Package 'MSstatsConvert'

Clean raw Proteome Discoverer data

Description

Clean raw Proteome Discoverer data

Usage

.cleanRawPD(
  msstats_object,
  quantification_column,
  protein_id_column,
  sequence_column,
  remove_shared,
  remove_protein_groups = TRUE,
  intensity_columns_regexp = "Abundance"
)

Arguments

msstats_object	an object of class MSstatsSpectroMineFiles.
quantification_column	chr, name of a column used for quantification.
protein_id_column	chr, name of a column with protein IDs.
sequence_column	chr, name of a column with peptide sequences.
remove_shared	lgl, if TRUE, shared peptides will be removed.
remove_protein_groups	if TRUE, proteins with numProteins > 1 will be removed.
intensity_columns_regexp	regular expressions that defines intensity columns. Defaults to "Abundance", which means that columns that contain the word "Abundance" will be treated as corresponding to intensities for different channels.

Value

data.table

---

Helper method to validate input has necessary columns

Description

Helper method to validate input has necessary columns

Usage

.validatePDTMTInputColumns(
  pd_input,
  protein_id_column,
  num_proteins_column,
  channels
)

Arguments

pd_input	data.frame input
protein_id_column	column name for protein passed from user
num_proteins_column	column name for number of protein groups passed from user
channels	list of column names for channels

---

Convert output of converters to data.frame

Description

Convert output of converters to data.frame

Usage

## S3 method for class 'MSstatsValidated'
as.data.frame(x, ...)

Arguments

x	object of class MSstatsValidated
...	Additional arguments to be passed to or from other methods.

Value

data.frame

---

Convert output of converters to data.table

Description

Convert output of converters to data.table

Usage

## S3 method for class 'MSstatsValidated'
as.data.table(x, ...)

Arguments

x	object of class MSstatsValidated
...	Additional arguments to be passed to or from other methods.

Value

data.tables

---

Import Diann files

Description

Import Diann files

Usage

DIANNtoMSstatsFormat(
  input,
  annotation = NULL,
  global_qvalue_cutoff = 0.01,
  qvalue_cutoff = 0.01,
  pg_qvalue_cutoff = 0.01,
  useUniquePeptide = TRUE,
  removeFewMeasurements = TRUE,
  removeOxidationMpeptides = TRUE,
  removeProtein_with1Feature = TRUE,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  MBR = TRUE,
  quantificationColumn = "FragmentQuantCorrected",
  ...
)

Arguments

input	name of MSstats input report from Diann, which includes feature-level data.
annotation	name of 'annotation.txt' data which includes Condition, BioReplicate, Run.
global_qvalue_cutoff	The global qvalue cutoff
qvalue_cutoff	local qvalue cutoff for library
pg_qvalue_cutoff	local qvalue cutoff for protein groups Run should be the same as filename.
useUniquePeptide	should unique pepties be removed
removeFewMeasurements	should proteins with few measurements be removed
removeOxidationMpeptides	should peptides with oxidation be removed
removeProtein_with1Feature	should proteins with a single feature be removed
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.
MBR	True if analysis was done with match between runs
quantificationColumn	Use 'FragmentQuantCorrected'(default) column for quantified intensities. 'FragmentQuantRaw' can be used instead.
...	additional parameters to data.table::fread.

Value

data.frame in the MSstats required format.

Author(s)

Elijah Willie

Examples

input_file_path = system.file("tinytest/raw_data/DIANN/diann_input.tsv", 
                                package="MSstatsConvert")
annotation_file_path = system.file("tinytest/raw_data/DIANN/annotation.csv", 
                                package = "MSstatsConvert")
input = data.table::fread(input_file_path)
annot = data.table::fread(annotation_file_path)
output = DIANNtoMSstatsFormat(input, annotation = annot, MBR = FALSE, 
                                use_log_file = FALSE)
head(output)

---

Import DIA-Umpire files

Description

Import DIA-Umpire files

Usage

DIAUmpiretoMSstatsFormat(
  raw.frag,
  raw.pep,
  raw.pro,
  annotation,
  useSelectedFrag = TRUE,
  useSelectedPep = TRUE,
  removeFewMeasurements = TRUE,
  removeProtein_with1Feature = FALSE,
  summaryforMultipleRows = max,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  ...
)

