Fig. 2: Arginylation analysis of whole-proteome peptides using in-house software.

a, Software flowchart of customized ArginylomePlot. Input data are mzXML and peptide identification files. Output data are MS1, MS2 and the summary of unbiased arginylation sites. b, Experimental workflow for arginylation of tryptic peptides from HEK293T (ATE1 KO) cells. c, Numbers of identified MS1 pairs, arginylation sites, unique peptides and unique proteins. d, H/L ratio distribution of all MS1 pairs and their corresponding numbers of MS1 scans (doublets, error ≤10 ppm). The retention times of peptide IDs belonging to a pair were averaged. The software will extract matching MS1 scans within 1.25 min (±1.25 min) of the averaged retention times. e, Analysis of the N-terminal residues of all unique arginylated peptides. Q is arginylated after deamidation (Q → E). f, Sequence logo calculated from unmodified forms of all unique arginylated peptides. The frequency plot is generated by WebLogo. The peptide sequences were aligned and extended to include 14 positions downstream of the arginylation sites as the P1′ position. g, Comparison of tryptic and nontryptic N-terminal of all arginylated peptides. A nontryptic N-terminal may indicate endogenously exposed N-termini of proteins.