Protein Interactions by Infrared Multiphoton Dissociation-MS. Crosslinker for Identification of. Photoactive Chemical
|
|
- Brianne King
- 5 years ago
- Views:
Transcription
1 Photoactive Chemical Crosslinker for Identification of Protein Interactions by Infrared Multiphoton Dissociation-MS Myles W. Gardner, Jennifer S. Brodbelt
2 Chemical Crosslinking of Proteins Protein structural analysis technique Covalently conjugate two specific targets, spatially constrained, with linker molecule Intramolecular crosslinking: tertiary structure Intermolecular crosslinking: quaternary structure Intermolecular Crosslinks Intramolecular Crosslink a 3 S 11.4 Å S 3 a
3 LC MS/MS Protein Crosslinking Protocol Crosslink protein 1. SEC, SDS-PAGE 2. Enzymatic Digest LC-MS/MS Time (min) Identification of Crosslinked Products and Determination of Crosslinked Residues
4 Current Methods for the Identification of Crosslinked Peptides Tri-functional crosslinkers with affinity tag a sulfo-sbed: Biotinylated H S H (CH 2 ) 4 H (CH 2 ) 4 CH H C H S S S 3 a Separate crosslinked peptides from uninformative, unmodified peptides prior to LC-MS/MS Isotope labeled Crosslinkers b BS 3 -d 4 / BS 3 : mass = 4 Da Detect peptide pairs in LC-MS a 3 S D D D D S 3 a a Alley, S.C.; Ishmael, F.T.; Jones, A.D.; Benkovic, S.J. J. Am. Chem. Soc. 2, 122, b Pearson, K.M.; Pannell, L.K.; Fales, H.M. Rapid Commun. Mass Spectrom. 22, 16, 149.
5 Crosslinking Goals Goal: Rapidly distinguish crosslinked peptides from unmodified peptides using quadrupole ion trap-ms IR-active chromophoric crosslinker phospho functional group Infrared Multiphoton Dissociation-MS Selective dissociation of crosslinked peptides Tandem MS/MS information to identify crosslink location
6 1 1 Phospho -groups and IRMPD IRMPD-MS of PMIDA and BIDA PMIDA = ms -H 2 P 3 H P H C 2 laser = 1.6 µm Photoactive Crosslinking Reagent BIDA a = ms Conventional Crosslinking Reagent H H H H Bond Stretch P-H P--C cm µm =P-H P-CH Silverstein, R.M. et al. Spectrometric Identification of rganic Compounds, 4 th ed. Wiley: ew York. 1981: pg a Back, J.W.; Hartog, A.F.; Dekker, H.L.; Muijsers, A..; de Koning, L.J.; de Jong, L.. J. Am. Soc. Mass Spectrom. 21, 12, 222.
7 PMIDA-Peptide Crosslinking H P H H PMIDA H + 2 H 3 C C H EDC 1-ethyl-3-(3- dimethylaminopropyl) carbodiimide hydrochloride CH 3 Cl CH 3 H 3 C H H P H unstable -Acylisourea Active intermediate H CH 3 dry DMS -(phosphonomethyl)- iminodiacetic acid H H H 3 C CH 3 H 3 C CH 3 H P H Protein/Peptide R H 2 H P H H dry DMS 2 2 H H R R Crosslinked Product 9% DMS, 1% 2 mm HEPES ph ~8 (v/v) + 2 H 3 C H PMIDA Crosslinker HS-ester intermediate C H H CH 3 CH 3 Isourea by-product HS -hydroxysuccinimide
8 Experimental: Reaction Procedure Activation Reaction 5. µmol PMIDA, 12.5 µmol EDC, 12.5 µmol HS 3 µl dry DMS 15 min, room temp. Peptide Crosslinking Protein Crosslinking 1:4 molar ratio peptide : PMIDA 1:5 molar ratio Protein:PMIDA 2 mm HEPES, ph 8 2 hours, room temp Desalting by C 18 solid-phase extraction Tryptic digest ESI-MS 18 hours 37 C IRMPD-MS LC-IRMPD-MS
9 ESI-IRMPD-MS Instrumentation ZnSe Window 1.6mm Reflective Mirrors Ring Electrode (5 mm hole) 5 W cw C 2 Laser, 1.6 µm (Synrad) Modified Finnigan LCQ Deca XP Samples: 1-2 µm in 95/4/1 MeH/H 2 /acetic acid (v/v) Flow rate: 3 µl/min, ESI = +4.5 kv IRMPD experiments: 5W for 1 15ms LC-IRMPD-MS C 18 column (2.1 5 mm, 3.5 µm); 98/2/.2 H 2 /AC/formic acid (v/v) to 6/4/.2 data-dependent IRMPD 5 W, 5 ms
10 MS Results: PMIDA + Peptide Crosslinking 1 [P+PMIDAH+2H] 2+ [P+PMIDA+H] 1+ Substance P + PMIDA/EDC/HS H 2 - R P K P Q Q F F G L M [P+PMIDAH+H] 1+ [P+2H] 2+ [P+H] 1+ PMIDA-HS Intra/Inter = +191 Da Dead-end = +29 Da H P H P+PMIDA P H H P+PMIDAH H 2 -R P K P Q Q F F G L M - H 2 H 6.8 Å H R H P K P H H P Q Q F F G L M H 2 H Intramolecular Crosslink Dead-end Modification
11 Reconstructed Full MS Reconstructed IRMPD-MS, 15ms nly PMIDA-modified peptides undergo IRMPD allowing for confident assignment and differentiation from non-crosslinked peptides Intensity (x 1 6, arb) Screening for Crosslinked Products in a Ten Peptide Mock Mixture 1x Laser off Laser on
12 .6 Relative Decrease in Ion Abundance Upon IR Irradiation Laser ff Laser n, 15 ms Relative Ion Abundance.1. Angiotensin I 3+ Angiotensin II Bradykinin CFIRCPRG-H eurotensin Angiotensin I Substance P Thymopentin Melittin 4+ Substance P -H eurotensin γ-endorphin Melittin Angiotensin II Bradykinin CFIRCPRG-H Angiotensin I Substance P Melittin Substance P Substance P -H eurotensin γ-endorphin PMIDA Relative abundance of PMIDA modified peptides decreases by >85% upon IRMPD whereas unmodified peptides abundance decreases by <5%.
