{Changes in version 0.3-11 (2012-01-29)}{

  \itemize{
    \item R >= 2.14.1 required due to changes in the vignette file structure.
  }

}

\section{Changes in version 0.3-8 (2011-10-10)}{

  \itemize{
    \item Function ReadMspFile added.
  }

}

\section{Changes in version 0.3-6 (2011-08-26)}{

  \itemize{
    \item Function ConvertConcentration added.
  }

}

\section{Changes in version 0.3-2 (2011-04-08)}{

  \itemize{
    \item Warning message in ListFormula modified to include the elemental formula (helps in tracking down the source of the warning when called multiple times within another function).
  }

}
  

\section{Changes in version 0.3-1 (2011-03-18)}{

  \itemize{
    \item NEWS file started.
  }
  
}
