Maldi ms ppt online

Liquid chromatography- mass spectrometry Harini Chandra a This is a common analytical tool that combines physical separation by liquid chomatography with.

Relative abundance m/z Part 3, Step 7: 1 5 3 2 4 Reflector TOF 2TOF 1 Collision cell Tandem MS/MS - MALDI-TOF-TOF-MS Part 3, Step 8: ActionAudio NarrationDescription of the action As shown in animation. First show the black boxes with the/animation. First show all the components of the instrument – the syringe, four rods, cube, blue rectangle, gray square with the dotted lines & the detector. Next show appearance of the coloured circles. Only the red one must move through the rods and after entering the/


日期時間授 課 內 容授課教師 7/2 ( 一 ) 10:10-12:00 Introduction to the course and Introduction to Nomics 張玉生 7/3( 二 ) 10:10-12:00Proteomics and human diseases 余兆松 7/3(

1188, 1438) (755, 974, 1244, 1374) (854, 935, 1021, 1067, 1184, 1386, 1438) (M/Z) How to identify proteins by MALDI-TOF MS? Linking between genomics/bioinformatics/proteomics 170 116.3 66.3 55.4 29 21.5 pH 310 4 3 12 (1) (2) (3) (4) Bruker’/ Max-Planck Unified (MAPU) proteome database. MAPU contains several body fluid proteomes; including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also been analyzed in depth. /


Functional Organization of the Yeast Proteosome by Systematic Analysis of Protein Complexes Nature.Vol 415. 10 January 2002. Anne-Claude Gavin, Markus.

successful identification.  There are several types of mass spectrometry- this experiment focused on MALDI/MALDI-TOF and MS/MS. Tandem Mass. Spec. (MS/MS)  MS/MS consists of: an ion source, the first mass analyzer, the gas-phase collision cell/-C110) by shared components. It illustrates the connection between the protein and complex levels of organization. Red lines indicate physical interactions as listed in YPD22. More Findings  Orthologous proteins preferentially interact with complexes enriched with/


Proteomics and mass spectrometry Manimalha Balasubramani.

MALDI TOF Voyager DE PRO ESI TOF Ultimate 3000 with micrOTOF MALDI TOF - principle KE = zeV = 1mv 2 2 MS of serum albumin MALDI TOF ESI TOF Tandem mass spectrometer MALDI TOF/TOF MS and MS/MS Ion Trap MS, MS 2, MS 3, ….MS n Quadrupole-q-TOF ESI QqTOF …installation phase…. FT MS …bottom line/ Quantitative proteomics Protein-protein interactions Sample preparation Quantitative Proteomics From 2D gels ….to MALDI or ESI MS Control Test Cy3 Cy5 Pool Image analysis with Delta2D, Decodon Quantitate Export spot /


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

IMAC beads placed directly on MALDI target Matrix solution spotted onto target MALDI-MS of peptides bound to IMAC bead MALDI-MS/MS (*) to identify phosphorylation site(s) MALDI-MS spectrum obtained from peptide bound to IMAC beads applied directly to MALDI target MALDI-MS/MS (Q-TOF) to locate/ of total protein and phosphoproteins 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 Diamond phosphoprotein gel stain (blue/


Analytical Mass Spectrometry1 Peter J Baugh Quay Pharma Training Progamme Day 4, September 28, 2004.

combinations of U, V and m with the assumption that r o and  are constant. The mass scan lines consist of ion values having a constant a/q ratio. Transmission of an ion occurs when U and V/recorded. Analytical Mass Spectrometry27 Diagram – 10 FAB mechanism Analytical Mass Spectrometry28 Diagram –11 Plasma Desorption MS Analytical Mass Spectrometry29 Diagram – 12 MALDI MS Analytical Mass Spectrometry30 5.Ionisation methods and interfaces for chromatography: Ionisation devices have been specially designed for/


Ionic liquids in analytical chemistry and their applications in mass spectrometry 13 September 2006 Farzad Fani Pakdel.

