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8Th Uppsala Conference & School on Electron 8th Uppsala Conference & School on Electron Capture and Transfer Dissociation 2011 (UPPCON 2011) Villars-sur-Ollon, Switzerland 6-10 February 2011 ISBN: 978-1-61782-367-1 Printed from e-media with permission by: Curran Associates, Inc. 57 Morehouse Lane Red Hook, NY 12571 Some format issues inherent in the e-media version may also appear in this print version. Copyright© (2011) by the Biomolecular Mass Spectrometry Laboratory (LSMB) All rights reserved. Printed by Curran Associates, Inc. (2011) For permission requests, please contact the Biomolecular Mass Spectrometry Laboratory (LSMB) at the address below. Biomolecular Mass Spectrometry Laboratory (LSMB) Yury O Tsybin EPFL-SB-ISIC LSMB, BCH 4307 CH-1015 Lausanne Switzerland Phone: 41 21 693 97 51 Fax: 41 21 693 98 95 [email protected] Additional copies of this publication are available from: Curran Associates, Inc. 57 Morehouse Lane Red Hook, NY 12571 USA Phone: 845-758-0400 Fax: 845-758-2634 Email: [email protected] Web: www.proceedings.com TABLE OF CONTENTS SESSION I – FUNDAMENTAL ASPECTS OF ECD/ETD I ECD/ETD Mechanism: Seven Burning Questions..............................................................................................................1 Roman A. Zubarev Hydrogen Economics in Peptide Dissociation: Abundant Or Deficient? ..........................................................................2 Ryan Julian Influence of the Charge Carrier on the Electron Capture Dissociation of Peptides ........................................................3 Julia Chamot-Rooke Transition Metal Ions: Charge Carriers That Mediate the Electron Capture Dissociation Pathways of Peptides...................................................................................................................................................................................4 T. W. Dominic Chan The Effect of Post-translational Modifications on the Electron Capture Dissociation Behavior of Peptide Ions............................................................................................................................................................................5 Helen Cooper SESSION II – ECD/ETD DEVELOPMENT AND APPLICATIONS IN LIFE SCIENCES How to Make ETD Faster and Better ..................................................................................................................................6 Joshua Coon Electron Transfer Energy Deposition: Progress in Studies of Protein Biology ................................................................7 Alma Burlingame Benefits of Lys-N and ETD in a Proteomics Workflow ......................................................................................................8 A. F. Maarten Altelaar Activated-ion Electron Transfer Dissociation (AI-ETD) Performed in a Dedicated ETD Reaction Cell on a Hybrid Mass Spectrometer Leads to Unprecedented Proteomic Sensitivity ............................................................9 Aaron Ledvina Study on the Role of Hydrogen Transfer to Improve Peptide Identification from an ABRF-IPRG- 2011 ETD Data Set Using PFIND....................................................................................................................................... 11 Rui-Xiang Sun SESSION III – FUNDAMENTAL ASPECTS OF ECD/ETD II Cascade Dissociation of Peptide “Z” Ions: Mechanism and Energetics.......................................................................... 12 Frantisek Turecek Ideas About How Electrons Fragment Peptides in Electron Transfer Dissociation (ETD) Mass Spectrometry........................................................................................................................................................................ 13 Jack Simons Electronic Structure and ECD Mechanism: Effects of Modeling Methods and Peptides Conformation..................... 14 Gilles Frison Electron Capture Induced Dissociation of Dipeptide Dications: Where Does the Charge Go? .................................... 15 Camilla Skinnerup Jensen Size-dependent Analysis of ECD Fragments Reveals That W-Ions Originate from a Pathway Distinct from Major Z-Ions............................................................................................................................................................... 16 Guillaume Van Der Rest SESSION IV – FRAGMENTATION OF NEGATIVE IONS WITH ELECTRONS AND PHOTONS Recent Progress in the Application of Electron Detachment Dissociation for the Structural Analysis of Glycosaminoglycans ............................................................................................................................................................ 17 I. Jonathan Amster Electron Detachment Dissociation for Top-down Mass Spectrometry of Acidic Proteins ............................................ 