mqScpData: Example MaxQuant/SCoPE2 output
In scp: Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

Description Usage Format Details See Also

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

1	data("mqScpData")

An object of class data.frame with 1197 rows and 139 columns.

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.

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

scp documentation built on Nov. 8, 2020, 8:20 p.m.