Arguments

raw.frag	name of FragSummary_date.xls data, which includes feature-level data.
raw.pep	name of PeptideSummary_date.xls data, which includes selected fragments information.
raw.pro	name of ProteinSummary_date.xls data, which includes selected peptides information.
annotation	name of annotation data which includes Condition, BioReplicate, Run information.
useSelectedFrag	TRUE will use the selected fragment for each peptide. 'Selected_fragments' column is required.
useSelectedPep	TRUE will use the selected peptide for each protein. 'Selected_peptides' column is required.
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.
...	additional parameters to data.table::fread.

Value

data.frame in the MSstats required format.

Author(s)

Meena Choi, Olga Vitek

Examples

diau_frag = system.file("tinytest/raw_data/DIAUmpire/dia_frag.csv", 
                             package = "MSstatsConvert")
diau_pept = system.file("tinytest/raw_data/DIAUmpire/dia_pept.csv", 
                             package = "MSstatsConvert")
diau_prot = system.file("tinytest/raw_data/DIAUmpire/dia_prot.csv", 
                             package = "MSstatsConvert")
annot = system.file("tinytest/raw_data/DIAUmpire/annot_diau.csv", 
                    package = "MSstatsConvert")
diau_frag = data.table::fread(diau_frag) 
diau_pept = data.table::fread(diau_pept) 
diau_prot = data.table::fread(diau_prot) 
annot = data.table::fread(annot)
diau_frag = diau_frag[, lapply(.SD, function(x) if (is.integer(x)) as.numeric(x) else x)]
# In case numeric columns are not interpreted correctly

diau_imported = DIAUmpiretoMSstatsFormat(diau_frag, diau_pept, diau_prot, 
                                         annot, use_log_file = FALSE)
head(diau_imported)

---

Import FragPipe files

Description

Import FragPipe files

Usage

FragPipetoMSstatsFormat(
  input,
  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 FragPipe msstats.csv export. ProteinName, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge, IsotopeLabelType, Condition, BioReplicate, Run, Intensity are required.
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.
...	additional parameters to data.table::fread.

Value

data.frame in the MSstats required format.

Author(s)

Devon Kohler

Examples

fragpipe_raw = system.file("tinytest/raw_data/FragPipe/fragpipe_input.csv",
                              package = "MSstatsConvert")
fragpipe_raw = data.table::fread(fragpipe_raw)
fragpipe_imported = FragPipetoMSstatsFormat(fragpipe_raw, use_log_file = FALSE)
head(fragpipe_imported)

---

Get one of files contained in an instance of MSstatsInputFiles class.

Description

Get one of files contained in an instance of MSstatsInputFiles class.

Usage

getInputFile(msstats_object, file_type)

## S4 method for signature 'MSstatsInputFiles'
getInputFile(msstats_object, file_type = "input")

## S4 method for signature 'MSstatsPhilosopherFiles'
getInputFile(msstats_object, file_type = "input")

Arguments

msstats_object	object that inherits from MSstatsPhilosopherFiles class.
file_type	character name of a type file. Usually equal to "input".

Value

data.table

data.table

data.table

Examples

evidence_path = system.file("tinytest/raw_data/MaxQuant/mq_ev.csv", 
                            package = "MSstatsConvert")
pg_path = system.file("tinytest/raw_data/MaxQuant/mq_pg.csv", 
                      package = "MSstatsConvert")
evidence = read.csv(evidence_path)
pg = read.csv(pg_path)
imported = MSstatsImport(list(evidence = evidence, protein_groups = pg),
                         "MSstats", "MaxQuant")
class(imported)
head(getInputFile(imported, "evidence"))

---

Import MaxQuant files

Description

Import MaxQuant files

Usage

MaxQtoMSstatsFormat(
  evidence,
  annotation,
  proteinGroups,
  proteinID = "Proteins",
  useUniquePeptide = TRUE,
  summaryforMultipleRows = max,
  removeFewMeasurements = TRUE,
  removeMpeptides = FALSE,
  removeOxidationMpeptides = FALSE,
  removeProtein_with1Peptide = FALSE,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  ...
)

