Literature DB >> 21953093

Sequence scrambling in shotgun proteomics is negligible.

Anton A Goloborodko1, Mikhail V Gorshkov, David M Good, Roman A Zubarev.   

Abstract

Analysis of 15,897 low-energy (CAD) and 10,878 higher-energy (HCD) collisional dissociation mass spectra of doubly protonated tryptic peptides taken with high resolution revealed that the rate of sequence scrambling due to b-ion cyclization is negligible (<1%) and can be safely ignored as a possible source of erroneous sequence assignment in shotgun proteomics. On the other hand, there is significant presence of normal (non-scrambled) internal fragments in HCD, which should be taken into account by MS/MS search engines.

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Year:  2011        PMID： 21953093     DOI： 10.1007/s13361-011-0130-z

Source DB:  PubMed          Journal:  J Am Soc Mass Spectrom        ISSN： 1044-0305            Impact factor:   3.109


  14 in total

Review 1.  Fragmentation pathways of protonated peptides.

Authors:  Béla Paizs; Sándor Suhai
Journal:  Mass Spectrom Rev       Date:  2005 Jul-Aug       Impact factor: 10.946

2.  Implementation of electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer.

Authors:  Graeme C McAlister; Doug Phanstiel; David M Good; W Travis Berggren; Joshua J Coon
Journal:  Anal Chem       Date:  2007-04-19       Impact factor: 6.986

3.  SwedCAD, a database of annotated high-mass accuracy MS/MS spectra of tryptic peptides.

Authors:  Maria Fälth; Mikhail M Savitski; Michael L Nielsen; Frank Kjeldsen; Per E Andren; Roman A Zubarev
Journal:  J Proteome Res       Date:  2007-08-21       Impact factor: 4.466

4.  Peptide sequence scrambling through cyclization of b(5) ions.

Authors:  Alex G Harrison
Journal:  J Am Soc Mass Spectrom       Date:  2008-07-03       Impact factor: 3.109

5.  To b or not to b: the ongoing saga of peptide b ions.

Authors:  Alex G Harrison
Journal:  Mass Spectrom Rev       Date:  2009 Jul-Aug       Impact factor: 10.946

6.  Influence of size on apparent scrambling of sequence during CID of b-type ions.

Authors:  Samuel Molesworth; Sandra Osburn; Michael Van Stipdonk
Journal:  J Am Soc Mass Spectrom       Date:  2009-08-12       Impact factor: 3.109

7.  Direct analysis of protein complexes using mass spectrometry.

Authors:  A J Link; J Eng; D M Schieltz; E Carmack; G J Mize; D R Morris; B M Garvik; J R Yates
Journal:  Nat Biotechnol       Date:  1999-07       Impact factor: 54.908

8.  A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer.

Authors:  Graeme C McAlister; W Travis Berggren; Jens Griep-Raming; Stevan Horning; Alexander Makarov; Doug Phanstiel; George Stafford; Danielle L Swaney; John E P Syka; Vlad Zabrouskov; Joshua J Coon
Journal:  J Proteome Res       Date:  2008-07-10       Impact factor: 4.466

9.  The effect of interfering ions on search algorithm performance for electron-transfer dissociation data.

Authors:  David M Good; Craig D Wenger; Joshua J Coon
Journal:  Proteomics       Date:  2010-01       Impact factor: 3.984

10.  Post-acquisition ETD spectral processing for increased peptide identifications.

Authors:  David M Good; Craig D Wenger; Graeme C McAlister; Dina L Bai; Donald F Hunt; Joshua J Coon
Journal:  J Am Soc Mass Spectrom       Date:  2009-03-14       Impact factor: 3.109
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  22 in total

1.  Occurrence of C-terminal residue exclusion in peptide fragmentation by ESI and MALDI tandem mass spectrometry.

Authors:  Mathieu Dupré; Sonia Cantel; Jean Martinez; Christine Enjalbal
Journal:  J Am Soc Mass Spectrom       Date:  2011-11-18       Impact factor: 3.109

2.  Investigation of scrambled ions in tandem mass spectra. Part 1. Statistical characterization.

Authors:  Nai-ping Dong; Yi-zeng Liang; Lun-zhao Yi
Journal:  J Am Soc Mass Spectrom       Date:  2012-04-27       Impact factor: 3.109

3.  Conformation-specific spectroscopy of peptide fragment ions in a low-temperature ion trap.

Authors:  Tobias N Wassermann; Oleg V Boyarkin; Béla Paizs; Thomas R Rizzo
Journal:  J Am Soc Mass Spectrom       Date:  2012-03-30       Impact factor: 3.109

4.  Mass spectrometry analysis of 2-nitrophenylhydrazine carboxy derivatized peptides.

Authors:  Junmei Zhang; Rowaida Al-Eryani; Haydn L Ball
Journal:  J Am Soc Mass Spectrom       Date:  2011-08-04       Impact factor: 3.109

5.  Carbonyl charge solvation patterns may relate to fragmentation classes in collision-activated dissociation.

Authors:  Hongqian Yang; David M Good; David van der Spoel; Roman A Zubarev
Journal:  J Am Soc Mass Spectrom       Date:  2012-06-12       Impact factor: 3.109

6.  Fragmentation reactions of b(5) and a (5) ions containing proline--the structures of a(5) ions.

Authors:  Alex G Harrison
Journal:  J Am Soc Mass Spectrom       Date:  2011-09-20       Impact factor: 3.109

7.  Structures of a(n)* ions derived from protonated pentaglycine and pentaalanine: results from IRMPD spectroscopy and DFT calculations.

Authors:  Junfang Zhao; Justin Kai-Chi Lau; Josipa Grzetic; Udo H Verkerk; Jos Oomens; K W Michael Siu; Alan C Hopkinson
Journal:  J Am Soc Mass Spectrom       Date:  2013-09-12       Impact factor: 3.109

8.  Non-direct sequence ions in the tandem mass spectrometry of protonated peptide amides--an energy-resolved study.

Authors:  Alex G Harrison; Cagdas Tasoglu; Talat Yalcin
Journal:  J Am Soc Mass Spectrom       Date:  2013-08-06       Impact factor: 3.109

9.  Fragmentation reactions of methionine-containing protonated octapeptides and fragment ions therefrom: an energy-resolved study.

Authors:  Alex G Harrison
Journal:  J Am Soc Mass Spectrom       Date:  2013-08-14       Impact factor: 3.109

10.  Evidence for sequence scrambling in collision-induced dissociation of y-type fragment ions.

Authors:  Mahsan Miladi; Brett Harper; Touradj Solouki
Journal:  J Am Soc Mass Spectrom       Date:  2013-08-28       Impact factor: 3.109
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