Esi tof ms ppt online

IC-IIFC meeting V.K.Handu and Manjiri Pande Technical Physics Division, Bhabha Atomic Research Center, Mumbai, India.

SPECTROMETERS for CLUSTER STUDIES & SURFACE ANALYSIS A Magnetron B Cluster source C Ion optics D Reflectron E ESI-TOF setup HIGH RESOLUTION DUAL TIME OF FLIGHT (TOF) CLUSTER BEAM SETUP Comprises of two TOF-MS at mutually perpendicular directions and is coupled to a molecular/ion beam source with : 1)Time scale of / analog and TTL i/p and o/p Feed Back DC Power supplies RF OUTPUT RF Input Water Dir. Coupler VCA 5 kW Amplifier Line-UP, option-1 BG Y 888 MRF 6V23 00 1 W, 30 dB100 W, 20 dB 8 × 800 W 19 dB 1/


1 Proprietary & Confidential The world leader in serving science Proprietary & Confidential Introduction to Liquid Phase Mass Spectrometry Andrew Baca.

Source Detector Full Scan (FS) Ion Source Detector Diagonal line represents the energies that are scanned to allow one ion at a specific mass to /run EMR for peptide Quan > 4 orders linear dynamic range Sensitivity: ESI/APCI 500 fg injected on column s/n 500:1 Performance Value/MS/MS for confirmation and ID Mass resolution: 140,000 Performance Value Target market: TOF competitor Multiple component screening and quantitation Ease of use for non-MS operators – no method development Target market: Q-TOF/


LC MSMS based 주요 기능 및 분석 요약 MSMS market survey MSMS market survey 용.

MS 3 의 활용 3.5 Precusor Ion Scan (SCAN/SIM), Neutral Loss (SCAN/SCAN) 3.6 Mass Defect Filtering 4. MSMS 의 주요 응용 영역 MSMS Terminology _ Separation/Purification Orthogonal In-source CID EI/CI ESI/APCI APPI MALDI Odd Ion Even Ion m/z Separation 1 SQ TOF/MSMS market survey 용 시료전처리 종류 및 분석장비 Sohxlet Precipitation Ultrafiltration LLE (On/Off–line, Micro) QuEChERS GPC/RAM SPE (On/Off–line, Micro) ImmunoAC MIP LC MSMS GC MSMS (Compound Specific Information) LC MS GC MS (RT, 유도체화 ) LC FLD LC UV/Vis GC ECD/NPD GC FID /


Metabolomics and Proteomics Core Facilities are composed of several major operations that involve a variety of expertise for metabolomic and proteomic.

Core Centers High throughput protein/metabolite profiling with LC-MS n or GCxGC- MS Various off-line HPLC separations and molecule isolation Identification and characterization of /MS/MS scan with rapid scanning speed and very high sensitivity. The XCT plus is coupled to the Chip Cube system for low sample volume analyses. AB QSTAR Pulsar (Q/TOF) coupled to nanoUPLC (Waters) combines ESI ionization with the hybrid quadrupole TOF analyzer for multi charge, high resolution analysis. AB 4800 MALDI TOF/TOF/


List of supplementary materials Supplemental Fig. 1. PCR primers for the cloning of GST-fused STIM1-UI in pGEX-4T-1 or STIM1-SBR in pMO91. Supplemental.

cell. The produced ions were analyzed using an orthogonal TOF analyzer and fitted with a reflector, a micro-channel plate detector, and a time-to-digital converter. Mode, ESI+; MS parameter and scan type, positive TOF MS; intensity threshold, 1 count; MCA No., GS1:/predicted as possible phosphorylation sites. Two phosphorable amino acids in helix I in Fig. 7a are indicated by red lines. A higher score means a higher possibility for phosphorylation. Numbers indicate the amino acid sequences of mouse STIM1-SBR/


Mass Spectrometry I Basic Data Processing. Mass spectrometry A mass spectrometer measures molecular masses. The mass unit is called dalton, which is 1/12.

0 2792.23 2868.0 2793.23 1234.0 … peak list Three Components of an MS A typical mass spectrometer contains – Ionizer – Mass analyzer – Detector Ion source charges the /ESI. – John B. Fenn & Koichi Tanaka 2002 Nobel Prize in Chemistry for Electrospray and MALDI Mass analyzer separates ions according to the mass to charge ratio (m/z) of the ions. – Iontrap, TOF/ Hull A convex hull is such that all the data points are above the lines and their extensions. How to calculate convex hull? Stack S contains all the /


The first part presents slides that had been on the handout for March 28; We will go through these fast! I will deposit the modified version on the web.

