Protein ubiquitination feature annotation

Format

A data frame with 21436 rows and 12 variables:

protein_id: character, RefSeq identifier in format [accession].[version], e.g., NP_001004415.1. Note: contaminants should be identified with the following nomenclature: "Contaminant_XXXX"
redundant_ids: character, pipe-separated list of additional RefSeq identifiers with redundant peptide-matching sequences to protein_id that cannot be resolved by inference due to lack of unique peptides
is_contaminant: logical, whether protein_id is a contaminant
peptide_score: double, MSGF+ SpecE Value or Spectrum Mill score (1/bestScore)
sequence: character, peptide sequence determined by MSGF+ or Spectrum Mill analysis of LC-MS/MS features
organism_name: character, organism whose protein collection database was used for LC-MS/MS peptide identification, e.g., Rattus norvegicus
ptm_id: character, concatenation of protein_id and the modified amino acid residue (e.g., serine residue, 20 denoted as S20s), with "-" as a separator
ptm_peptide: character, concatenation of ptm_id and peptide with "-" as a separator. Values in this column are unique.
confident_score: double, score indicating confidence of modified amino acid residue localization by LC-MS/MS fragmentation as calculated by Ascore algorith (0-1000) or Spectrum Mill (0-1)
confident_site: logical, whether a modified site was confidently localized by LC-MS/MS fragmentation
tissue: character, tissue abbreviation, one of TISSUE_ABBREV
assay: character, assay "UBIQ"

pass1b-06/results/proteomics-untargeted/*/prot-ub/*rii-results.txt