Tidyproteomics: an open-source R package and data object for quantitative proteomics post analysis and visualization

Table 1 The main data import structure utilizes a fragmented non-redundant scheme to minimize the size and complexity of the data

Data	Variable	Description
Experiments	sample_id	An 8-character string identifier
	import_file	The import file
	sample_file	The individual LCMS sample file
	sample	The sample name
	replicate	The sample replicate
Quantitative	sample_id	...
	sample	...
	replicate	...
	identifier	Proteins: protein Peptides: protein, peptide, modification
	abundance_…	the quantitative accounting value, existing as raw and "normalized" (eg. median, linear, loess, randomforest)
Accounting	sample_id	...
	identifier	Proteins: protein Peptides: protein, peptide, modification
	imputed	0-1 value, indicating the ratio of peptides imputed
	num_…	an integer accounting of peptides, unique_peptides and proteins
Annotations	identifier	Proteins: protein Peptides: protein, peptide, modification
	term	The annotation group(eg. molecular function)
	annotation	The annotation name (eg. metal ion binding)

Additionally, the Annotations table is setup in a one-to-many organization that does not enforce rigidity of term definitions across all measurement variables (eg. for each protein)

ISSN: 1471-2105