SpectronauttoMSstatsPTMFormat: Convert Spectronaut output into MSstatsPTM format

In Vitek-Lab/MSstatsPTM: Statistical Characterization of Post-translational Modifications

Convert Spectronaut output into MSstatsPTM format

Description

Converters label-free Spectronaut data into MSstatsPTM format. Requires PSM output from Spectronaut and a custom made annotation file, mapping the run name to the condition and bioreplicate. Can optionally take a seperate PSM file for a global profiling run. If no global profiling run provided, the function can extract the unmodified peptides from the PTM PSM file and use them as a global profiling run (not recommended).

Usage

SpectronauttoMSstatsPTMFormat(
  input,
  annotation = NULL,
  fasta_path = NULL,
  protein_input = NULL,
  annotation_protein = NULL,
  use_unmod_peptides = FALSE,
  intensity = "PeakArea",
  mod_id = "\\[Phospho \\(STY\\)\\]",
  fasta_protein_name = "uniprot_iso",
  remove_other_mods = TRUE,
  filter_with_Qvalue = TRUE,
  qvalue_cutoff = 0.01,
  useUniquePeptide = TRUE,
  removeFewMeasurements = TRUE,
  removeProtein_with1Feature = FALSE,
  summaryforMultipleRows = max,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL
)

Arguments

input	name of Spectronaut PTM output, which is long-format. ProteinName, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge, IsotopeLabelType, Condition, BioReplicate, Run, Intensity, F.ExcludedFromQuantification are required. Rows with F.ExcludedFromQuantification=True will be removed.
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.
fasta_path	string containing path to the corresponding fasta file for the modified peptide dataset.
protein_input	name of Spectronaut global protein output, which is as in the same format as input parameter.
annotation_protein	name of annotation file for global protein data, in the same format as above.
use_unmod_peptides	If protein_input is not provided, unmodified peptides can be extracted from input to be used in place of a global profiling run. Default is FALSE.
intensity	'PeakArea'(default) uses not normalized peak area. 'NormalizedPeakArea' uses peak area normalized by Spectronaut. Default is NULL
mod_id	Character that indicates the modification of interest. Default is ⁠\\(Phospho\\)⁠. Note ⁠\\⁠ must be included before special characters.
fasta_protein_name	Name of fasta column that matches with protein name in evidence file. Default is uniprot_iso.
remove_other_mods	Remove peptides which include modfications other than the one listed in mod_id. Default is TRUE. For example, in an experiment targeting Phosphorylation, setting this parameter to TRUE would remove peptides like (Acetyl (Protein N-term))AAAAPDSRVS(Phospho (STY))EEENLK. Set this parameter to FALSE to keep peptides with extraneous modifications.
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.
summaryforMultipleRows	max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.
use_log_file	logical. If TRUE, information about data processing will be saved to a file.
append	logical. If TRUE, information about data processing will be added to an existing log file.
verbose	logical. If TRUE, information about data processing wil be printed to the console.
log_file_path	character. Path to a file to which information about data processing will be saved. If not provided, such a file will be created automatically. If 'append = TRUE', has to be a valid path to a file.

Value

a list of two data.tables named 'PTM' and 'PROTEIN' in the format required by MSstatsPTM.

Examples

head(spectronaut_input)
head(spectronaut_annotation)

msstats_input = SpectronauttoMSstatsPTMFormat(spectronaut_input, 
                  annotation=spectronaut_annotation, 
                  fasta_path=system.file("extdata", "spectronaut_fasta.fasta", package="MSstatsPTM"),
                  use_unmod_peptides=TRUE,
                  mod_id = "\\[Phospho \\(STY\\)\\]",
                  fasta_protein_name = "uniprot_iso"
                  )

head(msstats_input$PTM)
head(msstats_input$PROTEIN)

Vitek-Lab/MSstatsPTM documentation built on Sept. 26, 2024, 9:28 p.m.