example_proteome: Example protein data in long format
In proBatch: Tools for Diagnostics and Corrections of Batch Effects in Proteomics

Description Usage Format Source

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

1	example_proteome

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)