) Not commercially available yet The relation between signal and IL structure is not well understood Quantitative analysis for mixtures was not shown Out line Ionic liquids in analytical chemistry:  Mass spectrometry: MALDI (Matrix assisted laser desorption ionization) Matrix properties in MALDI-MS Ionic liquids as matrices Quantitative and reproducible Electrospray  Chromatography  Extraction  Electrochemistry  Electrophoresis  Spectroscopy Electrospray ionization in hexane 1 st ESI in non/


Lecture 7: Mass Spectrometry, Instrumental

main difference was that Aston’s instrument focused ions with different speeds into a single line Francis Aston (1877-1945) Mass Spectrometry: The Beginning At first, it looked like MS would be good mostly for analyzing isotopes. Prior to WWII, the stable isotopes of / are probably most applicable to biological analytes, but there are plenty of other ways that ions can form! Ions from MALDI So the predominant mechanism for analyte ion formation is just a proton transfer, which would be quite gentle. We just/


2D-Gel Analysis Jennifer Wagner Image retrieved from

sample 2)Separate proteins by 2DGE 3)Visualize proteins and excise spots of interest 4)Digest proteins with trypsin 5)Use MALDI-MS to measure molecular mass 6)Use LC-MS/MS or MALDI-MS/MS to obtain sequence information Hu, et al., 2005 2D-gel analysis “Typical” steps: 1)Isolate sample 2)Separate proteins/paper mentioned proteomic analysis and fingerprinting being used as a diagnostic tool for certain diseases. Along those lines, would it be possible to use these types of analyses for personalized medicine?


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

for Isoelectric focusing (IEF): Lysis solution: 8M 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 sample IPG strip rehydration and sample loading 2/2D gel electrophoresis Immage system Identification of 2-DE-separated proteins in a high-throughput way using biomass spectrometry MALDI TOF/TOF MSLC/MS n What is a mass spectrometer and what does it do? Gary Siuzdak (1996) Mass Spectrometry for /


Methodology for Stable Isotope Labeling by Amino acids in Cell culture ( SILAC)  Related Los: Isobaric tag properties, Trypsin properties > Prior Viewing.

(if any) ‏ Description of the action/ interactivity For data analysis and interpretation please go through IDD:31- MALDI TOF data analysis. Search the processed MALDI- MS data against the relevant protein database by taking all the required modifications into consideration. After collection of spectrum/ is (with which isotopic atom??) Answers: a) 2 Da b) 6 Da c) 8 Da d) 10 Da 2. Which cell lines can be used for SILAC analysis Answers: a) HeLa, b) C127, c) HEK293, d) none, e) all Questionnaire: APPENDIX 1/


Human blood, urine, saliva and other samples Identification of highly interacting genes Label-free nanobiotechnologies (APA,QMC_D and Mass Spectrometry)

T cells. Subnetwork connecting the four leader genes which are “ neutral ” according to their expression pattern are shown with a dotted line. Figure 1. TP53 profile expression, which is differentially expressed between tolerant patients and those who have rejected renal graft. It is/ 10 7 6.0  10 7 8.0  10 7 1.0  10 8 10x10 p53 10x10 master mix Lc-ESI MS/MS MALDI-TOF Voyager Figure 2 Fluorescence analysis of SNAP-NAPPA a) Proteins were synthesized by two different IVTT systems, 1-Step Human Coupled IVT /


1 October 14, 2010 GBMSDG Talk Mass Spectrometry as the Premier Analytical Tool in Drug Discovery and Drug Development Walter Korfmacher Exploratory Drug.

(PK) information on a compound 34ASMS 2010 ADME-PK Studies Brain-- D Drug Levels— LC-MS/MS MS Image— MALDI-MS/MS Liver— D Drug Levels— LC-MS/MS Plasma— A Drug Levels— LC-MS/MS PK Parameters Dose NCE (Drug) PO/IV Ref: “Using Mass Spectrometry for Drug Metabolism Studies/any of the animal test species should be considered for safety assessment. Bottom line: Find human metabolites and then be sure they are “covered” in the tox species. Bottom line: Find human metabolites and then be sure they are “covered” in /


The Biostatistical & Bioinformatics Challenges in the High Dimensional Data Derived from High Throughput Assays: Today and Tomorrow Yu Shyr (), Ph.D. Yu.

to extract and quantify the common features across the spectra.  We propose a new comprehensive MALDI-TOF MS data preprocessing method using feedback concepts associated with several new algorithms.  This new package successfully/: investigators, day, spot, machine, lab, etc. Source of Variability for MALDI-TOF Data  Specimen Collection/Handling Effects - Tumor: surgical related effects - Cell Line: culture condition  Biological Heterogeneity in Specimen  Biological Heterogeneity in Population  Laser/


