Electron Transfer Dissociation (ETD) Innovation with Integrity. Look Beneath the Surface. Ion Trap MS

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1 Electron Transfer Dissociation (ETD) Look Beneath the Surface Innovation with Integrity Ion Trap MS

2 Bruker Daltonics Leader in ETD Technology amazon Featuring ETD Since its commercial introduction in 2005, Bruker has been the leader in highly efficient and sensitive electron transfer dissociation (ETD) and proton transfer reaction (PTR) technology. We are constantly developing cutting-edge solutions for in-depth characterization of proteins and top-down sequencing analysis using our ETD technology. Using smart combinations of CID and ETD our customers obtain the greatest possible depth of information. Both complementary and confirmatory identification of post-translational modifications (PTM) provide you with the complete picture in challenging protein analyses.

3 ETD Applications From PTM to Top-Down Analysis As a complementary fragmentation technique to CID, ETD is of major importance for: Localization of PTMs, such as phosphorylation, sulfonation, and nitrosylation Analysis of O- and N-glycopeptides Characterization of disulfide linkages Identification of non-tryptic peptides, such as those with multiple basic residues Determination of protein termini by top-down sequencing Nebulizer High-transmission dual ion funnel transfer line Ion guide In vacuum RF detection Ion trap High energy conversion detector Fast acquisition circuitry Off-axis geometry Vacuum Stage 1 Reagent anion source Fast-scanning analyzer Stage 2 Stage 3 Stage 4 Atmospheric- Pressure Ion Source

4 ETD and PTR on the amazon Technology Leadership Key technical facts ETD cleaves N-Cα bonds producing c- and z-ions Labile bonds of PTMs remain intact The most efficient reagent Fluoranthene is used for both ETD and PTR Highest sensitivity for low-abundance peptides on an LC timescale: Identification of 18 peptides with a Mascot score > 20 from 500 amol BSA on column The ETD reaction CID and ETD fragmentation The 3D advantage The 3D advantage of the spherical ion trap is the decisive factor for the highest efficiency ETD and PTR reactions: Robust and fast trapping of cations and anions for direct ETD reaction Better cross section for efficient ionion-reactions in 3D ion traps due to compression into the same small globular volume Roepstorff nomenclature scheme The 3D advantage ESI source Dual Ion funnel Reagent anion source 3D Ion Trap

5 PTM Analysis A Must for Protein Characterization Complete PTM characterization The regulatory function of many proteins is controlled by reversible PTMs such as sulfonation and phosphorylation. PTM analysis includes identification and unambiguous site localization. ETD is the method of choice for site-profiling of biologically important PTMs. In contrast to CID, ETD preserves the modification on the peptide backbone and therefore enables a definite assignment of the modification site. CID spectra generate significant neutral loss of sulfonation and phosphorylation (-SO 3 or -H 3 PO 4 ) and only a few lowabundance peptide fragments. Because it is a very labile PTM, sulfonation is especially difficult to analyze using CID. However, ETD supports peptide sequencing and site-localization of all PTMs and is therefore an invaluable tool for extensive protein characterization. Identification and localization of sulfonation Neutral loss of SO 3 detected in CID. Peptide sequence identification by ETD: ALAPE(sulfo)YAK. Identification and localization of phosphorylation Neutral loss of H 3 PO 4 detected in CID. Peptide sequence identification and PTM localization by ETD: THTTALAGR(phospho)SP(phospho)SPASGR.

6 Complete Glycopeptide Analysis by Fragment Triggered ETD Glycopeptide analysis is of particular interest in glycomics, because detailed information about glycan, peptide and glycosylation site is needed to understand relationships between structure, location and function. Localization of O-glycosylation sites Tools for in-depth characterization of N- and O-glycopeptides: CaptiveSpray nanobooster Dramatic enhancement of glycopeptide ionization and shift to higher charge states for highest ETD spectra quality CID Identification of glycan composition and structure with GlycoQuest ETD Sequencing of glycopeptides and localization of glycosylation sites Fragment triggered ETD enables targeted glycopeptide profiling. ETD is only triggered if diagnostic oxonium ions have been detected in the preceding CID spectrum. This allows for simultaneous protein identification and effective glycopeptide profiling. Structure elucidation of an EPO O-glycopeptide (precursor [M+3H] 3+ = m/z). Top: CID spectrum; Bottom: ETD spectrum with assignment of glycosylated serine S *. Localization of N-glycosylation sites Serotransferrin N-glycopeptide profiling using Fragment triggered ETD (precursor [M+3H] 3+ = m/z). The glycosylated asparagine is marked with an asterisk.

7 ETD-Based Mapping of Disulfide Bonds Disulfide linkage of cysteine residues is an important PTM with regards to protein folding, structure, and biological function. Preferred disulfide bond cleavage by ETD Because it favors the cleavage of S-S bonds, ETD is key to disulfide linkage analysis. After cleavage, the sequences of the resulting peptides can be determined by CID MS 3. The figure on the right shows MS and ETD MS 2 spectra of a pair of interchain disulfide-bound peptides from a monoclonal IgG2. Precursor ions with charge states up to 4+ are generated with the CaptiveSpray nanobooster source. MS and ETD MS 2 spectra of linked peptides The major fragments m/z and result from the cleavage of the disulfide bond and are used as precursor ions for the following CID fragmentation. CID data allow sequencing of the peptides as shown for SFNRGEC from the light chain. The amazon speed ETD supports a variety of different workflows, ranging from a completely untargeted, data dependent MS 3 to a fully targeted smartmrm approach with predefined precursors for ETD and CID. LC: light chain, HC: heavy chain Peptide sequencing by CID Peptide sequence SFNRGEC from the IgG2 light chain identified by CID MS 3.