13 1 Irradiation of PMIDA-Modified Peptides: Very Selective Dissociation [Substance P + PMIDA + H] 1+ a 8 +PMIDA b 9 +PMIDA ms H- R P K P Q Q F F G L M P y -H 2 P 8 -H 3 3 y [Substance P+BIDA+H] 1+ 1 [Substance P+H] ms 15ms o dissociation o dissociation
14 1 8 Selective Photodissociation of PMIDA vs. BIDA Modified Substance P Laser off -H 2 -H 6 [Substance P+H] H Laser on 15ms 2 -H -H H -H PMIDA PMIDAH BIDA BIDAH Relative abundance of PMIDA modified peptide decreases by >85% upon IRMPD whereas for BIDA modified peptide, abundance decreases by <1%. -H
15 IRMPD-MS for Elucidation of Crosslink Site [Substance P + PMIDA + 2H] ms H- R P K P Q Q F F G L M x5 b 9 2+ b 1 2+ x5 1 b 3 1+ y 8 1+ [PQ-28] 1+ y 1 1+ y 3 1+ a 6 2+ b 7 2+ b 8 2+ a 5 1+ a 8 -H 2 1+ b FGG b 6 1+ b y 4 PMIDA PMIDA fragment ions and losses of PMIDA IRMPD also allows one to determine sites of modifications, in addition to selectively dissociately only PMIDA modified peptides.
16 LC-IRMPD-MS of Peptide Mock Mixture Full MS Total Ion Chromatogram PMIDA modified peptide A B C D E F G H Time (min) A. [Bradykinin + 2H] 2+ IRMPD-MS, 5W, 5 ms 1 E. [γ-endorphin + 2H] B. [Angiotensin II + 2H] C. [eurotensin + 3H] F. [Substance P + PMIDAH H 2 + MeH+ 2H] G. [Substance P + PMIDA + 2H] D. [Angiotensin I + 3H] H. [Melittin + 4H]
17 Protein Crosslinking: Cytochrome c Deconvoluted MS a B A C Cytochrome c MW=1236 Da Mass ESI-MS PMIDA PMIDAH Protein Databank ore.do?structureid=1hrc a Zhang, Z; Marshall, A.G. J. Am. Soc. Mass Spectrom. 1998, 9,
18 Time (min) LC-IRMPD-MS of Crosslinked Cytochrome c Digest Full MS Total Ion PMIDA modified Chromatogram peptide A B C D E F A. Y74-K IRMPD-MS, 5W, 5 ms 1 D. [E61-K72] B. I9-K E. [I9-K25 + PMIDAH] C. M8-K F. [I9-K25 + Heme + PMIDAH]
19 IRMPD-Mass Spectrum of I9-K25+ PMIDAH [I9 K25 + Heme + PMIDAH + 4H] 4+ Heme I F V Q K C A Q C H T V E K G G K 5 ms b 12 -H 2 2+ y 1 1+ y 2 1+ a 5 -H y 3 or 1+ b 2 y 6 2+ y b 7 2+ y y y y 14 -H 3 3+ b a 1 2+ a 5 -H 3 1+ b a 8 1+ PMIDAH Heme internal fragment ions PMIDAH fragment losses a 16 -H 3 2+ y b LC-IRMPD-MS yields diagnostic tandem MS data to determine crosslinked residues for PMIDA modified peptides.
20 Conclusions Developed 2-step method to crosslink peptides with iminodiacetic acids using EDC/HS coupling PMIDA readily photodissociates when subjected to IR irradiation Rapidly screen for and distinguish PMIDA-modified peptides in complex mixtures using IRMPD or LC-IRMPD-MS IRMPD produces diagnostic fragment ions that allow one to confidently identify the crosslink location
21 Acknowledgements Dr. Jennifer Brodbelt Joe Chipuk Barry Davis Byoung-Joon Ko Carolyn Mazzitelli Sarah Pierce Mike Pikulski Suncerae Smith Jeff Wilson Dr. Matthew Crowe Dr. Courtney Sherman Dr. Eric Anslyn Aaron Wright Himali Hewage Dr. Jae Schwartz Thermo Electron
REDOX PROTEOMICS. Roman Zubarev.
REDOX PROTEOMICS Roman Zubarev Roman.Zubarev@ki.se Physiological Chemistry I, Department for Medical Biochemistry & Biophysics, Karolinska Institutet, Stockholm What is (RedOx) Proteomics? Proteomics -
More informationTime (min) Supplementary Figure 1: Gas decomposition products of irradiated DMC.