Arguments

evidence	name of 'evidence.txt' data, which includes feature-level data.
annotation	name of 'annotation.txt' data which includes Raw.file, Condition, BioReplicate, Run, IsotopeLabelType information.
proteinGroups	name of 'proteinGroups.txt' data. It needs to matching protein group ID. If proteinGroups=NULL, use 'Proteins' column in 'evidence.txt'.
proteinID	'Proteins'(default) or 'Leading.razor.protein' for Protein ID.
useUniquePeptide	TRUE (default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
summaryforMultipleRows	max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.
removeFewMeasurements	TRUE (default) will remove the features that have 1 or 2 measurements across runs.
removeMpeptides	TRUE will remove the peptides including 'M' sequence. FALSE is default.
removeOxidationMpeptides	TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default.
removeProtein_with1Peptide	TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default.
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.
...	additional parameters to data.table::fread.

Value

data.frame in the MSstats required format.

Note

Warning: MSstats does not support for metabolic labeling or iTRAQ experiments.

Author(s)

Meena Choi, Olga Vitek.

Examples

mq_ev = data.table::fread(system.file("tinytest/raw_data/MaxQuant/mq_ev.csv",
                                      package = "MSstatsConvert"))
mq_pg = data.table::fread(system.file("tinytest/raw_data/MaxQuant/mq_pg.csv",
                                      package = "MSstatsConvert"))
annot = data.table::fread(system.file("tinytest/raw_data/MaxQuant/annotation.csv",
                                      package = "MSstatsConvert"))
maxq_imported = MaxQtoMSstatsFormat(mq_ev, annot, mq_pg, use_log_file = FALSE)
head(maxq_imported)

---

Import Metamorpheus files

Description

Import Metamorpheus files

Usage

MetamorpheusToMSstatsFormat(
  input,
  annotation = NULL,
  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 Metamorpheus output file, which is tabular format. Use the AllQuantifiedPeaks.tsv file from the Metamorpheus output.
annotation	name of 'annotation.txt' data which includes Condition, BioReplicate.
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.
...	additional parameters to data.table::fread.

Value

data.frame in the MSstats required format.

Author(s)

Anthony Wu

Examples

input = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv", 
                                package = "MSstatsConvert")
input = data.table::fread(input)
annot = system.file("tinytest/raw_data/Metamorpheus/Annotation.tsv", 
                                package = "MSstatsConvert")
annot = data.table::fread(annot)
metamorpheus_imported = MSstatsConvert:::MetamorpheusToMSstatsFormat(input, annotation = annot)
head(metamorpheus_imported)

---

Creates balanced design by removing overlapping fractions and filling incomplete rows

Description

Creates balanced design by removing overlapping fractions and filling incomplete rows

Usage

MSstatsBalancedDesign(
  input,
  feature_columns,
  fill_incomplete = TRUE,
  handle_fractions = TRUE,
  fix_missing = NULL,
  remove_few = TRUE
)

Arguments

input	data.table processed by the MSstatsPreprocess function
feature_columns	str, names of columns that define spectral features
fill_incomplete	if TRUE (default), Intensity values for missing runs will be added as NA
handle_fractions	if TRUE (default), overlapping fractions will be resolved
fix_missing	str, optional. Defaults to NULL, which means no action. If not NULL, must be one of the options: "zero_to_na" or "na_to_zero". If "zero_to_na", Intensity values equal exactly to 0 will be converted to NA. If "na_to_zero", missing values will be replaced by zeros.
remove_few	lgl, if TRUE, features with one or two measurements across runs will be removed.

Value

data.frame of class MSstatsValidated

Examples

unbalanced_data = system.file("tinytest/raw_data/unbalanced_data.csv", 
                              package = "MSstatsConvert")
unbalanced_data = data.table::as.data.table(read.csv(unbalanced_data))
balanced = MSstatsBalancedDesign(unbalanced_data, 
                                 c("PeptideSequence", "PrecursorCharge",
                                   "FragmentIon", "ProductCharge"))
dim(balanced) # Now balanced has additional rows (with Intensity = NA)
# for runs that were not included in the unbalanced_data table

---

Clean files generated by a signal processing tools.