HEPES buffer, [M+K]+). Dunn et al. (2005) Evaluation of automated electrospray-TOF MS for metabolic fingerprinting of the plant metabolome. Metabolomics 1, 137. Some metabolites are/ electrophoresis; DIESI, direct-infusion ESI, which can be linked to Fourier transform ion cyclotron resonance mass spectrometry (FT- ICR-MS); NMR, nuclear magnetic resonance;/authentic β-caryophyllne Absence of β-Car. in some (mostly US) maize lines Reproductive success and β-caryophyllene Pactol – low amounts Graf – high amounts/


Pr. Jean-Louis Habib Jiwan UCL – Département de chimie Les détecteurs de masse : une révolution en chromatographie 2ème partie : chromatographie.

mai 2007 EI CI ESI APCI APPI MALDI GC LC DESITLC On line Off line Couplings : MALDI - LC Pr. Jean-Louis Habib JiwanUCL – Département de chimieIPL mai 2007 Source : documentation Applied Biosystem LC MALDI - MS On line couplings : acquisition /partement de chimieIPL mai 2007 Acquisition modes : Advanced methods on hybrid instruments FT ICR ORBITRAP TOF ION TRAP LC Chromatographic separation Ion source MS n capabilities HRMS Accurate mass capabilities Pr. Jean-Louis Habib JiwanUCL – Département de chimieIPL/


Application of Proteomics in Biological Research An introduction Jau-Song Yu Department of Cell and Molecular Biology Chang Gung University.

Urea 4% NP-40 or CHAPS 40mM Tris base Sample preparation Cell line Lysis solution Sonication vacuum Lysis solution Centrifugation Measurement of [protein] 2-DE/Analogy between mass analysis and the dispersion of light Components of a mass spectrometer MALDI-TOF MS (Matrix-assisted laser desorption/ionization-Time of flight ) ( 基質輔助雷射脫附游離 - 飛行時間質譜儀 ) Target/the method that John B. Fenn published in 1988, electrospray ionisation (ESI), charged droplets of protein solution are produced which shrink as the water/


Techniques of isolation and analysis in the natural product research u Sample preparation, isolation techniques u Identification methods, structure elucidation.

MS/MS and MS (n) Comparison quadrupole – ion trap (selectivity of detection) quadrupole GC-MS ion trap Spectrum of hexadec-9-en-1-ol ion trap quadrupole GC-MS Spectrum of hexadecan-1-ol ion trap quadrupole GC-MS GC-TOF Principles of TOF MS/MS) u large amounts of mobile phase has to be removed u particle beam interface u thermospray (TSP) u electrospray (ESI) u chemical ionisation in atmospheric pressure (APCI) LC-MS/accuracy provided good (base-line) separation of enantiomeric pairs u high sensitivity,/


01/04/2013KYMOS2 Biologics Biopharmaceutical Testing Bioanalysis and Immunogenicity Biologics Characterization Quality Control and GMP Batch Release Typology.

ESI-MS and MALDI-TOF  Peptide Mapping: digestion and peptide profile by HPLC-UV  Protein Sequencing: digestion and peptide sequencing by HPLC/MS-MS (Q- TOF, Q-TRAP)  N- and C- Terminal Sequence: MALDI-TOF ISD and EDMAN Degradation  Disulfide Bonds: HPLC-UV and HPLC-MS/ Proxima Imaging System for electrophoresis data processing Pharmacia PhastSystem High Speed Electrophoresis Symbiosis Pharma On line solid phase extraction system Agilent 2100 Bioanalyzer: microfluidics-based platform for cell, DNA, RNA and/


Producing Recombinant Glycoproteins in the Baculovirus-Insect Cell System Donald L. Jarvis, Jason R. Hollister, Jared J. Aumiller Department of Molecular.

Identify missing functions. l Identify human/mammalian genes. l Place under control of insect promoters. l Genetically transform insect cell lines. l Isolate transgenic insect cells that constitutively express these genes. Jarvis et al., 1998; Jarvis et al., 2003, Jarvis/al., 2002 MALDI-TOF Results Sf9 Sfß4GalT Sfß4GalT/ST6 SfSWT-1 Hollister et al., 2002 1810 2123 1664 16481283 14451607 SfSWT-1 ESI-MS/MS Results Hollister et al., 2002 1810 2123 1664 16481283 14451607 SfSWT-1 ESI-MS/MS Results Hollister et al/


Microliter-Volume NMR The Wellplate and Microvial as an Efficient Medium of Sample Transport Among Automated Methods of Analysis.