200000 C 2 CH 3 CH 3 DMC 180000 160000 140000 Intensity 120000 100000 80000 60000 40000 C 2 H 6 CH 3 CH 2 CH 3 CH 3 CCH 3 EMC DEC 20000 C 3 H 8 HCCH 3 5 10 15 20 25 Time (min) Supplementary Figure 1: Gas
More informationCharacterization of Disulfide Linkages in Proteins by 193 nm Ultraviolet Photodissociation (UVPD) Mass Spectrometry. Supporting Information
Characterization of Disulfide Linkages in Proteins by 193 nm Ultraviolet Photodissociation (UVPD) Mass Spectrometry M. Montana Quick, Christopher M. Crittenden, Jake A. Rosenberg, and Jennifer S. Brodbelt
More informationApplication of LC/Electrospray Ion Trap Mass Spectrometry for Identification and Quantification of Pesticides in Complex Matrices
Application ote #LCMS-2 esquire series Application of LC/Electrospray Ion Trap Mass Spectrometry for Identification and Quantification of Pesticides in Complex Matrices Introduction The simple monitoring
More informationfor the Identification of Phosphorylated Peptides
Application of a Data Dependent Neutral-Loss Experiment on the Finnigan LTQ for the Identification of Phosphorylated Peptides Gargi Choudhary Diane Cho Thermo Electron, San Jose, CA Abstracted from posters
More informationSupplementary Material (ESI) for Chemical Communications This journal is (c) The Royal Society of Chemistry 2008
Experimental Details Unless otherwise noted, all chemicals were purchased from Sigma-Aldrich Chemical Company and were used as received. 2-DOS and neamine were kindly provided by Dr. F. Huang. Paromamine
More informationCharged Surface Hybrid C18 for High Resolution LC and LC/MS Peptide Separations
Charged Surface Hybrid C18 for High Resolution LC and LC/MS Peptide Separations Higher Quality Peptide Separations Using Hybrid Particle-Based Reversed-Phase Columns and CSH Technology Matthew Lauber,
More informationMass Spectrometry. Mass spectrometer MALDI-TOF ESI/MS/MS. Basic components. Ionization source Mass analyzer Detector
Mass Spectrometry MALDI-TOF ESI/MS/MS Mass spectrometer Basic components Ionization source Mass analyzer Detector 1 Principles of Mass Spectrometry Proteins are separated by mass to charge ratio (limit
More informationProtein and peptide separations,
A Quarterly Technical Newsletter Spring Grace Vydac: Leading the Way in Separations for Proteomics Protein and peptide separations, always important to protein chemists and enzymologists, have recently
More informationApplying a Novel Glycan Tagging Reagent, RapiFluor-MS, and an Integrated UPLC-FLR/QTof MS System for Low Abundant N-Glycan Analysis
Applying a Novel Glycan Tagging Reagent, RapiFluor-MS, and an Integrated UPLC-FLR/QTof MS System for Low Abundant N-Glycan Analysis Ying Qing Yu Waters Corporation, Milford, MA, USA APPLICATION BENEFITS
More informationPost-translational Modifications to Human Bile Acid CoA:Amino Acid N- acyltransferase
Post-translational Modifications to uman Bile Acid oa:amino Acid - acyltransferase Erin Shonsey UAB Graduate Student September 12, 2006 onjugation of Bile Acids SoA + + 3 2 2 S 3 - hbat oa-s 2 2 S - 3
More informationLecture 3. Tandem MS & Protein Sequencing
Lecture 3 Tandem MS & Protein Sequencing Nancy Allbritton, M.D., Ph.D. Department of Physiology & Biophysics 824-9137 (office) nlallbri@uci.edu Office- Rm D349 Medical Science D Bldg. Tandem MS Steps:
More informationBiomolecular Mass Spectrometry
Lipids ot different than other organic small molecules Carbohydrates Polymers of monosaccharides linked via glycosidic bonds (acetals/ ketals) many different combinationsvery interesting no time ucleic
More informationComparison of mass spectrometers performances
Comparison of mass spectrometers performances Instrument Mass Mass Sensitivity resolution accuracy Quadrupole 1 x 10 3 0.1 Da* 0.5-1.0 pmol DE-MALDI 2 x 10 4 20 ppm 1-10 fmol peptide 1-5 pmol protein Ion
More informationCharacterization of an Unknown Compound Using the LTQ Orbitrap
Characterization of an Unknown Compound Using the LTQ rbitrap Donald Daley, Russell Scammell, Argenta Discovery Limited, 8/9 Spire Green Centre, Flex Meadow, Harlow, Essex, CM19 5TR, UK bjectives unknown
More informationSupporting information
Supporting information Figure legends Supplementary Table 1. Specific product ions obtained from fragmentation of lithium adducts in the positive ion mode comparing the different positional isomers of
More informationMass Spectrometry Infrastructure
Mass Spectrometry Infrastructure Todd Williams, Ph.D. Director KU Mass Spectrometry and Analytical Proteomics Laboratory Mass Spectrometry Lab B025 Malott Hall Mission The Mass Spectrometry and analytical
More informationMS/MS as an LC Detector for the Screening of Drugs and Their Metabolites in Race Horse Urine
Application Note: 346 MS/MS as an LC Detector for the Screening of Drugs and Their Metabolites in Race Horse Urine Gargi Choudhary and Diane Cho, Thermo Fisher Scientific, San Jose, CA Wayne Skinner and
More informationSUPPORTING INFORMATION. Lysine Carbonylation is a Previously Unrecognized Contributor. to Peroxidase Activation of Cytochrome c by Chloramine-T