Description

Clean files generated by a signal processing tools.

Clean DIAUmpire files

Clean MaxQuant files

Clean OpenMS files

Clean OpenSWATH files

Clean Progenesis files

Clean ProteomeDiscoverer files

Clean Skyline files

Clean SpectroMine files

Clean Spectronaut files

Clean Philosopher files

Clean DIA-NN files

Clean Metamorpheus files

Usage

MSstatsClean(msstats_object, ...)

## S4 method for signature 'MSstatsDIAUmpireFiles'
MSstatsClean(msstats_object, use_frag, use_pept)

## S4 method for signature 'MSstatsMaxQuantFiles'
MSstatsClean(
  msstats_object,
  protein_id_col,
  remove_by_site = FALSE,
  channel_columns = "Reporterintensitycorrected"
)

## S4 method for signature 'MSstatsOpenMSFiles'
MSstatsClean(msstats_object)

## S4 method for signature 'MSstatsOpenSWATHFiles'
MSstatsClean(msstats_object)

## S4 method for signature 'MSstatsProgenesisFiles'
MSstatsClean(msstats_object, runs, fix_colnames = TRUE)

## S4 method for signature 'MSstatsProteomeDiscovererFiles'
MSstatsClean(
  msstats_object,
  quantification_column,
  protein_id_column,
  sequence_column,
  remove_shared,
  remove_protein_groups = TRUE,
  intensity_columns_regexp = "Abundance"
)

## S4 method for signature 'MSstatsSkylineFiles'
MSstatsClean(msstats_object)

## S4 method for signature 'MSstatsSpectroMineFiles'
MSstatsClean(msstats_object)

## S4 method for signature 'MSstatsSpectronautFiles'
MSstatsClean(msstats_object, intensity)

## S4 method for signature 'MSstatsPhilosopherFiles'
MSstatsClean(
  msstats_object,
  protein_id_col,
  peptide_id_col,
  channels,
  remove_shared_peptides
)

## S4 method for signature 'MSstatsDIANNFiles'
MSstatsClean(
  msstats_object,
  MBR = TRUE,
  quantificationColumn = "FragmentQuantCorrected"
)

## S4 method for signature 'MSstatsMetamorpheusFiles'
MSstatsClean(msstats_object)

Arguments

msstats_object	object that inherits from MSstatsInputFiles class.
...	additional parameter to specific cleaning functions.
use_frag	TRUE will use the selected fragment for each peptide. 'Selected_fragments' column is required.
use_pept	TRUE will use the selected fragment for each protein 'Selected_peptides' column is required.
protein_id_col	character, name of a column with names of proteins.
remove_by_site	logical, if TRUE, proteins only identified by site will be removed.
channel_columns	character, regular expression that identifies channel columns in TMT data.
runs	chr, vector of Run labels.
fix_colnames	lgl, if TRUE, one of the rows will be used as colnames.
quantification_column	chr, name of a column used for quantification.
protein_id_column	chr, name of a column with protein IDs.
sequence_column	chr, name of a column with peptide sequences.
remove_shared	lgl, if TRUE, shared peptides will be removed.
remove_protein_groups	if TRUE, proteins with numProteins > 1 will be removed.
intensity_columns_regexp	regular expressions that defines intensity columns. Defaults to "Abundance", which means that columns that contain the word "Abundance" will be treated as corresponding to intensities for different channels.
intensity	chr, specifies which column will be used for Intensity.
peptide_id_col	character name of a column that identifies peptides
channels	character vector of channel labels
remove_shared_peptides	logical, if TRUE, shared peptides will be removed based on the IsUnique column from Philosopher output
MBR	True if analysis was done with match between runs
quantificationColumn	Use 'FragmentQuantCorrected'(default) column for quantified intensities. 'FragmentQuantRaw' can be used instead.