21,55-22,66, 23,61-25,02 NL: 5,92E5 F: - c ESI Full ms [ 140,01-1000,02] 200 250 300 350 400 450 500 550 600 650 700/extract MS spectra TOF MS spectra CONTROL WOUNDED C12H17O3 209.1256 spiked Total crude extract TOF MS spectra CONTROL RANKED LIST OF INDUCED IONS WOUNDED UPLC-TOF-ES-MS of A. thaliana CAP-NMR Multiple collection triggered by MS m/ in your solvent Run before every Nth sample or at startup Checks Signal / Noise and Line Shape to assure good results. Stops if out of spec. 67 67 Copyright © 2006 /


Mass Analyzers III Quadrupoles Chem 5181 – Fall 2007 Joel Kimmel.

, m/z = +100 and m/z = -100) 4.Peak shapes in an averaged TOF mass spectrum are affected by differences in the initial positions of ions within the region where the /stability apex requires increases in U and V m/z Scanning in a Quadrupole MS From De Hoffmann Scan line shows U/Vo = ½(0.233 / 0.706) Increase in mass /9, 569-579 A common application of rf-only multipoles involves collisional cooling. In an ESI source, the expansion into vacuum produces a ion beam with broad energy distribution Ion optics /


Improving the Reliability of Peptide Identification by Tandem Mass Spectrometry Nathan Edwards Department of Biochemistry and Molecular & Cellular Biology.

Sample + _ Mass Analyzer Detector MALDI Electro-Spray Ionization (ESI) Time-Of-Flight (TOF) Quadrapole Ion-Trap Electron Multiplier (EM) 4 High Bandwidth /MS MS m/z 10 Tandem Mass Spectrometry (MS/MS) Precursor selection m/z 11 Tandem Mass Spectrometry (MS/MS) Precursor selection + collision induced dissociation (CID) MS/MS m/z 12 The big picture... MS/MS/ for translation start site 18 Novel Splice Isoform Human Jurkat leukemia cell-line Lipid-raft extraction protocol, targeting T cells von Haller, et al./


Affinity Chromatography and Ion Exchange Chromatography Shannon E. Spence.

(SCOT). the inner wall of the capillary is lined with a thin layer of support material such as/. Chemical Ionization (CI) 3. Electron Impact (EI) 4. Electrospray Ionization (ESI) 5, Fast Atom Bombardment (FAB) 6. Field Desorption / Field Ionization /common known mass analyzers are quadrupoles, time- of-flight (TOF) analyzers, magnetic sectors, Fourier transform and quadrupole ion traps/usually coupled to a quadrupole analyzer. Analyzers Tandem (MS-MS) mass spectrometers are instruments that have more than one/


In 1989 along the coast of Emilia Romagna…

(murine fibrosarcoma) cell lines IC 50 10.9  g/ml on J774 (murine monocyte/macrophage) cell lines *IC 50 16.5  g/ml WEHI 164 (murine fibrosarcoma) cell lines IC 50 10.9  g/ml on J774 (murine monocyte/macrophage) cell lines P.Ciminiello, C. Dell/TOF, Ion Trap High Vacuum (10 -5 to 10 -6 torr) Syringe, CE, HPLC COMPONENTS OF TANDEM MASS SPECTROMETER Inlet system HPLC SOURCE ESI Ion trap DATA Advantage: High sensitivity in Full Scan Drawback Non linear calibration curves XIC m/z 1173.5 B XIC A B C D TIC MS/


EBI is an Outstation of the European Molecular Biology Laboratory. Introduction to Mass Spectrometry Dr. Juan Antonio VIZCAINO PRIDE Group coordinator.

EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan@ebi.ac.uk Sample Fractionation: Peptide separation Chromatography and MS are ‘on-line’ for ESI approaches. This is not possible for MALDI. ‘Retention Time’ is an essential piece of information to be taken into account/ Juan A. Vizcaíno juan@ebi.ac.uk Mass Spec Principles Ionization Source Sample + _ Mass Analyzer/s -Time of Flight (TOF) -Ion Trap (IT) -Quadrupole (Q) -FTICR -Orbitrap Detector EBI Roadshow Rotterdam, 12 June 2012 Juan A. Vizcaíno juan/


Journal Club 埼玉医科大学 総合医療センター 内分泌・糖尿病内科 Department of Endocrinology and Diabetes, Saitama Medical Center, Saitama Medical University 松田 昌文 Matsuda, Masafumi.

listed above. Peptide molecular weights were confirmed by ESI or MALDI-TOF mass spectrometry. Purified peptides were lyophilized, aliquotted, and stored at 4 °C. Cell lines. All cell lines used were confirmed to be mycoplasma free and tested/ frozen immediately. All samples were stored at −20 °C. Compound concentrations in plasma were determined by LC-MS/MS and respective pharmacokinetic parameters were determined by Non-Compartmental Analysis (NCA) with the industry standard software Phoenix WinNonlin /


Direct Experimental Observation of Functional Protein Isoforms by Tandem Mass Spectrometry Nathan Edwards Center for Bioinformatics and Computational Biology.