Electronic Supplementary Material (ESI) for Chemical Science. This journal is The Royal Society of Chemistry 2019 SUPPORTING INFORMATION Lysine Carbonylation is a Previously Unrecognized Contributor to
More informationSupporting Information
Supporting Information Wiley-VC 2007 69451 Weinheim, Germany Electrospray Ionization Mass Spectrometric Study on the irect rganocatalytic α-alogenation of Aldehydes Cesar A. Marquez, Francesco Fabbretti
More informationMass Spectrometry. - Introduction - Ion sources & sample introduction - Mass analyzers - Basics of biomolecule MS - Applications
- Introduction - Ion sources & sample introduction - Mass analyzers - Basics of biomolecule MS - Applications Adapted from Mass Spectrometry in Biotechnology Gary Siuzdak,, Academic Press 1996 1 Introduction
More informationUPLC/MS Monitoring of Water-Soluble Vitamin Bs in Cell Culture Media in Minutes
UPLC/MS Monitoring of Water-Soluble Vitamin Bs in Cell Culture Media in Minutes Catalin E. Doneanu, Weibin Chen, and Jeffrey R. Mazzeo Waters Corporation, Milford, MA, U.S. A P P L I C AT ION B E N E F
More informationDevelopment of a near-infrared fluorescent probe for monitoring hydrazine in serum and living cells
Supporting Information for Development of a near-infrared fluorescent probe for monitoring hydrazine in serum and living cells Sasa Zhu, Weiying Lin,* Lin Yuan State Key Laboratory of Chemo/Biosensing
More informationUV Tracer TM Maleimide NHS ester
UV Tracer TM Maleimide HS ester Product o.: 1020 Product ame: UV-Tracer TM Maleimide-HS ester Chemical Structure: Chemical Composition: C 41 H 67 5 18 Molecular Weight: 1014.08 Appearance: Storage: Yellow
More informationFused-Core Particles:
Fused-Core Particles: Varying Shell Thickness and Pore Size Stephanie A. Schuster; Joseph J. Kirkland; Brian M. Wagner; Barry E. Boyes; William L. Johnson; Timothy J. Langlois; Joseph J. DeStefano Advanced
More informationAnalysis of Choline and its Metabolites on the Finnigan LTQ
Analysis of Choline and its Metabolites on the Finnigan LTQ Gargi Choudhary Diane Cho Thermo Electron, San Jose, CA Abstracted from a poster presented at Montreux 3 LC/MS Symposium, with co-authors: Brad
More informationProteomics/Peptidomics
Proteomics/Peptidomics System biology tools and preclinical models for translational research in endometriosis, ESHRE Campus workshop, 4-5 September 2009 E. Waelkens Proteomics: What? Proteins Proteomics
More informationO O H. Robert S. Plumb and Paul D. Rainville Waters Corporation, Milford, MA, U.S. INTRODUCTION EXPERIMENTAL. LC /MS conditions
Simplifying Qual/Quan Analysis in Discovery DMPK using UPLC and Xevo TQ MS Robert S. Plumb and Paul D. Rainville Waters Corporation, Milford, MA, U.S. INTRODUCTION The determination of the drug metabolism
More informationNew Developments in LC-IMS-MS Proteomic Measurements and Informatic Analyses
New Developments in LC-IMS-MS Proteomic Measurements and Informatic Analyses Erin Shammel Baker Kristin E. Burnum-Johnson, Xing Zhang, Cameron P. Casey, Yehia M. Ibrahim, Matthew E. Monroe, Tao Liu, Brendan
More informationOrganic Semiconducting Nanoparticles as Efficient Photoacoustic Agents for Lightening Early Thrombus and
Supporting Information rganic Semiconducting anoparticles as Efficient Photoacoustic Agents for Lightening Early Thrombus and Monitoring Thrombolysis in Living Mice Cao Cui,, Zhen Yang,, Xiang Hu, Jinjun
More informationChapter 12: Mass Spectrometry: molecular weight of the sample
Structure Determination: hapter 12: Mass Spectrometry- molecular weight of the sample; formula hapter 12: Infrared Spectroscopy- indicated which functional groups are present hapter 13: Nuclear Magnetic
More informationCAMAG TLC-MS INTERFACE
CAMAG TLC-MS INTERFACE 93.1 249.2 40 30 97.1 20 10 250.2 0 200 400 m/z WORLD LEADER IN PLANAR-CHROMATOGRAPHY Identification and elucidation of unknown substances by hyphenation of TLC / HPTLC and MS The
More informationMass spectra of peptides and proteins - and LC analysis of proteomes Stephen Barnes, PhD
Mass spectra of peptides and proteins - and LC analysis of proteomes Stephen Barnes, PhD 4-7117 sbarnes@uab.edu Overview A mass spectrum Electrospray MS Analysis of intact proteins Molecular weight calculations
More informationPHOTOCATALYTIC DECONTAMINATION OF CHLORANTRANILIPROLE RESIDUES IN WATER USING ZnO NANOPARTICLES. DR. A. RAMESH, Ph.D, D.Sc.,
PHOTOCATALYTIC DECONTAMINATION OF CHLORANTRANILIPROLE RESIDUES IN WATER USING ZnO NANOPARTICLES DR. A. RAMESH, Ph.D, D.Sc., raamesh_a@yahoo.co.in 1 OBJECTIVES Determination of persistence and photolysis
More informationSupporting Information
Supporting Information Wiley-VCH 2008 69451 Weinheim, Germany Chemoselective Peptide Cyclization via Induced Traceless Staudinger Ligation Rolf Kleineweischede, Christian P.R. Hackenberger* Institute for
More informationRapid, Simple Impurity Characterization with the Xevo TQ Mass Spectrometer
Robert Plumb, Michael D. Jones, and Marian Twohig Waters Corporation, Milford, MA, USA INTRODUCTION The detection and characterization of impurities and degradation products of an active pharmaceutical
More informationOne Gene, Many Proteins. Applications of Mass Spectrometry to Proteomics. Why Proteomics? Raghothama Chaerkady, Ph.D.
