Example MaxQuant/SCoPE2 output

Source: R/data.R

A data.frame with 1088 observations and 139 variables, as produced by reading a MaxQuant output file with read.delim().

  • Sequence: a character vector

  • Length: a numeric vector

  • Modifications: a character vector

  • Modified.sequence: a character vector

  • Deamidation..N..Probabilities: a character vector

  • Oxidation..M..Probabilities: a character vector

  • Deamidation..N..Score.Diffs: a character vector

  • Oxidation..M..Score.Diffs: a character vector

  • Acetyl..Protein.N.term.: a numeric vector

  • Deamidation..N.: a numeric vector

  • Oxidation..M.: a numeric vector

  • Missed.cleavages: a numeric vector

  • Proteins: a character vector

  • Leading.proteins: a character vector

  • protein: a character vector

  • Gene.names: a character vector

  • Protein.names: a character vector

  • Type: a character vector

  • Set: a character vector

  • MS.MS.m.z: a numeric vector

  • Charge: a numeric vector

  • m.z: a numeric vector

  • Mass: a numeric vector

  • Resolution: a numeric vector

  • Uncalibrated...Calibrated.m.z..ppm.: a numeric vector

  • Uncalibrated...Calibrated.m.z..Da.: a numeric vector

  • Mass.error..ppm.: a numeric vector

  • Mass.error..Da.: a numeric vector

  • Uncalibrated.mass.error..ppm.: a numeric vector

  • Uncalibrated.mass.error..Da.: a numeric vector

  • Max.intensity.m.z.0: a numeric vector

  • Retention.time: a numeric vector

  • Retention.length: a numeric vector

  • Calibrated.retention.time: a numeric vector

  • Calibrated.retention.time.start: a numeric vector

  • Calibrated.retention.time.finish: a numeric vector

  • Retention.time.calibration: a numeric vector

  • Match.time.difference: a logical vector

  • Match.m.z.difference: a logical vector

  • Match.q.value: a logical vector

  • Match.score: a logical vector

  • Number.of.data.points: a numeric vector

  • Number.of.scans: a numeric vector

  • Number.of.isotopic.peaks: a numeric vector

  • PIF: a numeric vector

  • Fraction.of.total.spectrum: a numeric vector

  • Base.peak.fraction: a numeric vector

  • PEP: a numeric vector

  • MS.MS.count: a numeric vector

  • MS.MS.scan.number: a numeric vector

  • Score: a numeric vector

  • Delta.score: a numeric vector

  • Combinatorics: a numeric vector

  • Intensity: a numeric vector

  • Reporter.intensity.corrected.0: a numeric vector

  • Reporter.intensity.corrected.1: a numeric vector

  • Reporter.intensity.corrected.2: a numeric vector

  • Reporter.intensity.corrected.3: a numeric vector

  • Reporter.intensity.corrected.4: a numeric vector

  • Reporter.intensity.corrected.5: a numeric vector

  • Reporter.intensity.corrected.6: a numeric vector

  • Reporter.intensity.corrected.7: a numeric vector

  • Reporter.intensity.corrected.8: a numeric vector

  • Reporter.intensity.corrected.9: a numeric vector

  • Reporter.intensity.corrected.10: a numeric vector

  • RI1: a numeric vector

  • RI2: a numeric vector

  • RI3: a numeric vector

  • RI4: a numeric vector

  • RI5: a numeric vector

  • RI6: a numeric vector

  • RI7: a numeric vector

  • RI8: a numeric vector

  • RI9: a numeric vector

  • RI10: a numeric vector

  • RI11: a numeric vector

  • Reporter.intensity.count.0: a numeric vector

  • Reporter.intensity.count.1: a numeric vector

  • Reporter.intensity.count.2: a numeric vector

  • Reporter.intensity.count.3: a numeric vector

  • Reporter.intensity.count.4: a numeric vector

  • Reporter.intensity.count.5: a numeric vector

  • Reporter.intensity.count.6: a numeric vector

  • Reporter.intensity.count.7: a numeric vector

  • Reporter.intensity.count.8: a numeric vector

  • Reporter.intensity.count.9: a numeric vector

  • Reporter.intensity.count.10: a numeric vector

  • Reporter.PIF: a logical vector

  • Reporter.fraction: a logical vector

  • Reverse: a character vector

  • Potential.contaminant: a logical vector

  • id: a numeric vector

  • Protein.group.IDs: a character vector

  • Peptide.ID: a numeric vector

  • Mod..peptide.ID: a numeric vector

  • MS.MS.IDs: a character vector

  • Best.MS.MS: a numeric vector

  • AIF.MS.MS.IDs: a logical vector

  • Deamidation..N..site.IDs: a numeric vector

  • Oxidation..M..site.IDs: a logical vector

  • remove: a logical vector

  • dart_PEP: a numeric vector

  • dart_qval: a numeric vector

  • razor_protein_fdr: a numeric vector

  • Deamidation..NQ..Probabilities: a logical vector

  • Deamidation..NQ..Score.Diffs: a logical vector

  • Deamidation..NQ.: a logical vector

  • Reporter.intensity.corrected.11: a logical vector

  • Reporter.intensity.corrected.12: a logical vector

  • Reporter.intensity.corrected.13: a logical vector

  • Reporter.intensity.corrected.14: a logical vector

  • Reporter.intensity.corrected.15: a logical vector

  • Reporter.intensity.corrected.16: a logical vector

  • RI12: a logical vector

  • RI13: a logical vector

  • RI14: a logical vector

  • RI15: a logical vector

  • RI16: a logical vector

  • Reporter.intensity.count.11: a logical vector

  • Reporter.intensity.count.12: a logical vector

  • Reporter.intensity.count.13: a logical vector

  • Reporter.intensity.count.14: a logical vector

  • Reporter.intensity.count.15: a logical vector

  • Reporter.intensity.count.16: a logical vector

  • Deamidation..NQ..site.IDs: a logical vector

  • input_id: a logical vector

  • rt_minus: a logical vector

  • rt_plus: a logical vector

  • mu: a logical vector

  • muij: a logical vector

  • sigmaij: a logical vector

  • pep_new: a logical vector

  • exp_id: a logical vector

  • peptide_id: a logical vector

  • stan_peptide_id: a logical vector

  • exclude: a logical vector

  • residual: a logical vector

  • participated: a logical vector

  • peptide: a character vector

data("mqScpData")

Format

An object of class data.frame with 1361 rows and 149 columns.

Details

The dataset is a subset of the SCoPE2 dataset (version 2, Specht et al. 2019, BioRXiv). The input file evidence_unfiltered.csv was downloaded from a Google Drive repository. The MaxQuant evidence file was loaded and the data was cleaned (renaming columns, removing duplicate fields,...). MS runs that were selected in the scp1 dataset (see ?scp1) were kept along with a blank run. The data is stored as a data.frame.

See also

readSCP() for an example on how mqScpData is parsed into a QFeatures object.