Sample + _ Mass Analyzer Detector MALDI Electro-Spray Ionization (ESI) Time-Of-Flight (TOF) Quadrapole Ion-Trap Electron Multiplier (EM) 6 High /translation frames “Dark” open-reading-frames 19 Splice Isoform Human Jurkat leukemia cell-line Lipid-raft extraction protocol, targeting T cells von Haller, et al. MCP /% (80%) acid + lys-C + trypsin: 85% (94%) Repeated LC-MS/MS Precursor Exclusion / Inclusion lists MALDI / ESI Protein separation and/or orthogonal fractionation Anal Chem, Vol. 76, pp. 4193-4201/


A basic overview of Proteomics Bioinformatics Unit Lab Meeting F.M. Mancuso 21/02/2012.

Encyclopedia. Wikimedia Foundation, Inc. Typical MS experiment (I) Protein Identification (and quantitation) TOF, Q, IT MALDI, ESI HPLC Cells, tissue Algorithms Typical MS experiment (II) Mass Spectrometry (MS) Stages Introduce sample to the instrument Generate/III) Boxes in blue and yellow represent two experimental conditions. Horizontal lines indicate when samples are combined. Dashed lines indicate points at which experimental variation and thus quantification errors can occur. Bantscheff et /


on Metabolomics Bioinformatics for Life Scientists

ionization (ESI) Laser desorption ionization (LDI) PRACTICAL ASPECTS Number of scans/second Implications in LC/MS and GC/MS: Quantification /MS WORKFLOW RAW LC-MS DATA TO mZXML: PROTEOWIZARD [Nature Biotechnology, 30 (918–920) (2012)] LC-MS WORK-FLOW XCMS PRE-PROCESSING http://metlin.scripps.edu/download/ Free & Open Source Based on R On-line version Suitable for: -GC-MS -LC-MS/MS/MS data of unknowns to model compounds.” 63 Step 4: Compare RT and MS/MS of standards Standard7α-hydroxy-cholesterol 367.33 Q-TOF/


Quantitative Proteomics: Applications and Strategies October 2013 Gustavo de Souza IMM, OUS.

/min No precolumn or split ESI 15 cm Fenn et al., Science 246:64-71, 1989. LC-MS MS-based quantitation Inlet Ion Source Mass Analyzer Detector MALDI ES Time-of-Flight Quadrupole Ion Trap Quadrupole-TOF LC Peak intensities can vary / of Dialyzed Serum non-dialzed serum contains free (unlabeled) amino acids! No alterations to cell phenotype C2C12 myoblast cell line Labeled cells behaved as expected under differentiation protocols Why SILAC is convenient? Convenient - no extra step introduced to experiment,/


Improving Genome Annotation using Proteomics Nathan Edwards Center for Bioinformatics and Computational Biology University of Maryland, College Park.

Sample + _ Mass Analyzer Detector MALDI Electro-Spray Ionization (ESI) Time-Of-Flight (TOF) Quadrapole Ion-Trap Electron Multiplier (EM) 4 High /translation frames “Dark” open-reading-frames 16 Splice Isoform Human Jurkat leukemia cell-line Lipid-raft extraction protocol, targeting T cells von Haller, et al. MCP /% (80%) acid + lys-C + trypsin: 85% (94%) Repeated LC-MS/MS Precursor Exclusion / Inclusion lists MALDI / ESI Protein separation and/or orthogonal fractionation Anal Chem, Vol. 76, pp. 4193-4201/


Mass Spectrometry for Protein Quantification and Identification of Posttranslational Modifications Joseph A. Loo Department of Biological Chemistry David.

needed. Use MS to determine PTM of isolated protein Enzymatic or chemical degradation of modified protein HPLC separation of peptides MALDI and/or ESI used to identify PTM MS/MS used to/ in a 2-D gel blue red Proteins from a Jurkat T-cell lymphoma line cell lysate were separated by 2-D gel electrophoresis and stained with Pro-Q / Step 11: Chemical Derivatisation of the Peptide Digest Step 12: MS Analysis Step 13: Calibration of the MALDI-ToF MS Step 14: Preparing for a Database Search Step 15: PMF Database/


Mass Spectrometry in the analysis of Persistent Organic Pollutants Anton Kočan, Jana Klánová.