Applications of Mass Spectrometry to Proteomics Raghothama Chaerkady, Ph.D. McKusick-Nathans Institute of Genetic Medicine and the Department of Biological Chemistry Why Proteomics? One Gene, Many Proteins
More informationBiological Mass spectrometry in Protein Chemistry
Biological Mass spectrometry in Protein Chemistry Tuula Nyman Institute of Biotechnology tuula.nyman@helsinki.fi MASS SPECTROMETRY is an analytical technique that identifies the chemical composition of
More informationJose Castro-Perez, Henry Shion, Kate Yu, John Shockcor, Emma Marsden-Edwards, Jeff Goshawk Waters Corporation, Milford, MA, U.S. and Manchester, UK
HIGH-THRUGHPUT REACTIVE METABLITE SCREEIG FR DICLFEAC BY UPLC AD XEV TQ MS WITH SCAWAVE Jose Castro-Perez, Henry Shion, Kate Yu, John Shockcor, Emma Marsden-Edwards, Jeff Goshawk Waters Corporation, Milford,
More informationAnalyzing Trace-Level Impurities of a Pharmaceutical Intermediate Using an LCQ Fleet Ion Trap Mass Spectrometer and the Mass Frontier Software Package
Analyzing Trace-Level Impurities of a Pharmaceutical Intermediate Using an LCQ Fleet Ion Trap Mass Spectrometer and the Mass Frontier Software Package Chromatography and Mass Spectrometry Application Note
More informationMass Spectrometric Analysis of Eight Common Chemical Explosives Using Ion Trap Mass Spectrometer
Mass Spectrometric Analysis of Explosives Bull. Korean Chem. Soc. 2013, Vol. 34, No. 12 3659 http://dx.doi.org/10.5012/bkcs.2013.34.12.3659 Mass Spectrometric Analysis of Eight Common Chemical Explosives
More informationBabu Antharavally, Ryan Bomgarden, and John Rogers Thermo Fisher Scientific, Rockford, IL
A Versatile High-Recovery Method for Removing Detergents from Low-Concentration Protein or Peptide Samples for Mass Spectrometry Sample Preparation and Analysis Babu Antharavally, Ryan Bomgarden, and John
More informationAgilent Protein In-Gel Tryptic Digestion Kit
Agilent 5188-2749 Protein In-Gel Tryptic Digestion Kit Agilent Protein In-Gel Tryptic Digestion Kit Instructions Kit Contents The Protein In-Gel Tryptic Digestion Kit includes sufficient reagents for approximately
More informationBioanalytical Quantitation of Biotherapeutics Using Intact Protein vs. Proteolytic Peptides by LC-HR/AM on a Q Exactive MS
Bioanalytical Quantitation of Biotherapeutics Using Intact Protein vs. Proteolytic Peptides by LC-HR/AM on a Q Exactive MS Jenny Chen, Hongxia Wang, Zhiqi Hao, Patrick Bennett, and Greg Kilby Thermo Fisher
More informationEvaluation of Chemical Labeling Strategies for Monitoring HCV RNA using Vibrational Microscopy
Electronic Supplementary Information Evaluation of Chemical Labeling Strategies for Monitoring HCV RA using Vibrational Microscopy Matthew oestheden 1,2, Qingyan Hu 1, Angela M. Tonary 1, Li-Lin Tay 3,
More informationThe distribution of log 2 ratio (H/L) for quantified peptides. cleavage sites in each bin of log 2 ratio of quantified. peptides
Journal: Nature Methods Article Title: Corresponding Author: Protein digestion priority is independent of their abundances Mingliang Ye and Hanfa Zou Supplementary Figure 1 Supplementary Figure 2 The distribution
More informationUNIVERSITY OF GUELPH CHEM 4540 ENZYMOLOGY Winter 2005 Quiz #2: March 24, 2005, 11:30 12:50 Instructor: Prof R. Merrill ANSWERS
UNIVERSITY F GUELPH CHEM 4540 ENZYMLGY Winter 2005 Quiz #2: March 24, 2005, 11:30 12:50 Instructor: Prof R. Merrill ANSWERS Instructions: Time allowed = 80 minutes. Total marks = 30. This quiz represents
More informationDon t miss a thing on your peptide mapping journey How to get full coverage peptide maps using high resolution accurate mass spectrometry
Don t miss a thing on your peptide mapping journey How to get full coverage peptide maps using high resolution accurate mass spectrometry Kai Scheffler, PhD BioPharma Support Expert,LSMS Europe The world
More informationEssential Lipidomics Experiments using the LTQ Orbitrap Hybrid Mass Spectrometer
Application Note: 367 Essential Lipidomics Experiments using the LTQ rbitrap Hybrid Mass Spectrometer Thomas Moehring 1, Michaela Scigelova 2, Christer S. Ejsing 3, Dominik Schwudke 3, Andrej Shevchenko
More informationShotgun Proteomics MS/MS. Protein Mixture. proteolysis. Peptide Mixture. Time. Abundance. Abundance. m/z. Abundance. m/z 2. Abundance.