Value

data.table

data.table

data.table

data.table

data.table

data.table

data.table

data.table

data.table

data.table

data.table

data.table

Examples

evidence_path = system.file("tinytest/raw_data/MaxQuant/mq_ev.csv", 
                            package = "MSstatsConvert")
pg_path = system.file("tinytest/raw_data/MaxQuant/mq_pg.csv", 
                      package = "MSstatsConvert")
evidence = read.csv(evidence_path)
pg = read.csv(pg_path)
imported = MSstatsImport(list(evidence = evidence, protein_groups = pg),
                         "MSstats", "MaxQuant")
cleaned_data = MSstatsClean(imported, protein_id_col = "Proteins")
head(cleaned_data)

---

MSstatsConvert: An R Package to Convert Data from Mass Spectrometry Signal Processing Tools to MSstats Format

Description

MSstatsConvert helps convert data from different types of mass spectrometry experiments and signal processing tools to a format suitable for statistical analysis with the MSstats and MSstatsTMT packages.

Main functions

MSstatsLogsSettings for logs management, MSstatsImport for importing files created by signal processing tools, MSstatsClean for re-formatting imported files into a consistent format, MSstatsPreprocess for preprocessing cleaned files, MSstatsBalancedDesign for handling fractions and creating balanced data.

---

Import files from signal processing tools.

Description

Import files from signal processing tools.

Usage

MSstatsImport(input_files, type, tool, tool_version = NULL, ...)

Arguments

input_files	list of paths to input files or data.frame objects. Interpretation of this parameter depends on values of parameters type and tool.
type	chr, "MSstats" or "MSstatsTMT".
tool	chr, name of a signal processing tool that generated input files.
tool_version	not implemented yet. In the future, this parameter will allow handling different versions of each signal processing tools.
...	optional additional parameters to data.table::fread.

Value

an object of class MSstatsInputFiles.

Examples

evidence_path = system.file("tinytest/raw_data/MaxQuant/mq_ev.csv", 
                            package = "MSstatsConvert")
pg_path = system.file("tinytest/raw_data/MaxQuant/mq_pg.csv", 
                      package = "MSstatsConvert")
evidence = read.csv(evidence_path)
pg = read.csv(pg_path)
imported = MSstatsImport(list(evidence = evidence, protein_groups = pg),
                         "MSstats", "MaxQuant")
class(imported)
head(getInputFile(imported, "evidence"))

---

Set how MSstats will log information from data processing

Description

Set how MSstats will log information from data processing

Usage

MSstatsLogsSettings(
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  base = "MSstats_log_",
  pkg_name = "MSstats"
)

Arguments

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.
base	start of the file name.
pkg_name	currently "MSstats", "MSstatsPTM" or "MSstatsTMT". Each package can use its own separate log settings.

Value

TRUE invisibly in case of successful logging setup.

Examples

# No logging and no messages
MSstatsLogsSettings(FALSE, FALSE, FALSE)
# Log, but do not display messages
MSstatsLogsSettings(TRUE, FALSE, FALSE)
# Log to an existing file
file.create("new_log.log")
MSstatsLogsSettings(TRUE, TRUE, log_file_path = "new_log.log")
# Do not log, but display messages
MSstatsLogsSettings(FALSE)

---

Create annotation

Description

Create annotation

Usage

MSstatsMakeAnnotation(input, annotation, ...)

Arguments

input	data.table preprocessed by the MSstatsClean function
annotation	data.table
...	key-value pairs, where keys are names of columns of annotation

Value

data.table

Examples

evidence_path = system.file("tinytest/raw_data/MaxQuant/mq_ev.csv", 
                            package = "MSstatsConvert")
pg_path = system.file("tinytest/raw_data/MaxQuant/mq_pg.csv", 
                      package = "MSstatsConvert")
evidence = read.csv(evidence_path)
pg = read.csv(pg_path)
imported = MSstatsImport(list(evidence = evidence, protein_groups = pg),
                         "MSstats", "MaxQuant")
cleaned_data = MSstatsClean(imported, protein_id_col = "Proteins")
annot_path = system.file("tinytest/raw_data/MaxQuant/annotation.csv", 
                         package = "MSstatsConvert")
mq_annot = MSstatsMakeAnnotation(cleaned_data, read.csv(annot_path),
                                 Run = "Rawfile")
head(mq_annot)