Ion trap Time-of-flight Ion-cyclotron resonance Electron impact (EI) Chemical ionization (CI) Electrospray (ESI) Fast-atom bombardment (FAB) Laser ionization (LIMS) Resonance ionization (RIMS) ˇThermal ionization (TIMS)/ 15  s and m/z 50 in ~ 4.6  s By TOF-MS, up to 50 000 full spectra can be measured in a second Since full/ computer program to be converted to the line spectrum 142156170184198212226241 m/z A. Kočan, Slovak Medical University GC-MS Uses Identification and quantification of volatile and/


Mass spectrometry and proteomics

method MALDI Electrospray (Proteins must be charged and dry) Mass analyzer MALDI-TOF Quadrapole MALDI-QqTOF AA seq and MW QqTOF AA seq and protein modif. Definitions ESI- Electron Spray Ionization is a technique used in mass spectrometry to produce ions/green or red, respectively. The numbers denote fold expression change. The arrows denote activation and the blocked lines denote inhibition. Used tandem MS The global pattern of protein expression in rat myc-null cells was compared with that of myc-plus cells/


Chapter 3 Despair Inc.. POLYMERIZATION KINETICS REVIEW.

polystyrene. The molecular weight of each fraction is given. The dashed lines show the predictions of the Flory-Huggins theory for two of the /TOF - time-of-flight) ● Imbeds polymer in a matrix of low MW organic compound ● Irradiates the matrix with UV laser ● Matrix transfer the absorbed energy to polymer and vaporize the polymer ● Integrated peak areas  the number of ions ● M n, M w can be calculated Soft ionization method field desorption (FD-MS) laser desorption (LD-MS) electrospray ionization (ESI-MS/


Bioinformatics Summer School Young-Jin Lee Iowa State University.

with a Specific Protease Trypsin  Analyze peptides with a Mass spectrometer Usually MALDI-TOF, but it can be any type as long as the mass is accurate/ Digest Protein with tyrpsin  Determine the m/z of a peptide ion MALDI, ESI  Isolate the peptide ion from any other ions (inside the mass spectrometer) /line crosses 83. The log of this value — the E-value — is -8.2, as shown.  It is not trivial to reconstruct Proteins from identified peptides More than one protein may contain the same peptide sequence MS/MS/


1 K1.8BR beamline の 円筒型検出器群 (CDS) の Commissioning について Y.Sada (Kyoto-u) ストレンジネス研究 会.

Now we ready cooling test of 3 He beamline detecoters Ready! Beam Hodoscope(BHD,PA),Chamber(PDC,BLC) etc Slit (MS etc) /kick angle (ESI) study O.K! CDS/ 3 He Target Beam line 5 CDS Commissioning 6 Cylindrical Detector System Detectors to measure the decayed particles from 3 HeTarget,And get invariant mass 6 Expected/Methods in Physics Research A 455 (2000) 294-304 20 dPt/Pt 21 22 23 24 PID P pi+ Pi- Very preliminary (no fine tune and TOF) 25 1.0 0.8 0.6 0.4 0.2 0 Efficiency 1 2 3 4 5 6 7 8 9 10 11 12 13 14 /


Bioananalytical separation group Max Mousseron Institute, Montpellier, France Proteolysis inside a coated capillary : new development for the Quality Control.

m i.d. L T : 50 cm. Detection: 214 nm Repeatability of D-PES methodology for mAbs Humanized mAb 16 In-line vs Off-line methodology Off-line In-line Trastuzumab (Herceptin®) Separation buffer: citric acid /  -aminocaproic acid, I 25 mM, pH 5. T: 25°C. /separation methods. Separation runs of 120 min were performed at 20 kV CESI 8000 High Performance Separation ESI Module from Sciex Separations AB SCIEX triple TOF 5600 MS with Nanospray  III Ion Source Curtain gas: 5 PSI Ion spray voltage: 1600 V Interface /


Quantitative Proteomics Research: Breast and Prostate Cancer Biology Spiros D. Garbis, PhD Investigator, Faculty Member Center for Basic Research II Division.

