Representative De novo analysis of a MALDI-TOF-TOF spectrum. (A) The x- and y-axes show the mass to charge (m/z) ratio and the % abundance of the precursor ion fragments, respectively. The MS/MS spectrum was analyzed by PEAKS de novo sequencing software to generate 'RSALQAAHDAVAQEGQCR'. (B) The table details peptide fragments 'b-ions, y-ions and a-ions' and the neutral losses of water and ammonia for b-ions and y-ions as well as the immonium ions to develop confident and complete peptide sequence de novo from MS/MS spectrum. (C) The SPIDER homology search of this peptide resulted in sequence from Ubiquitin carboxyl-terminal hydrolase isozyme L1 as 'NEAIQAAHDAVAQEGQCR'.