Abundance Abundance Abundance Abundance Abundance Shotgun Proteomics Protein Mixture 1 2 3 MS/MS proteolysis m/z 2 3 Time µlc m/z MS 1 m/z Peptide Mixture m/z Block Diagram of a Mass Spectrometer Sample
More informationIon fragmentation of small molecules in mass spectrometry
Ion fragmentation of small molecules in mass spectrometry Jeevan Prasain jprasain@uab.edu 6-2612 Nomenclature: the main names and acronyms used in mass spectrometry Molecular ion: Ion formed by addition
More informationAutomating Mass Spectrometry-Based Quantitative Glycomics using Tandem Mass Tag (TMT) Reagents with SimGlycan
PREMIER Biosoft Automating Mass Spectrometry-Based Quantitative Glycomics using Tandem Mass Tag (TMT) Reagents with SimGlycan Ne uaca2-3galb1-4glc NAcb1 6 Gal NAca -Thr 3 Ne uaca2-3galb1 Ningombam Sanjib
More informationMASS SPECTROMETRY BASED METABOLOMICS. Pavel Aronov. ABRF2010 Metabolomics Research Group March 21, 2010
MASS SPECTROMETRY BASED METABOLOMICS Pavel Aronov ABRF2010 Metabolomics Research Group March 21, 2010 Types of Experiments in Metabolomics targeted non targeted Number of analyzed metabolites is limited
More informationINTRODUCTION CH 3 CH CH 3 3. C 37 H 48 N 6 O 5 S 2, molecular weight Figure 1. The Xevo QTof MS System.
Fast and Sensitive in vitro Metabolism Study of Rate and Routes of Clearance for Ritonavir using UPLC CUPLED with the Xevo QTof MS System Jose Castro-Perez, Kate Yu, John Shockcor, Henry Shion, Emma Marsden-Edwards,
More information5 Identification of Binding Partners of the Annexin A2 / P11 Complex by Chemical Cross-Linking
5 Identification of Binding Partners of the Annexin A2 / P11 Complex by Chemical Cross-Linking In the quest of the omics sciences for holistic schemes, the identification of binding partners of proteins
More informationPhosphorylation of proteins Steve Barnes Feb 19th, 2002 in some cases, proteins are found in a stable, hyperphosphorylated state, e.g.
Phosphorylation of proteins Steve Barnes Feb 19th, 2002 in some cases, proteins are found in a stable, hyperphosphorylated state, e.g., casein more interestingly, in most other cases, it is a transient
More information2. Ionization Sources 3. Mass Analyzers 4. Tandem Mass Spectrometry
Dr. Sanjeeva Srivastava 1. Fundamental of Mass Spectrometry Role of MS and basic concepts 2. Ionization Sources 3. Mass Analyzers 4. Tandem Mass Spectrometry 2 1 MS basic concepts Mass spectrometry - technique
More informationTandem mass spectrometry analysis of prostaglandins and isoprostanes
Tandem mass spectrometry analysis of prostaglandins and isoprostanes Jeevan Prasain jprasain@uab.edu 6-2612 verview Introduction to PGs and their synthesis Mass spectrometry characterization of PGs and
More informationSEPARATION OF BRANCHED PFOS ISOMERS BY UPLC WITH MS/MS DETECTION
SEPARATION OF BRANCHED PFOS ISOMERS BY UPLC WITH MS/MS DETECTION Marian Twohig 1, Nicholas Ellor 1, Keith Worrall 2, Tim Jenkins 2, Gordon Kearney 2 1 Waters Corporation, 1 Cummings Center, Beverly, MA
More informationPrimary Structure Analysis. Automated Evaluation. LC-MS Data Sets
Primary Structure Analysis by Automated Evaluation of LC-MS Data Sets Mass Spec 29 Dr. Wozny, MassMap GmbH & Co. KG 1 LC-MS Peptide Mapping Origin of Signals Peptides with and without post-translational
More informationAn Alternative Approach: Top-Down Bioanalysis of Intact Large Molecules Can this be part of the future? Lecture 8, Page 27
An Alternative Approach: Top-Down Bioanalysis of Intact Large Molecules Can this be part of the future? Lecture 8, Page 27 Top-down HRAM Bioanalysis of Native Proteins/Molecules Relative Abundance 100
More informationUsing Software Tools to Improve the Detection of Impurities by LC/MS. Application Note. Christine Miller Agilent Technologies.
Using Software Tools to Improve the Detection of Impurities Application Note Christine Miller Introduction The analysis of raw materials and finished products for or impurities presents a challenge in
More informationUltra Performance Liquid Chromatography Coupled to Orthogonal Quadrupole TOF MS(MS) for Metabolite Identification
22 SEPARATION SCIENCE REDEFINED MAY 2005 Ultra Performance Liquid Chromatography Coupled to Orthogonal Quadrupole TOF MS(MS) for Metabolite Identification In the drug discovery process the detection and
More informationMALDI-TOF. Introduction. Schematic and Theory of MALDI
MALDI-TOF Proteins and peptides have been characterized by high pressure liquid chromatography (HPLC) or SDS PAGE by generating peptide maps. These peptide maps have been used as fingerprints of protein
More informationTissue and Fluid Proteomics Chao-Cheng (Sam) Wang
Tissue and Fluid Proteomics Chao-Cheng (Sam) Wang UAB-03/09/2004 What is proteomics? A snap shot of the protein pattern!! What can proteomics do? To provide information on functional networks and/or involvement
More informationIssue in Honor of Prof. Edmund Lukevics ARKIVOC 2006 (v) 86-91
Issue in onor of Prof. Edmund Lukevics ARKIVC 2006 (v) 86-91 Polycyclic heterocycles with acidic - groups VIII 1 The synthesis of some binuclear - acids with free rotary 1,2,4- triazole, 6-azauracil and
More informationUsing Multiple Mass Defect Filters and Higher Energy Collisional Dissociation on an LTQ Orbitrap XL for Fast, Sensitive and Accurate Metabolite ID
