Analysis of low complex region peptides derived from mollusk shell matrix proteins using CID, high-energy collisional dissociation, and electron transfer dissociation on an LTQ-orbitrap: Implications for peptide to spectrum match

Identification of proteins involved in mollusk biomineralization by proteomics approach is gaining importance. These proteins are often characterized by low-complexity regions (LCRs) made of repeating motifs that are constituted by few amino acids (e.g. IGG, DD, KK, and GGG). In this work, we have analyzed the fragmentation of model LCR peptides under different fragmentation regimes (CID, high-energy collisional dissociation [HCD], and electron transfer dissociation [ETD]) and its consequences on peptide to spectrum matches (PSMs) using two search algorithms (Mascot and PEAKS DB). For both search tools, higher number of PSMs was obtained using CID spectra, followed by HCD and ETD. Intense fragment ions present in the lower m/z region of HCD led to lower PSM scores and absence of low mass cut off seems to offer little advantage for the identification of LCR peptides. Generally, doubly charged peptides under ETD conditions did not fragment to yield sequence information rich spectra. The spectral quality is affected by the nature of the repeating motifs in the peptide. The performance of both Mascot and PEAKS DB (de novo based search tool) vary according to the fragment regime employed to acquire MS/MS spectra.