PeptideProphet Explained Brian C. Searle Proteome Software Inc. www.proteomesoftware.com 1336 SW Bertha Blvd, Portland OR 97219 (503) 244-6027 An explanation.

the standard way of evaluating the peptides matched by a search of MS/MS spectra against a protein database. The threshold model sorts search results /zero error and everything identified (sensitivity = 100%). PeptideProphet corresponds to the curved line. Squares 1–5 are thresholds chosen by other authors. This graph shows / for: –different instruments (QTOF, TOF-TOF, IonTrap) –ionization sources (electrospray vs MALDI) –sample complexities (2D gel spot vs MudPIT) –different databases (SwissProt vs NR)/


Lecture 4 Technologies for DNA Methylation Analyses Andrea Baccarelli, MD, PhD, MPH Laboratory of Environmental Epigenetics Harvard School of Public Health.

Name: MK3 Tost et al. Biotechniques 2003 Karin Michel. Epigenetic Epidemiology, pag 41 MALDI-TOF Sequenom Mass-Array MALDI-TOF MS Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry Developed by Sequenom, Inc (MassArray/ 3 (© Garland Science 2007) Global Methylation Most methylation in repeated elements: – LINE-1 elements: >500K/haploid genome – Alu elements: >1,100K/haploid genome LINE-1/Alu methylation is correlated with global content (Weisenberger, 2005) Function of repeated/


Biofluids, Saliva and Clinical Chemistry Ken Parker 2-12-2016.

see marijuana active ingredients over CHCA background if desired From: Direct screening of herbal blends for new synthetic cannabinoids by MALDI-TOF MS. Rossella Gottardo, Anna Chiarini, Ilaria Dal Prà, Catia Seri,c Claudia Rimondo, Giovanni Serpelloni, Ubaldo Armatob and Franco/, and Detlef Suckau. Precision of Heavy−Light Peptide Ratios Measured by MALDI-TOF Mass Spectrometry J Proteome Res. 2012;11:1868-78. Biomarker Discovery Matrix methods Line up all of the mass measurments using bins Get a matrix of /


1 © SGS SA 2015 ALL RIGHTS RESERVED CONFERENCE SERIES LLC CONFERENCES Conference Series LLC is a pioneer and leading science event organizer, which publishes.

early stage, characterization surveys may help to guide choice of an appropriate cell line. Build similarity concept. 12 © SGS SA 2015 ALL RIGHTS RESERVED COMPARISON OF/MS / MALDI-MS Intact mass vs. Deglycosylated ES-MS / MALDI-MS Heterogeneity & Extent of Glycosylation Quantitative Monosaccharide Composition GC-MS HPAEC-PAD Quantitative Sialic Acid Content Derivatised Glycans Glycan Composition Glycan Sequence MALDI-MS MALDI-MS/MS PMAA GC-MS Inter- monosaccharide Linkages Antennary Profile ESI-MS 2AB-LC-MS/


Canadian Bioinformatics Workshops www.bioinformatics.ca.

=H + EI Breaks up Molecules in Predictable Ways Molecular ion Electron Impact MS of CH 3 OH Soft Ionization Methods Lecture 2.1 63 337 nm UV laser MALDI cyano-hydroxy cinnamic acid Gold tip needle Fluid (no salt) ESI + _/ Spectra Need “Fixin’” Chemical shift referencing (TMS, DSS) – Calibrates/normalizes chemical shifts Shimming – Fixes line shape to look Lorentzian Phasing – Fixes line shape to look “absorptive” Water suppression/removal – Removes large water signal Baseline correction – Makes spectrum look/


NUTRIGENOMICS: A SYSTEM BIOLOGY TOOL FOR ANIMAL HEALTH

in high vacuum of the MS and MALDI. MS has very high speed, sensitivity, specificity, resolution of mass ability and mass precision for protein documentation processes. When MS is merged with LC-GC or with MS, then its efficiency can further/spectrometers. http://www.piercenet.com/guide/mass-spectrometry-sample-prep-workflow Proteomics study example In colorectal cancer cell lines, butyrate treatment induced apoptosis and inhibited proliferation after 48 h. Proteomics and gene expression arrays were used to/


Canadian Bioinformatics Workshops www.bioinformatics.ca.