Application ote: 417 Using Multiple Mass Defect Filters and Higher Energy Collisional Dissociation on an LTQ rbitrap XL for Fast, Sensitive and Accurate Metabolite ID Yingying Huang 1, Shirley Liu 2, Shichang
More informationSupplementary Information
Supplementary Information Levulinic esters from the acid-catalysed reactions of sugar and alcohol as part of bio-refinery Xun Hu and Chun-Zhu Li* Fuels and Energy Technology Institute, Curtin University
More informationDetermination of N-Nitrososarcosine (NSAR) in tobacco
JTI-Ökolab Vienna, Austria Determination of N-Nitrososarcosine (NSAR) in tobacco Madeleine Werneth, Jutta Pani, Bernhard Mayer-Helm 2014 CORESTA CONGRESS - ST46 Québec City, Canada 12-16 October 2014 Background
More informationAdvances in Hybrid Mass Spectrometry
The world leader in serving science Advances in Hybrid Mass Spectrometry ESAC 2008 Claire Dauly Field Marketing Specialist, Proteomics New hybrids instruments LTQ Orbitrap XL with ETD MALDI LTQ Orbitrap
More informationMass Spectrometry Course Árpád Somogyi Chemistry and Biochemistry MassSpectrometry Facility) University of Debrecen, April 12-23, 2010
Mass Spectrometry Course Árpád Somogyi Chemistry and Biochemistry MassSpectrometry Facility) University of Debrecen, April 12-23, 2010 Introduction, Ionization Methods Mass Analyzers, Ion Activation Methods
More informationMethyltrioxorhenium-Catalyzed Highly Selective Dihydroxylation of 1,2-Allenylic Diphenyl Phosphine Oxides
Electronic Supplementary Material (ESI) for Chemical Communications. This journal is The Royal Society of Chemistry 2015 Methyltrioxorhenium-Catalyzed Highly Selective Dihydroxylation of 1,2-Allenylic
More information[ APPLICATION NOTE ] A Generic Kit-Based Approach for LC-MS/MS Quantification of Urinary Albumin for Clinical Research APPLICATION BENEFITS
A Generic Kit-Based Approach for LC-MS/MS Quantification of Urinary Albumin for Clinical Research Mary Lame, Caitlin Dunning, and Erin Chambers Waters Corporation, Milford, MA, USA APPLICATION BENEFITS
More informationReceived: 21 September 2009 / Revised: 2 November 2009 / Accepted: 3 November 2009 / Published online: 25 November 2009 # Springer-Verlag 2009
Anal Bioanal Chem (2010) 396:1273 1280 DOI 10.1007/s00216-009-3292-9 ORIGINAL PAPER Quantitative analysis of urinary phospholipids found in patients with breast cancer by nanoflow liquid chromatography
More informationRapid Lipid Profiling of Serum by Reverse Phase UPLC-Tandem Quadrupole MS
Rapid Lipid Profiling of Serum by Reverse Phase UPLC-Tandem Quadrupole MS Mark Ritchie and Evelyn Goh Waters Pacific Pte Ltd., Singapore A P P L I C AT ION B E N E F I T S Delivers a rapid 10-min MRM method
More informationTopic 6 Structure Determination Revision Notes
1) Introduction Topic 6 Structure Determination Revision Notes Mass spectrometry, infrared spectroscopy and NMR spectroscopy can be used to determine the structure of unknown compounds 2) Mass spectrometry
More informationChemical Biology, Option II Mechanism Based Proteomic Tagging Case History CH1
Proteome Wide Screening of Serine Protease Activity Proc Natl Acad Sci 1999, 97, 14694; Proteomics 2001, 1, 1067; Proc Natl Acad Sci 2002, 99, 10335; Biochemistry 2001, 40, 4005; J. Am. Chem. Soc., 2005,
More informationTandem mass spectrometry is becoming the
Fragmentation of Phosphopeptides in an Ion Trap Mass Spectrometer Jon P. DeGnore and Jun Qin Laboratory of Biophysical Chemistry, National Heart, Lung, and Blood Institute, National Institutes of Health,
More informationMass Spectrometry Introduction
Mass Spectrometry Introduction Chem 744 Spring 2013 What MS is and is not MS is NOT a spectroscopic method. Molecules are not absorbing EM radiation MS is the generation, separation and characterization
More informationOn the Nature of the Chemical Noise in MALDI Mass Spectra
On the Nature of the Chemical Noise in MALDI Mass Spectra Andrew N. Krutchinsky and Brian T. Chait* Rockefeller University, New York, New York, USA The so-called chemical noise background imposes a major
More informationProteomics of body liquids as a source for potential methods for medical diagnostics Prof. Dr. Evgeny Nikolaev
Proteomics of body liquids as a source for potential methods for medical diagnostics Prof. Dr. Evgeny Nikolaev Institute for Biochemical Physics, Rus. Acad. Sci., Moscow, Russia. Institute for Energy Problems
More informationA Definitive Lipidomics Workflow for Human Plasma Utilizing Off-line Enrichment and Class Specific Separation of Phospholipids
A Definitive Lipidomics Workflow for Human Plasma Utilizing Off-line Enrichment and Class Specific Separation of Phospholipids Jeremy Netto, 1 Stephen Wong, 1 Federico Torta, 2 Pradeep Narayanaswamy, 2
More informationTechnical Note # TN-31 Redefining MALDI-TOF/TOF Performance
Bruker Daltonics Technical Note # TN-31 Redefining MALDI-TOF/TOF Performance The new ultraflextreme exceeds all current expectations of MALDI-TOF/TOF technology: A proprietary khz smartbeam-ii TM MALDI
More informationFEBS 1138 January Paul R. Buckland and Bernard Rees Smith