18 Katherin Breuker Vibrational and Ion-electron Activation for Negative Ion MS/MS Analysis of Sulfopeptides ...................................... 19 Katherine E. Hersberger From EDD of Oligonucleotides to EID of Mononucleotides ............................................................................................ 20 Carlos Afonso Electron Photodetachment Dissociation (EPD) Experiments .......................................................................................... 21 Philippe Dugourd SESSION V – PEPTIDE AND PROTEIN RADICAL CHEMISTRY AND STRUCTURE ECD Without EC: Programming Peptides for Self Destruction with Reactive Radical Centers.................................. 22 Jack Beauchamp Deciphering Protein Folding Mechanisms by Mass Spectrometry Using Top-down ECD and Radical Labeling................................................................................................................................................................................ 23 Lars Konermann ECD After Gas-phase H/D Exchange As a Probe for Protein Ion Tertiary Structure .................................................. 24 Sergio Castro ETD MS/MS for Detailed Protein Analysis: A Closer Look at the Invisible Regime of the “Iceberg” ........................ 25 Ralf Hartmer SESSION VI – ECD/ETD METHOD AND TECHNIQUE DEVELOPMENT Recent ECD FT-ICR MS Results Using a Graphite Nanopearl Planar Field-emission Cold Cathode ........................ 26 Pat Langridge-Smith The Implementation and Characterization of Electron Transfer Dissociation (ETD) on an Ion Mobility Enabled Q-TOF Mass Spectrometer .................................................................................................................. 27 Keith Compson A-, B-, C-, D-, W-, Y-, and Z-ions of Peptides and Proteins Generated Simultaneously by MALDI ISD .................... 28 Kai Scheffler SESSION VII – BEYOND ELECTROSPRAY IONIZATION ECD/ETD Electron Capture by Metal Cationized Peptides and Metal Ions in Aqueous Nanodrops: Connections to Solution Electrochemistry............................................................................................................................................... 29 Evan Williams Dissociation Dynamics of Electronically Excited Peptides in a Cold Ion Trap............................................................... 30 Thomas Rizzo Electron Transfer Reactions for Imaging MS................................................................................................................... 31 Ron Heeren POSTER PRESENTATIONS Role of Conformation in H· Transfer During ECD of Peptides: Lessons from Class II Lasso Peptides....................... 32 Carlos Afonso Probing Gas Phase Peptide Structures: Insight from Simulations May Confirm Structural Preferences in Radical Induced Tandem Mass Spectrometry ......................................................................................... 33 Hisham Ben Hamidane Electron Capture Process Under LDI of Dyes from Rough Graphite............................................................................. 34 Vitaliy Chagovets Mass Spectrometry of Silver Clusters................................................................................................................................35 Jelena Cveticanin Identification of O-Glycopeptides and Sulfopeptides by ETD-MS.................................................................................. 36 Zsuzsanna Darula Gas-phase Holo-myoglobin Ions Preserve Solution-phase Heme Location .................................................................... 37 Atim Enyenihi High Throughput Analysis of Gonadotropin-releasing Hormone III Analog-daunorubicin Complex by Fully Automated Chip-based Nanoelectrospray Ionization and Multistage Cid/etd Mass Spectrometry........................................................................................................................................................................ 38 Corina Flangea Improved Peptide Identification by Electron Transfer Dissociation and Beam-type Collision Induced Dissociation .......................................................................................................................................................................... 39 Christian Frese Charge As You Like! Efficient Manipulation of Charge Distributions in (-)ESI of Proteins and RNA....................... 40 Barbara Ganisl Type IV Pili of Neisseria Meningitidis Five PTMs One Experiment: a Comparison of ECD and ETD for Comprehensive Fragmentation .................................................................................................................................... 41 Joseph Gault Analysis of Small Inhibitory RNA (siRNA) Using
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