---

Preprocess outputs from MS signal processing tools for analysis with MSstats

Description

Preprocess outputs from MS signal processing tools for analysis with MSstats

Usage

MSstatsPreprocess(
  input,
  annotation,
  feature_columns,
  remove_shared_peptides = TRUE,
  remove_single_feature_proteins = TRUE,
  feature_cleaning = list(remove_features_with_few_measurements = TRUE,
    summarize_multiple_psms = max),
  score_filtering = list(),
  exact_filtering = list(),
  pattern_filtering = list(),
  columns_to_fill = list(),
  aggregate_isotopic = FALSE,
  ...
)

Arguments

input	data.table processed by the MSstatsClean function.
annotation	annotation file generated by a signal processing tool.
feature_columns	character vector of names of columns that define spectral features.
remove_shared_peptides	logical, if TRUE shared peptides will be removed.
remove_single_feature_proteins	logical, if TRUE, proteins that only have one feature will be removed.
feature_cleaning	named list with maximum two (for MSstats converters) or three (for MSstatsTMT converter) elements. If handle_few_measurements is set to "remove", feature with less than three measurements will be removed (otherwise it should be equal to "keep"). summarize_multiple_psms is a function that will be used to aggregate multiple feature measurements in a run. It should return a scalar and accept an na.rm parameter. For MSstatsTMT converters, setting remove_psms_with_any_missing will remove features which have missing values in a run from that run.
score_filtering	a list of named lists that specify filtering options. Details are provided in the vignette.
exact_filtering	a list of named lists that specify filtering options. Details are provided in the vignette.
pattern_filtering	a list of named lists that specify filtering options. Details are provided in the vignette.
columns_to_fill	a named list of scalars. If provided, columns with names defined by the names of this list and values corresponding to its elements will be added to the output data.frame.
aggregate_isotopic	logical. If TRUE, isotopic peaks will by summed.
...	additional parameters to data.table::fread.

Value

data.table

Examples

evidence_path = system.file("tinytest/raw_data/MaxQuant/mq_ev.csv", 
                            package = "MSstatsConvert")
pg_path = system.file("tinytest/raw_data/MaxQuant/mq_pg.csv", 
                      package = "MSstatsConvert")
evidence = read.csv(evidence_path)
pg = read.csv(pg_path)
imported = MSstatsImport(list(evidence = evidence, protein_groups = pg),
                         "MSstats", "MaxQuant")
cleaned_data = MSstatsClean(imported, protein_id_col = "Proteins")
annot_path = system.file("tinytest/raw_data/MaxQuant/annotation.csv", 
                         package = "MSstatsConvert")
mq_annot = MSstatsMakeAnnotation(cleaned_data, read.csv(annot_path),
                                 Run = "Rawfile")
                               
# To filter M-peptides and oxidatin peptides 
m_filter = list(col_name = "PeptideSequence", pattern = "M", 
                filter = TRUE, drop_column = FALSE)
oxidation_filter = list(col_name = "Modifications", pattern = "Oxidation", 
                        filter = TRUE, drop_column = TRUE)
msstats_format = MSstatsPreprocess(
cleaned_data, mq_annot, 
feature_columns = c("PeptideSequence", "PrecursorCharge"),
columns_to_fill = list(FragmentIon = NA, ProductCharge = NA),
pattern_filtering = list(oxidation = oxidation_filter, m = m_filter)
)
# Output in the standard MSstats format
head(msstats_format)

---

Save session information

Description

Save session information

Usage

MSstatsSaveSessionInfo(
  path = NULL,
  append = TRUE,
  base = "MSstats_session_info_"
)

Arguments

path	optional path to output file. If not provided, "MSstats_session_info" and current timestamp will be used as a file name
append	if TRUE and file given by the path parameter already exists, session info will be appended to the file
base	beginning of a file name

Value

TRUE invisibly after session info was saved

Examples

MSstatsSaveSessionInfo("session_info.txt")
MSstatsSaveSessionInfo("session_info.txt", base = "MSstatsTMT_session_info_")

---

Import OpenMS files

Description

Import OpenMS files

Usage

OpenMStoMSstatsFormat(
  input,
  annotation = NULL,
  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 MSstats input report from OpenMS, which includes feature(peptide ion)-level data.
annotation	name of 'annotation.txt' data which includes Condition, BioReplicate, Run. Run should be the same as filename.
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.
...	additional parameters to data.table::fread.

