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
Version of Record online: 20 SEP 2012
© 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Special Issue: Focus on Emerging Gel-Free Separation and Detection Methods
Volume 12, Issue 19-20, pages 3069–3075, October 2012
How to Cite
Marie, A., Alves, S., Marie, B., Dubost, L., Bédouet, L. and Berland, S. (2012), 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. Proteomics, 12: 3069–3075. doi: 10.1002/pmic.201200143
- Issue online: 19 OCT 2012
- Version of Record online: 20 SEP 2012
- Accepted manuscript online: 8 AUG 2012 01:27AM EST
- Manuscript Accepted: 25 JUL 2012
- Manuscript Revised: 9 JUL 2012
- Manuscript Received: 5 APR 2012
- Ministère de l'éducation nationale et de la Recherche
- Muséum National d'Histoire Naturelle
Disclaimer: Supplementary materials have been peer-reviewed but not copyedited.
Table 1: Mascot scores for peptide-spectrum matches of spectra acquired under different fragmentation regimes. Values in parenthesis under the score column represent ion identity threshold score and amino acids in red color denote the differences in the matched sequence with respect to the model peptide. Only the peptides that are classed in the first place are indicated.
Table 2: Mascot matches six different sequences for peptide P1 containing (IGG) motifs and matches to only one peptide for P2 containing (LGG) motifs although same fragment ions are matched (with minor differences).
Table 3: Table shows the isomeric fragment ions for b and y ion series for the peptide P4. Red color denotes fragment ions matched only by Mascot and ions shaded in yellow are matched by PEAKS DB
Table 4: PEAKS scores for the peptide-spectrum matches of spectra obtained under different fragmentation regimes: a) CID-FT MS/MS, B) HCD-FT MS/MS and C) ETD-FT MS/MS. ALC score indicates the average score of the positional confidence of each amino acid. Amino acids in red denote the difference in amino acid with respect to the model peptide.
Figure 1: ETD-FT MS/MS spectrum of the peptide P5 showing sequence rich fragment ions. Mascot matches to the correct peptide sequence, while PEAKS DB does not match to any sequence. Fragment ions corresponding to (z3+2) to (z17+2) ions are indicated with (*), fragment ion Z16+2 is not observed.
Figure 2A: ETD- FT MS/MS spectrum of the peptide P8 (WDDDDNDDWDDDDR) showing zn+2 fragment ions (n = 3, 5 -12) and whereas the peptide P9 (WGDDDNDDWDDDDR) does not fragment to give sequence specific fragment ions (Figure 2B).
Figure 3: HCD spectrum of peptide P6 (QQFQQQQQQQR) showing the y1 fragment ion (m/z = 175.11). Both Mascot and PEAKS DB do not take into account this information and matches to a peptide with amino acids at the N-terminal inversed (QQFQQQQQQRQ)
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