8 Top-Down Protein Characterization by ETD-Analysis of Hemoglobin Sequence variant analysis of full-length hemoglobin ETD fragmentation of full-length HbA -chain Until now, sequence variant analysis of full-length hemoglobin has been a major challenge. ETD fragmentation after precise isolation of the multiply charged Hb chains (for example, -chain 19+ charged) generates specific fragments that enable an unambiguous identification of the Hb specific sequence variant. Typical extracted ion chromatograms Hb A Control Hb C Homozygote Hb S Homozygote Typical Extracted Ion Chromatograms (EIC) of a control (HbA) and a homozygote Hemoglobin C and S sample. Several sequencespecific ETD fragments are used to generate the EIC traces for the different Hb chain variants.

9 Technical Specifications Technology-driven solutions Patented SmartICC for optimal ion storage SmartFrag Enhanced for reproducible high-quality MS/MS spectra generation and confident library searches Panorama fragmentation (PAN) enabling CID fragmentation without 1/3 cut-off MS/MS modes Highly efficient and sensitive ETD/PTR capabilities for PTM detection and top-down sequencing Data-dependent automs n Scheduled precursor list (SPL) supporting ETD and CID MS n in positive and negative mode SmartMRM for highly sensitive SPL - based targeted experiments Neutral-loss and fragment-triggered experiments for the analysis of posttranslational modifications (by ETD) Manual MS n up to MS 11 in all scan modes for structural elucidation Source options CaptiveSpray nanobooster: robust and reliable plug-and-play nano/cap ESI source for flow rates from nl/min ESI, APCI, APPI, and DIP source for direct analysis of solids and liquids Advion Triversa NanoMate Smart CE-MS coupling with grounded spray needle Software solutions ProteinScape including GlycoQuest glycan database search engine RapiDeNovo for de-novo sequencing of proteins ProfileAnalysis for statistical comparison of metabolite and proteomic profiles Compass OpenAccess client/serverbased system for walk-up users Compass Security Pack for regulated environments Scan speed and resolution Scan Mode Resolution u/sec m/z XtremeScan 2+ ions 52, UltraScan 3+ ions 32, Enhanced Resolution 4+ ions Maximum Resolution 8+ ions Extended Mass Range 27,

10 Bruker Daltonics is continually improving its products and reserves the right to change specifications without notice. BDAL , Further Reading Bruker brochures CaptiveSpray nanobooster The revolution in Proteomics Ionization Glyco Analysis Solutions Expanding the frontier in Glycobiology amazon speed Ion Trap Performance Beyond Imagination Bruker Application Notes App-Note LCMS-57 In-depth Characterization of Neutral and Acidic Glycopeptides by ZIC-HILIC Enrichment and Mass Spectrometry Jessica Wohlgemuth, Sven Andrecht, Merck KGaA, Darmstadt, Germany; Andrea Schneider, Anja Resemann, Arndt Asperger, Bruker Daltonik GmbH, Bremen, Germany (2010) App-Note LCMS-66 Straightforward N-glycopeptide analysis combining fast ion trap data acquisition with new ProteinScape functionalities Kristina Neue, Andrea Kiehne, Markus Meyer, Marcus Macht, Ulrike Schweiger-Hufnagel, Anja Resemann; Bruker Daltonik GmbH, Bremen, Germany (2012) App-Note LCMS-71 Identification of Proteins from a HeLa Cell Culture Sample Using the amazon speed ETD system Zoltan Czentnar, Andrea Kiehne, Kristina Neue, Markus Meyer; Bruker Daltonik GmbH, Bremen, Germany (2012) App-Note LCMS-75 Identification and Characterization of PTMs from a Complex Peptide Mixture Using the amazon speed ETD Anjali Alving, Matthew Willetts (2012) App-Note LCMS-76 Identification of a Second N-glycosylation Site in a Human PSA Sample by Combined CID/ETD Fragmentation Kristina Marx, Anja Resemann, Ulrike Schweiger-Hufnagel, Waltraud Evers, Andrea Kiehne, Markus Meyer; Bruker Daltonik GmbH, Bremen, Germany (2012) App-Note LCMS-93 amazon speed ETD: Exploring glycopeptides in protein mixtures using Fragment Triggered ETD and CaptiveSpray nanobooster Kristina Marx, Andrea Kiehne, Markus Meyer; Bruker Daltonik GmbH, Bremen, Germany (2014) For research use only. Not for use in diagnostic procedures. Bruker Daltonik GmbH Bremen Germany Phone +49 (0) Fax +49 (0) Bruker Daltonics Inc. Billerica, MA USA Phone +1 (978) Fax +1 (978) ms.sales.bdal@bruker.com -

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