align_features: Perform alignment of pre-determined MS1-features by MaxQuant...

In mathiaskalxdorf/IceR: Requantification of label-free DDA proteomics data pre-analyzed by MaxQuant.

Perform alignment of pre-determined MS1-features by MaxQuant over proteomics samples either analyzed on an Orbitrap machine (e.g. Q-Exactive or Orbitrap Fusion) or a TIMS-ToF Pro

Description

Perform alignment of pre-determined MS1-features by MaxQuant over proteomics samples either analyzed on an Orbitrap machine (e.g. Q-Exactive or Orbitrap Fusion) or a TIMS-ToF Pro

Usage

align_features(
  path_to_MaxQ_output,
  path_to_output,
  align_unknown = F,
  output_file_names_add = "IceR_analysis",
  mz_window = NA,
  min_mz_window = 0.001,
  RT_window = NA,
  min_RT_window = 1,
  min_num_ions_collapse = 10,
  feature_mass_deviation_collapse = 0.002,
  only_unmodified_peptides = F,
  sample_list = NA,
  remove_contaminants = T,
  MassSpec_mode = c("Orbitrap", "TIMSToF"),
  IM_window = NA,
  min_IM_window = 0.002
)

Arguments

path_to_MaxQ_output	Path to folder containing MaxQuant outputs (txt folder containing at least allpeptides.txt, evidence.txt, peptides.txt and proteinGroups.txt)
path_to_output	Path to folder where IceR results should be stored
align_unknown	Boolean value indicating if only peptide features or also unsequenced features should be aligend over samples. By default set to F.
output_file_names_add	IceR result name tag. By default IceR_analysis
mz_window	Numeric value indicating maximal m/z deviation around a center. By default set to NA which indicates that the function determines automatically this parameter based on sd of m/z of identified peptides between samples.
min_mz_window	Numberic value indicating how large the automatically determined m/z-window should be. By default set to 0.001 Da. Only required if m/z alignment window should be automatically determined. If set to NA, no minimal window size will be required.
RT_window	Numeric value indicating maximal RT deviation around a center. By default set to NA which indicates that the function determines automatically this parameter based on sd of RT of identified peptides between samples.
min_RT_window	Numberic value indicating how large the automatically determined RT-window should be. By default set to 1 min. Only required if RT alignment window should be automatically determined. If set to NA, no minimal window size will be required.
min_num_ions_collapse	Numeric value indicating how many unsequenced MaxQuant features have to be at least detected over all samples to result in an IceR feature. Only required if align_unknown is set to T. By default set to 10.
feature_mass_deviation_collapse	Numeric value indicating which minimal mass deviation is required to distinguish IceR features. By default set to 0.002 Da. IceR features with overlapping RT-windows and mass differences smaller than the specified value are merged.
only_unmodified_peptides	Boolean value indicating if only unmodified peptide sequences are used for alignment. By default set to F.
sample_list	Character vector (raw file names) listing which samples should be aligned. By default all samples occuring in MaxQuant outputs are aligned.
remove_contaminants	Boolean value indicating if peptide features labeled as contaminants should be removed. By default set to T.
MassSpec_mode	String being either "Orbitrap" or "TIMSToF" specifying by which type of Mass Spectrometer the data was generated. By default it expects Thermo Orbitrap data.
IM_window	Numeric value indicating maximal ion mobility (inverse K0) deviation around a center. By default set to NA which indicates that the function determines automatically this parameter based on sd of ion mobility of identified peptides between samples.
min_IM_window	Numberic value indicating how large the automatically determined ion mobility-window (inverse K0) should be. By default set to 0.002. Only required if ion mobility alignment window should be automatically determined. If set to NA, no minimal window size will be required.

Details

Performs the first steps of the IceR workflow: 1) Alignment window determination if not specified. 2) Alignment of MaxQuant features into IceR features. 3) Transfer of sequence information between MaxQuant features aligned into IceR features. 4) Extraction, modelling and prediction of RT- and m/z-correction factor per IceR feature and sample.

Value

Outputs are stored in the sub-directory Temporary_files within specified output folder. MaxQuant allpeptides.txt and evidence.txt are converted to RData files. QC plots of estimated alignment windows as well as of random forest modesl and generalized additive models are stored in a QC_plots.pdf. Relevant QC data is stored in Feature_alignment_QC_data.RData. Aligned IceR features are stored in Features_aligned_merged.txt

mathiaskalxdorf/IceR documentation built on Aug. 1, 2022, 8:03 a.m.