Volume 166, number 1 FEBS 1138 January 1984 A structural comparison receptors by of guinea pig thyroid and fat TSH photoaffinity labelling Paul R. Buckland and Bernard Rees Smith Endocrine Immunology Unit,
More informationHow to Use TOF and Q-TOF Mass Spectrometers
How to Use TOF and Q-TOF Mass Spectrometers October 2011 What do TOF and Q-TOF offer? TOF Fast scanning of full spectrum High resolution full scan spectra Accurate mass measurements Q-TOF Fast scanning
More informationOrganic Chemistry Laboratory Fall Lecture 3 Gas Chromatography and Mass Spectrometry June
344 Organic Chemistry Laboratory Fall 2013 Lecture 3 Gas Chromatography and Mass Spectrometry June 19 2013 Chromatography Chromatography separation of a mixture into individual components Paper, Column,
More informationSulfate Radical-Mediated Degradation of Sulfadiazine by CuFeO 2 Rhombohedral Crystal-Catalyzed Peroxymonosulfate: Synergistic Effects and Mechanisms
Supporting Information for Sulfate Radical-Mediated Degradation of Sulfadiazine by CuFeO 2 Rhombohedral Crystal-Catalyzed Peroxymonosulfate: Synergistic Effects and Mechanisms Submitted by Yong Feng, Deli
More informationQuantitative Analysis of Vit D Metabolites in Human Plasma using Exactive System
Quantitative Analysis of Vit D Metabolites in Human Plasma using Exactive System Marta Kozak Clinical Research Applications Group Thermo Fisher Scientific San Jose CA Clinical Research use only, Not for
More informationAuthor. Introduction. Small Molecule Pharmaceuticals & Generics
Agilent Bond Elut Plexa PCX Cation Exchange SPE A Destination to a Better Sensitivity in LC/MS Bioanalysis Resulting from Minimized Ion-Suppression Application Note Small Molecule Pharmaceuticals & Generics
More informationMultiplex Protein Quantitation using itraq Reagents in a Gel-Based Workflow
Multiplex Protein Quantitation using itraq Reagents in a Gel-Based Workflow Purpose Described herein is a workflow that combines the isobaric tagging reagents, itraq Reagents, with the separation power
More information[ APPLICATION NOTE ] High Sensitivity Intact Monoclonal Antibody (mab) HRMS Quantification APPLICATION BENEFITS INTRODUCTION WATERS SOLUTIONS KEYWORDS
Yun Wang Alelyunas, Henry Shion, Mark Wrona Waters Corporation, Milford, MA, USA APPLICATION BENEFITS mab LC-MS method which enables users to achieve highly sensitive bioanalysis of intact trastuzumab
More informationFacile Cu(II) mediated conjugation of thioesters and thioacids to peptides and proteins under mild conditions
Electronic Supplementary Material (ESI) for Organic & Biomolecular Chemistry. This journal is The Royal Society of Chemistry 2018 Facile Cu(II) mediated conjugation of thioesters and thioacids to peptides
More informationPrevious Class. Today. Detection of enzymatic intermediates: Protein tyrosine phosphatase mechanism. Protein Kinase Catalytic Properties
Previous Class Detection of enzymatic intermediates: Protein tyrosine phosphatase mechanism Today Protein Kinase Catalytic Properties Protein Phosphorylation Phosphorylation: key protein modification
More informationProtein sequence mapping is commonly used to
Reproducible Microwave-Assisted Acid Hydrolysis of Proteins Using a Household Microwave Oven and Its Combination with LC-ESI MS/MS for Mapping Protein Sequences and Modifications Nan Wang and Liang Li
More informationRapid Screening and Quantitation of Postharvest Fungicides on Citrus Fruits Using AxION DSA/TOF and Flexar SQ MS
APPLICATION NOTE Mass Spectrometry Author: Avinash Dalmia PerkinElmer, Inc. Shelton, CT USA Rapid Screening and Quantitation of Postharvest Fungicides on Citrus Fruits Using AxION DSA/TOF and Flexar SQ
More informationFundamentals of Soft Ionization and MS Instrumentation
Fundamentals of Soft Ionization and MS Instrumentation Ana Varela Coelho varela@itqb.unl.pt Mass Spectrometry Lab Analytical Services Unit Index Mass spectrometers and its components Ionization methods:
More informationSelective phosphatidylcholine double bond. fragmentation and localization using. Paternó-Büchi reactions and ultraviolet.
Electronic Supplementary Material (ESI) for Analyst. This journal is The Royal Society of Chemistry 2017 Selective phosphatidylcholine double bond fragmentation and localization using Paternó-Büchi reactions
More informationSequence Identification And Spatial Distribution of Rat Brain Tryptic Peptides Using MALDI Mass Spectrometric Imaging
Sequence Identification And Spatial Distribution of Rat Brain Tryptic Peptides Using MALDI Mass Spectrometric Imaging AB SCIEX MALDI TOF/TOF* Systems Patrick Pribil AB SCIEX, Canada MALDI mass spectrometric
More informationApplication Note # ET-17 / MT-99 Characterization of the N-glycosylation Pattern of Antibodies by ESI - and MALDI mass spectrometry
Bruker Daltonics Application Note # ET-17 / MT-99 Characterization of the N-glycosylation Pattern of Antibodies by ESI - and MALDI mass spectrometry Abstract Analysis of the N-glycosylation pattern on
More informationMALDI Imaging Drug Imaging Detlev Suckau Head of R&D MALDI Bruker Daltonik GmbH. December 19,
MALDI Imaging Drug Imaging Detlev Suckau Head of R&D MALDI Bruker Daltonik GmbH December 19, 2014 1 The principle of MALDI imaging Spatially resolved mass spectra are recorded Each mass signal represents
More information