raw_prot: raw_prot

In Vitek-Lab/MSstatsLiP: LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

raw_prot

Description

Example of input TrP dataset.

Usage

raw_prot

Format

A data.table consisting of 9,120 rows and 29 columns. Raw TrP data for use in testing and examples.

Details

Input to MSstatsLiP converter SpectronauttoMSstatsLiPFormat. Contains the following columns:

• R.Condition : Label of conditions (EG Disease/Control)

• R.FileName : Name of spectral processing run

• R.Replicate : Name of biological replicate

• PG.ProteinAccessions : Protein name

• PG.ProteinGroups : Protein name, can be multiple

• PG.Quantity : Protein Quantity

• PEP.GroupingKey : Peptide grouping

• PEP.StrippedSequence : Peptide sequence

• PEP.Quantity : Peptide quantity

• EG.iRTPredicted : Predicted value

• EG.Library : Name of library

• EG.ModifiedSequence : Peptide sequence including any post-translational modifications

• EG.PrecursorId : Peptide sequence wiht modifications including charge

• EG.Qvalue : Qvalue

• FG.Charge : Identified Ion charge

• FG.Id : Peptide sequence with charge

• FG.PrecMz : Prec Mz reading

• FG.Quantity : Initial quantity reading

• F.Charge : F.Charge

• F.FrgIon : Fragment ion

• F.FrgLossType : Label for loss type

• F.FrgMz : Mz reading

• F.FrgNum : numeric Frg

• F.FrgType : character label for Frg

• F.ExcludedFromQuantification : True/False boolean for if to exclude

• F.NormalizedPeakArea : Normalized peak intensity

• F.NormalizedPeakHeight : Normalized peak height

• F.PeakArea : Unnormalized peak area

• F.PeakHeight : Unnormalized peak height

Examples

head(raw_prot)

Vitek-Lab/MSstatsLiP documentation built on April 5, 2024, 3:25 a.m.