Literature DB >> 26111518

A calibration routine for efficient ETD in large-scale proteomics.

Christopher M Rose1,2, Matthew J P Rush1,2, Nicholas M Riley1,2, Anna E Merrill1,2, Nicholas W Kwiecien1,2, Dustin D Holden3, Christopher Mullen3, Michael S Westphall2, Joshua J Coon4,5,6.   

Abstract

Electron transfer dissociation (ETD) has been broadly adopted and is now available on a variety of commercial mass spectrometers. Unlike collisional activation techniques, optimal performance of ETD requires considerable user knowledge and input. ETD reaction duration is one key parameter that can greatly influence spectral quality and overall experiment outcome. We describe a calibration routine that determines the correct number of reagent anions necessary to reach a defined ETD reaction rate. Implementation of this automated calibration routine on two hybrid Orbitrap platforms illustrate considerable advantages, namely, increased product ion yield with concomitant reduction in scan rates netting up to 75% more unique peptide identifications in a shotgun experiment. Graphical Abstract ᅟ.

Entities:  

Keywords:  Calibration; ETD; Ion/ion; Kinetics; Mass spectrometry; Orbitrap; Proteomics

Mesh：

Substances：

Year:  2015        PMID： 26111518      PMCID： PMC5642106          DOI： 10.1007/s13361-015-1183-1

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


  62 in total

Review 1.  Ion/ion chemistry of high-mass multiply charged ions.

Authors:  S A McLuckey; J L Stephenson
Journal:  Mass Spectrom Rev       Date:  1998 Nov-Dec       Impact factor: 10.946

2.  Open mass spectrometry search algorithm.

Authors:  Lewis Y Geer; Sanford P Markey; Jeffrey A Kowalak; Lukas Wagner; Ming Xu; Dawn M Maynard; Xiaoyu Yang; Wenyao Shi; Stephen H Bryant
Journal:  J Proteome Res       Date:  2004 Sep-Oct       Impact factor: 4.466

3.  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

4.  Optimized Orbitrap HCD for quantitative analysis of phosphopeptides.

Authors:  Yi Zhang; Scott B Ficarro; Shaojuan Li; Jarrod A Marto
Journal:  J Am Soc Mass Spectrom       Date:  2009-03-28       Impact factor: 3.109

5.  Optimization of electron transfer dissociation via informed selection of reagents and operating parameters.

Authors:  Philip D Compton; Joseph V Strukl; Dina L Bai; Jeffrey Shabanowitz; Donald F Hunt
Journal:  Anal Chem       Date:  2012-01-06       Impact factor: 6.986

6.  Front-end electron transfer dissociation: a new ionization source.

Authors:  Lee Earley; Lissa C Anderson; Dina L Bai; Christopher Mullen; John E P Syka; A Michelle English; Jean-Jacques Dunyach; George C Stafford; Jeffrey Shabanowitz; Donald F Hunt; Philip D Compton
Journal:  Anal Chem       Date:  2013-08-19       Impact factor: 6.986

7.  A new probabilistic database search algorithm for ETD spectra.

Authors:  Rovshan G Sadygov; David M Good; Danielle L Swaney; Joshua J Coon
Journal:  J Proteome Res       Date:  2009-06       Impact factor: 4.466

8.  Collisions or electrons? Protein sequence analysis in the 21st century.

Authors:  Joshua J Coon
Journal:  Anal Chem       Date:  2009-05-01       Impact factor: 6.986

9.  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

10.  Neutron-encoded mass signatures for quantitative top-down proteomics.

Authors:  Timothy W Rhoads; Christopher M Rose; Derek J Bailey; Nicholas M Riley; Rosalynn C Molden; Amelia J Nestler; Anna E Merrill; Lloyd M Smith; Alexander S Hebert; Michael S Westphall; David J Pagliarini; Benjamin A Garcia; Joshua J Coon
Journal:  Anal Chem       Date:  2014-02-19       Impact factor: 6.986
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  28 in total

1.  Electron Transfer Dissociation of All Ions at All Times, MSETD, in a Quadrupole Time-of-Flight (Q-ToF) Mass Spectrometer.

Authors:  Christian N Cramer; Jeffery M Brown; Nick Tomczyk; Peter Kresten Nielsen; Kim F Haselmann
Journal:  J Am Soc Mass Spectrom       Date:  2016-12-02       Impact factor: 3.109

2.  Use of Multiple Ion Fragmentation Methods to Identify Protein Cross-Links and Facilitate Comparison of Data Interpretation Algorithms.

Authors:  Bingqing Zhao; Colin P Reilly; Caroline Davis; Andreas Matouschek; James P Reilly
Journal:  J Proteome Res       Date:  2020-06-04       Impact factor: 4.466

3.  Sulfur Pentafluoride is a Preferred Reagent Cation for Negative Electron Transfer Dissociation.

Authors:  Matthew J P Rush; Nicholas M Riley; Michael S Westphall; John E P Syka; Joshua J Coon
Journal:  J Am Soc Mass Spectrom       Date:  2017-03-27       Impact factor: 3.109

Review 4.  Radical solutions: Principles and application of electron-based dissociation in mass spectrometry-based analysis of protein structure.

Authors:  Frederik Lermyte; Dirk Valkenborg; Joseph A Loo; Frank Sobott
Journal:  Mass Spectrom Rev       Date:  2018-02-09       Impact factor: 10.946

5.  Neutral Loss Is a Very Common Occurrence in Phosphotyrosine-Containing Peptides Labeled with Isobaric Tags.

Authors:  Robert A Everley; Edward L Huttlin; Alison R Erickson; Sean A Beausoleil; Steven P Gygi
Journal:  J Proteome Res       Date:  2016-12-30       Impact factor: 4.466

6.  Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)-Enabled Intact Glycopeptide/Glycoproteome Characterization.

Authors:  Qing Yu; Bowen Wang; Zhengwei Chen; Go Urabe; Matthew S Glover; Xudong Shi; Lian-Wang Guo; K Craig Kent; Lingjun Li
Journal:  J Am Soc Mass Spectrom       Date:  2017-07-10       Impact factor: 3.109

7.  An Advanced Strategy for Comprehensive Profiling of ADP-ribosylation Sites Using Mass Spectrometry-based Proteomics.

Authors:  Ivo A Hendriks; Sara C Larsen; Michael L Nielsen
Journal:  Mol Cell Proteomics       Date:  2019-02-23       Impact factor: 5.911

8.  Implementation of Activated Ion Electron Transfer Dissociation on a Quadrupole-Orbitrap-Linear Ion Trap Hybrid Mass Spectrometer.

Authors:  Nicholas M Riley; Michael S Westphall; Alexander S Hebert; Joshua J Coon
Journal:  Anal Chem       Date:  2017-04-17       Impact factor: 6.986

9.  Electron-Based Dissociation Is Needed for O-Glycopeptides Derived from OpeRATOR Proteolysis.

Authors:  Nicholas M Riley; Stacy A Malaker; Carolyn R Bertozzi
Journal:  Anal Chem       Date:  2020-10-30       Impact factor: 6.986

Review 10.  A Perspective on the Confident Comparison of Glycoprotein Site-Specific Glycosylation in Sample Cohorts.

Authors:  Joshua A Klein; Joseph Zaia
Journal:  Biochemistry       Date:  2019-12-31       Impact factor: 3.162
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