-GEL DIGEST 2DGE OR 2D DIGE MALDI-TOF MS ANALYSIS DATA ANALYSIS PROTEIN ID & PROTEIN EXPRESSION ANALYSIS STABLE ISOTOPE LABELING MULTI-DIMENSIONAL CHROMATOGRAPHY MULTI-DIMENSIONAL CHROMATOGRAPHY ON-LINE LC-MS-MS ANALYSIS ON-LINE LC-MS-MS ANALYSIS Garbis SD, et al. J./Tandem Mass Spectrometry (MS/MS) Collision induced dissociation, CID MS fragmentation MS Precursor ionProduct ions MS-ΜS spectrum MS spectrum Reveals SEQUENCE and PTM information about the peptides Mixture of Peptide ions (LC-ESI) PEPTIDE PE PEP/


William Cho.

postoperative survival. Overexpression of let-7 miRNA in A549 lung adenocarcinoma cell line inhibited lung cancer cell growth in vitro. Takamizawa J, et al./2007;4(3):401-410. William Cho ESI: Electrospray ionization MALDI: Matrix-assisted laser desorption ionization SELDI: Surface-enhanced laser desorption ionization TOF: Time of flight 29 Surface-enhanced laser / Aquarius (Tecan) 31 Sample fractionation, chip binding and data acquisition in SELDI-TOF MS Cho WC, et al. Clin Cancer Res 2004;10:43-52. Cho WC/


99.86 127.96 172.00 189.98 206.00 224.02 281.12 325.06 307.10 307.16 281.11 206.04 224.02 190.02 171.95 145.95 146.01 128.00 99.97 m/z Relative abundance.

. Pyo-Mal Pyo-Suca Pyo-Glu Pyo-Suc Pyo-Kgl Supplemental Figure 3. HR-ESI-TOF-MS of viscosin. Bottom panel: measured HR-MS [M+Na] + m/z 1148.6798. Top panel: calculated HR-MS spectrum for the formula C 54 H 95 N 9 O 16 Na, the theoretical/ reactans (WLIP producer). The arrow points at the white line indicating the production of WLIP by P. reactans. B. White line agar assay between P. tolaasii and P. fluorescens SBW25 (viscosin producer). C.. White line agar assay between P. tolaasii and P. fluorescens BBc6R8 /


Proteomics and Glycoproteomics (Bio-)Informatics of Protein Isoforms Nathan Edwards Department of Biochemistry and Molecular & Cellular Biology Georgetown.

ESI) Time-Of-Flight (TOF) Quadrapole Ion-Trap Electron Multiplier (EM) Mass Spectrum 4 Mass is fundamental 5 Sample Preparation for MS/MS 6 Enzymatic Digest and Fractionation Single Stage MS 7 MS Tandem Mass Spectrometry (MS/MS) 8 Precursor selection Tandem Mass Spectrometry (MS/MS) 9 Precursor selection + collision induced dissociation (CID) MS/MS Why Tandem Mass Spectrometry? MS/MS/Splice Isoform 13 Splice Isoform Anomaly Human erythroleukemia K562 cell-line Depth of coverage study Resing et al. Anal. Chem/


Introduction to Arson Analysis

THE POLAR COMPOUNDS. MODERN HPLC SYSTEM API (ESI) Mass Spectra (Solvent Programming) CAN HAVE ONE/is about the size of a heavy fishing line. The Column The Heart Of The Gas /MS/MS) or ion trapping (MS/MS in time). In addition to ionization and fragmentation, an ion pre-isolation process and collision-induced dissociation precedes a secondary ion separation (filtering) and mass spectra formulation. New computer algorithms coupled with fast scanning detectors, such as time of flight mass spectrometry (TOF/


Improving the Sensitivity of Peptide Identification for Genome Annotation Nathan Edwards Department of Biochemistry and Molecular & Cellular Biology Georgetown.

_ Mass Analyzer Detector MALDI Electro-Spray Ionization (ESI) Time-Of-Flight (TOF) Quadrapole Ion-Trap Electron Multiplier (EM) Mass /MS/MS Enzymatic Digest and Fractionation Single Stage MS MS Tandem Mass Spectrometry (MS/MS) Precursor selection Tandem Mass Spectrometry (MS/MS) Precursor selection + collision induced dissociation (CID) MS/MS/be difficult: Correct spectral format Search parameter files and command-line Pre-processed sequence databases. Tracking spectrum identifiers Extracting peptide /


NUTRIGENOMICS: A SYSTEM BIOLOGY TOOL FOR ANIMAL HEALTH

GC). Mass spectrometry (MS)-rooted proteomic techniques for protein identification and quantification . MS technologies include electrospray ionization (ESI), soft ionization technique and/TOF-MS–based ProteinChip® System. Nature Methods 2, 393-395, 2005. MS Sample Preparation Workflow Mass spectrometry (or MS) is a powerful analytical tool for proteomics research and drug discovery. MS/ Proteomics study example In colorectal cancer cell lines, butyrate treatment induced apoptosis and inhibited proliferation/


Proteomic Characterization of Alternative Splicing and Coding Polymorphism Nathan Edwards Center for Bioinformatics and Computational Biology University.

