example_proteome: Example protein data in long format

In symbioticMe/proBatch: Tools for Diagnostics and Corrections of Batch Effects in Proteomics

Example protein data in long format

Description

This is OpenSWATH-output data from Aging study with all iRT, spike-in peptides, few representative peptides and proteins for signal improvement demonstration. Using matrix_to_long can be converted to example_proteome_matrix

Usage

example_proteome

Format

A data frame with 124655 rows and 7 variables:

peptide_group_label

peptide ID, which is regular feature level. This column is mostly used as feature_id_col

used for merging with "example_peptide_annotation"

Intensity

peptide group intensity in given sample. Used in function as measure_col

Protein

Protein group ID, specified as N/UniProtID1|UniProtID2|..., where N is number of protein peptide group maps to. If 1/UniProtID, then this is proteotypic peptide, in functions used as protein_col

FullRunName

name of the file, in most functions used for sample_id_col

m_score

column marking the quality of peptide IDs, used as qual_col throughout the script; when qual_value is 2 in this column, peptide has been imputed (requantified)

...

Source

PRIDE ID will be added upon the publication of the dataset

symbioticMe/proBatch documentation built on April 9, 2023, 11:59 a.m.