Value

data.frame in the MSstats required format.

Author(s)

Meena Choi, Olga Vitek.

Examples

openms_raw = data.table::fread(system.file("tinytest/raw_data/OpenMS/openms_input.csv", 
                                           package = "MSstatsConvert"))
openms_imported = OpenMStoMSstatsFormat(openms_raw, use_log_file = FALSE)
head(openms_imported)

---

Import OpenSWATH files

Description

Import OpenSWATH files

Usage

OpenSWATHtoMSstatsFormat(
  input,
  annotation,
  filter_with_mscore = TRUE,
  mscore_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 MSstats input report from OpenSWATH, which includes feature-level data.
annotation	name of 'annotation.txt' data which includes Condition, BioReplicate, Run. Run should be the same as filename.
filter_with_mscore	TRUE(default) will filter out the features that have greater than mscore_cutoff in m_score column. Those features will be removed.
mscore_cutoff	Cutoff for m_score. 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.
...	additional parameters to data.table::fread.

Value

data.frame in the MSstats required format.

Author(s)

Meena Choi, Olga Vitek.

Examples

os_raw = system.file("tinytest/raw_data/OpenSWATH/openswath_input.csv", 
                             package = "MSstatsConvert")
annot = system.file("tinytest/raw_data/OpenSWATH/annot_os.csv", 
                    package = "MSstatsConvert")
os_raw = data.table::fread(os_raw) 
annot = data.table::fread(annot)

os_imported = OpenSWATHtoMSstatsFormat(os_raw, annot, use_log_file = FALSE)
head(os_imported)

---

Import Proteome Discoverer files

Description

Import Proteome Discoverer files

Usage

PDtoMSstatsFormat(
  input,
  annotation,
  useNumProteinsColumn = FALSE,
  useUniquePeptide = TRUE,
  summaryforMultipleRows = max,
  removeFewMeasurements = TRUE,
  removeOxidationMpeptides = FALSE,
  removeProtein_with1Peptide = FALSE,
  which.quantification = "Precursor.Area",
  which.proteinid = "Protein.Group.Accessions",
  which.sequence = "Sequence",
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  ...
)

Arguments

input	PD report or a path to it.
annotation	name of 'annotation.txt' or 'annotation.csv' data which includes Condition, BioReplicate, Run information. 'Run' will be matched with 'Spectrum.File'.
useNumProteinsColumn	TRUE removes peptides which have more than 1 in # Proteins column of PD output.
useUniquePeptide	TRUE (default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
summaryforMultipleRows	max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.
removeFewMeasurements	TRUE (default) will remove the features that have 1 or 2 measurements across runs.
removeOxidationMpeptides	TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default.
removeProtein_with1Peptide	TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default.
which.quantification	Use 'Precursor.Area'(default) column for quantified intensities. 'Intensity' or 'Area' can be used instead.
which.proteinid	Use 'Protein.Accessions'(default) column for protein name. 'Master.Protein.Accessions' can be used instead.
which.sequence	Use 'Sequence'(default) column for peptide sequence. 'Annotated.Sequence' can be used instead.
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.
...	additional parameters to data.table::fread.

Value

data.frame in the MSstats required format.