Ionizer Sample + _ Mass Analyzer Detector MALDI Electro-Spray Ionization (ESI) Time-Of-Flight (TOF) Quadrapole Ion-Trap Electron Multiplier (EM) 10 High Bandwidth 11/Single Stage MS MS m/z 16 Tandem Mass Spectrometry (MS/MS) Precursor selection m/z 17 Tandem Mass Spectrometry (MS/MS) Precursor selection + collision induced dissociation (CID) MS/MS m/z / proteomics workflow for isoform detection Identify splice variants in cancer cell-lines (MCF-7) and clinical brain tumor samples dbPep for genomic annotation/


Proteomic Characterization of Alternative Splicing and Coding Polymorphism Nathan Edwards Center for Bioinformatics and Computational Biology University.

Ionizer Sample + _ Mass Analyzer Detector MALDI Electro-Spray Ionization (ESI) Time-Of-Flight (TOF) Quadrapole Ion-Trap Electron Multiplier (EM) 6 High Bandwidth 7/Single Stage MS MS m/z 12 Tandem Mass Spectrometry (MS/MS) Precursor selection m/z 13 Tandem Mass Spectrometry (MS/MS) Precursor selection + collision induced dissociation (CID) MS/MS m/z /evidence for translation start site 18 Novel Splice Isoform Human Jurkat leukemia cell-line Lipid-raft extraction protocol, targeting T cells von Haller, et al. /


OMICS Group International is an amalgamation of Open Access publications and worldwide international science conferences and events. Established in the.

and 45298 ions) and proprietary compound identification algorithm and spectral pattern matching algorithm Application of Software (Methods) MS: Compact (Q-TOF MS, Bruker Daltonik GmbH). ESI(+) with MS and autoMS/MS modes. Scan range: m/z 75-1000. Acquisition rate: 3 Hz. HPLC: U3000 RSLC(Thermo/.d SimMet Data Analysis Workflow Raw Data: Brukers native files viz.,.fid,.baf and.yep. profile data or line data types are supported. Other files: SCIEX’s.wiff, Thermo’s.raw,.zXML,.mzData. Model Experimental Design /


Improving the Sensitivity of Peptide Identification for Genome Annotation Nathan Edwards Department of Biochemistry and Molecular & Cellular Biology Georgetown.

ESI) Time-Of-Flight (TOF) Quadrapole Ion-Trap Electron Multiplier (EM) 4 Mass Spectrum 5 Mass is fundamental 6 Sample Preparation for MS/MS Enzymatic Digest and Fractionation 7 Single Stage MS MS 8 Tandem Mass Spectrometry (MS/MS) Precursor selection 9 Tandem Mass Spectrometry (MS/MS) Precursor selection + collision induced dissociation (CID) MS/MS 10 Unannotated Splice Isoform Human Jurkat leukemia cell-line/ format Search parameter files and command-line Pre-processed sequence databases. Tracking spectrum/


Metabolomics using SWATH™ Acquisition

and Quantitative data collection Stream lined a generic data collection practice of MS and NOW MS/MS simultaneously ….MS/MS data simultaneously collected is advantageous yet reproducibility and remains challenging Targeted MS/MS data collection is still the /(10mM NH4OaC) Positive and Negative TOF MS and MS/MSALL acquired sequentially in 3.3 minutes Data analysis, quantitation, results interpretation Sample infusion Make-up Flow Calibrant delivery (APCI) ESI Shotgun Lipidomics by Sequential Precursor Ion /


BioSci 145B lecture 8 page 1 © copyright Bruce Blumberg 2004. All rights reserved BioSci D145 Lecture #8 2/28/2006 Bruce Blumberg –2113E McGaugh Hall -

molecules “fly” and measures mass/charge (m/z) ratio MALDI-TOF –Matrix assisted laser desorption ionization – time of flight –Laser causes matrix/ fly to detector measured along with m/z ESI –electrospray ionization – molecules are sprayed, ionized and detected MS-MS –Tandem mass spec – has two mass analyzers/ Result called “floxed allele” –inject into blastocysts, select chimeras –establish lines –cross with Cre expressing line and analyze function BioSci 145B lecture 8 page 35 © copyright Bruce Blumberg/


Wi’07Bafna Proteomics via Mass Spectrometry (a bioinformatics perspective) Vineet Bafna www.cse.ucsd.edu/~vbafna.

