Converts raw PTM MS data from Spectronautt into the format needed for MSstatsPTM.

Takes as as input both raw PTM and global protein outputs from Spectronaut.

SpectronauttoMSstatsPTMFormat(
  PTM.data,
  fasta,
  Protein.data = NULL,
  annotation = NULL,
  intensity = "PeakArea",
  filter_with_Qvalue = TRUE,
  qvalue_cutoff = 0.01,
  useUniquePeptide = TRUE,
  removeFewMeasurements = TRUE,
  removeProtein_with1Feature = FALSE,
  removeNonUniqueProteins = TRUE,
  modificationLabel = "Phospho",
  removeiRT = TRUE,
  summaryforMultipleRows = max,
  which.Conditions = "all"
)

Arguments

PTM.data	name of PTM Spectronaut output, which is long-format.
fasta	A string of path to a FASTA file, used to match PTM peptides.
Protein.data	name of Global Protein Spectronaut output, which is long-format.
annotation	name of 'annotation.txt' data which includes Condition, BioReplicate, Run. If annotation is already complete in Spectronaut, use annotation=NULL (default). It will use the annotation information from input.
intensity	'PeakArea'(default) uses not normalized peak area. 'NormalizedPeakArea' uses peak area normalized by Spectronaut
filter_with_Qvalue	TRUE(default) will filter out the intensities that have greater than qvalue_cutoff in EG.Qvalue column. Those intensities will be replaced with zero and will be considered as censored missing values for imputation purpose.
qvalue_cutoff	Cutoff for EG.Qvalue. default is 0.01.
useUniquePeptide	TRUE(default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
removeFewMeasurements	TRUE (default) will remove the features that have 1 or 2 measurements across runs.
removeProtein_with1Feature	TRUE will remove the proteins which have only 1 feature, which is the combination of peptide, precursor charge, fragment and charge. FALSE is default.
removeNonUniqueProteins	TRUE will remove proteins that were not uniquely identified. IE if the protein column contains multiple proteins seperated by ";". TRUE is default
modificationLabel	String of modification name. Default is 'Phospho'.
removeiRT	TRUE will remove proteins that contain iRT. True is default
summaryforMultipleRows	max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.
which.Conditions	list of conditions to format into MSstatsPTM format. If "all" all conditions will be used. Default is "all".

Examples

# Output datasets of Spectronaut
## TODO: Add examples