Author(s)

Meena Choi, Olga Vitek

Examples

pd_raw = system.file("tinytest/raw_data/PD/pd_input.csv", 
                     package = "MSstatsConvert")
annot = system.file("tinytest/raw_data/PD/annot_pd.csv", 
                    package = "MSstatsConvert")
pd_raw = data.table::fread(pd_raw)
annot = data.table::fread(annot)

pd_imported = PDtoMSstatsFormat(pd_raw, annot, use_log_file = FALSE)
head(pd_imported)

---

Import Progenesis files

Description

Import Progenesis files

Usage

ProgenesistoMSstatsFormat(
  input,
  annotation,
  useUniquePeptide = TRUE,
  summaryforMultipleRows = max,
  removeFewMeasurements = TRUE,
  removeOxidationMpeptides = FALSE,
  removeProtein_with1Peptide = FALSE,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  ...
)

Arguments

input	name of Progenesis output, which is wide-format. 'Accession', 'Sequence', 'Modification', 'Charge' and one column for each run are required.
annotation	name of 'annotation.txt' or 'annotation.csv' data which includes Condition, BioReplicate, Run information. It will be matched with the column name of input for MS runs.
useUniquePeptide	TRUE (default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
summaryforMultipleRows	max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.
removeFewMeasurements	TRUE (default) will remove the features that have 1 or 2 measurements across runs.
removeOxidationMpeptides	TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default.
removeProtein_with1Peptide	TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default.
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.
...	additional parameters to data.table::fread.

Value

data.frame in the MSstats required format.

Author(s)

Meena Choi, Olga Vitek, Ulrich Omasits

Examples

progenesis_raw = system.file("tinytest/raw_data/Progenesis/progenesis_input.csv", 
                             package = "MSstatsConvert")
annot = system.file("tinytest/raw_data/Progenesis/progenesis_annot.csv", 
                    package = "MSstatsConvert")
progenesis_raw = data.table::fread(progenesis_raw) 
annot = data.table::fread(annot)

progenesis_imported = ProgenesistoMSstatsFormat(progenesis_raw, annot,
                                                use_log_file = FALSE)
head(progenesis_imported)

---

Import Skyline files

Description

Import Skyline files

Usage

SkylinetoMSstatsFormat(
  input,
  annotation = NULL,
  removeiRT = TRUE,
  filter_with_Qvalue = TRUE,
  qvalue_cutoff = 0.01,
  useUniquePeptide = TRUE,
  removeFewMeasurements = TRUE,
  removeOxidationMpeptides = FALSE,
  removeProtein_with1Feature = FALSE,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  ...
)

Arguments

input	name of MSstats input report from Skyline, which includes feature-level data.
annotation	name of 'annotation.txt' data which includes Condition, BioReplicate, Run. If annotation is already complete in Skyline, use annotation=NULL (default). It will use the annotation information from input.
removeiRT	TRUE (default) will remove the proteins or peptides which are labeled 'iRT' in 'StandardType' column. FALSE will keep them.
filter_with_Qvalue	TRUE(default) will filter out the intensities that have greater than qvalue_cutoff in DetectionQValue column. Those intensities will be replaced with zero and will be considered as censored missing values for imputation purpose.
qvalue_cutoff	Cutoff for DetectionQValue. 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.
removeOxidationMpeptides	TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default.
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.
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.
...	additional parameters to data.table::fread.

Value

data.frame in the MSstats required format.

Author(s)

Meena Choi, Olga Vitek

Examples

skyline_raw = system.file("tinytest/raw_data/Skyline/skyline_input.csv",
                          package = "MSstatsConvert")
skyline_raw = data.table::fread(skyline_raw)
skyline_imported = SkylinetoMSstatsFormat(skyline_raw)
head(skyline_imported)

---

Import Spectronaut files

Description

Import Spectronaut files

Usage

SpectronauttoMSstatsFormat(
  input,
  annotation = NULL,
  intensity = "PeakArea",
  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 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.
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.
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.
...	additional parameters to data.table::fread.

Value

data.frame in the MSstats required format.

Author(s)

Meena Choi, Olga Vitek

Examples

spectronaut_raw = system.file("tinytest/raw_data/Spectronaut/spectronaut_input.csv",
                              package = "MSstatsConvert")
spectronaut_raw = data.table::fread(spectronaut_raw)
spectronaut_imported = SpectronauttoMSstatsFormat(spectronaut_raw, use_log_file = FALSE)
head(spectronaut_imported)

---