Many proteins do not get separated. Wi’07Bafna LC-MS based separation As the peptides elute (separated by physiochemical properties), spectra is acquired. HPLC ESI TOF Spectrum (scan) p1 p2 pn p4 p3 Wi’07Bafna LC-MS Maps time m/z I Peptide 2 Peptide 1 x/ The tag based search extends efficiently to spliced-exon graphs. Wi’07Bafna Genomic Search Results ~18M spectra from a kidney cell line were searched against a human splice-exon graph. Validation of 39,000 exons and 11,000 introns Novel or extended exons in/


Proteomic Based Approaches In Developmental Biology.

Parts of a Mass Spectrometer Ion sourceMass analyzerDetector 1. MALDI 2. ESI 1. TOF 2. Ion trap 3. Quadrupole 4. Orbitrap 5. Magnetic sector /on the relative intensities of fragment peaks at fixed m/z values within an MS/MS spectrum. For example, iTRAQ and Tandem Mass TagsReporter:iTRAQTandem Mass Tags Replicate: Label/ one neutron C13 is chemically indistinguishable SILAC Everley et al., MCP 2004 Prostate cancer cell line PC3 PC3M (low metastatic potential) PC3M-LN4 (high metastatic potential) (98%) Ratio =/


CSE182 CSE182-L13 Mass Spectrometry Quantitation and other applications.

we have a ‘location’ for proteins/peptides CSE182 LC-MS based separation As the peptides elute (separated by physiochemical properties), spectra is acquired. HPLC ESI TOF Spectrum (scan) p1 p2 pn p4 p3 CSE182 LC-MS Maps time m/z I Peptide 2 Peptide 1 x / problems Tag is bulky, and can break off. Cys is low abundance MS 2 analysis to identify the peptide is harder. CSE182 SILAC A novel stable isotope labeling strategy Mammalian cell-lines do not ‘manufacture’ all amino-acids. Where do they come from? Labeled/


Fa 06CSE182 CSE182-L13 Mass Spectrometry Quantitation and other applications.

a ‘location’ for proteins/peptides Fa 06CSE182 LC-MS based separation As the peptides elute (separated by physiochemical properties), spectra is acquired. HPLC ESI TOF Spectrum (scan) p1 p2 pn p4 p3 Fa 06CSE182 LC-MS Maps time m/z I Peptide 2 Peptide 1 x/problems Tag is bulky, and can break off. Cys is low abundance MS 2 analysis to identify the peptide is harder. Fa 06CSE182 SILAC A novel stable isotope labeling strategy Mammalian cell-lines do not ‘manufacture’ all amino-acids. Where do they come from? /


CSE182 CSE182-L13 Mass Spectrometry Quantitation and other applications.

we have a ‘location’ for proteins/peptides CSE182 LC-MS based separation As the peptides elute (separated by physiochemical properties), spectra is acquired. HPLC ESI TOF Spectrum (scan) p1 p2 pn p4 p3 CSE182 LC-MS Maps time m/z I Peptide 2 Peptide 1 x / problems Tag is bulky, and can break off. Cys is low abundance MS 2 analysis to identify the peptide is harder. CSE182 SILAC A novel stable isotope labeling strategy Mammalian cell-lines do not ‘manufacture’ all amino-acids. Where do they come from? Labeled/


Jeffrey N. Peterson, CEO UBS Global Life Sciences Conference 9/22/2003 … EOTrol™ Dynamic Coatings Open New Horizons for Electrophoretic Separations 9/22/03.

Horizons for Electrophoretic Separations 9/22/03 - Press Release: Target Discovery Introduces First Product Line … … EOTrol™ Dynamic Coatings Open New Horizons for Electrophoretic Separations Target Discovery, Inc. /Labeled Protein Sample LIF Detector pI 2 pI 3 MW ESI-TOF Mass Spec Sequence Tag Algorithm MSGGFTA Terminal Sequence “N”/ & Software Deduce kinetics Metabolic Flux Confirmation with SIRMS  Stable Isotope Ratio MS of metabolites (MetaSIRMS™) Direct metabolic flux measure in vivo Track ratios &/


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