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.
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.
Added remove.placeholders argument to ReadMSPFile and ReadMSPDirectory to optionally remove zero intensity peaks from the resulting data frame.
Included iodine in ListFormula and MolecularWeight (thanks to G. Getzinger).
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).
Added example to WriteMspFile.Rd.
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.
Vingette changed to R Markdown format and complied using knitr.
Added trypsin.strict option to Digest function (thanks to S. Michalik).
Function Digest fixed. It now correctly determines peptide sequences when the number of missed cleavages is > 1 (thanks to S. Michalik).
R >= 2.14.1 required due to changes in the vignette file structure.
Function ReadMspFile added.
Function ConvertConcentration added.
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).
NEWS file started.