O=H + EI Breaks up Molecules in Predictable Ways Molecular ion Electron Impact MS of CH 3 OH Lecture 2.166 Soft Ionization Methods 337 nm UV laser MALDI cyano-hydroxy cinnamic acid Gold tip needle Fluid (no salt) ESI + _ /NMR Spectra Need “Fixin’” Chemical shift referencing (TMS, DSS) –Calibrates/normalizes chemical shifts Shimming –Fixes line shape to look Lorentzian Phasing –Fixes line shape to look “absorptive” Water suppression/removal –Removes large water signal Baseline correction –Makes spectrum look/


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

for Proteomics Mass spectrometry has been around since the turn of the century......why is MS based Proteomics so new? Ionization methods MALDI, Electrospray Protein chemistry & automation Chromatography, Gels, Computers Protein sequence databases A reference / Identification of protein isoforms: Optimize proteomics workflow for isoform detection Identify splice variants in cancer cell-lines (MCF-7) and clinical brain tumor samples dbPep for genomic annotation 46 Future Research Directions Proteomics/


Bioinformatics Summer School Young-Jin Lee Iowa State University.

for good results  Works almost exclusively for single protein only.  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)  Fragment the peptide ion  Determine mass of /where the red 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 spectra may match /


Beta-Galactosidase Digest from 500 fmole Loaded on a 1-D Gel A. B. C. Bovine Serum Albumin Digest from 250 fmole Loaded on a 1-D Gel Automation of In-Gel.

ABI provides a reproducible and automatable method for in-gel digestion and clean up of peptides prior to MALDI-TOF MS analysis. The successful automation of such complicated and lengthy procedures provides the throughput and simplicity necessary to /slices is placed on the vacuum manifold where destaining and extraction occur (after off-line incubation). Spotting digested proteins onto the ABI MALDI target takes place using the ABI MALDI Spotting Tower from Perkin Elmer. 1. Add 200 µl destain solution per /


Research In the Post-Genomics Era Martina McGloughlin, Biotechnology Program and Life Sciences Informatics Program UC Davis.

Acid based Sequencing Microarrays Photolithography Mirrors Spotted Chips Semi-conductor  Protein based 2-D, electrospray/nanospray MS: MALDI-TOF, LC/MS/MS, SELDI  Imaging/optical biology  Biosensors, Bioelectronics and Bionetworks (Nanotechnology) 20 Genomics, Proteomics and /Molecule Drugs Tissues & Cell Lines In situ Hybridization Clones Database DNA Libraries Database Annotated Sequence Database Assays & Validation Database Clustering Database Tissue & Cell Lines Database Small Molecule Database Micro /


Basic Scheme of Biological Phenomena

Sample preparation Prefractionation 2D - PAGE IEF SDS Proteome separation Spot excision in gel digestion MALDI-TOF-MS Spot analysis peptide fingerprinting peptide sequencing Database 10000 Counts 8000 6000 4000 2000 1000 1500 /2000 2500 3000 Mass (m/z) Comparison with Genebank (Bioinformatics) Identification of proteins Functional studies of identified proteins Protein Overexpression, Cell line/


Applications of nanotechniques in proteomics Harini Chandra Affiliations Nanotechniques have found an increasing number of applications for proteomic studies.

2, Step 4: ActionAudio Narration 1 5 3 2 4 Description of the action Centrifugation and detection Pellet Supernatant MALDI-TOF-TOF-MS MS Spectra Show a spinning motion of the contents on the left followed by the animation as shown on the right./ blue line and yellow circle group moving as shown in the animation followed by appearance of the graphs above. The authors carried out direct on-probe MS analysis using MALDI-TOF-TOF following separation of the nanoparticles by centrifugation. A clean MS profile was/


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

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 modes Pr. Jean/ 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 mai 2007 Acquisition/


DAH3.1 Mass Spectrometry Kathryn Lilley Part III Systems Biology

Workflow 1 MALDI/MS Peptide mass fingerprinting Excise Digest Spectrometry Western blotting GFP tagging Immuno- histochemistry Enzyme assay Workflow 1 MALDI/MS Peptide mass fingerprinting Excise Digest Apply to MALDI ToF Matrix Assisted Laser Desorption Ionisation (MALDI) Sample is/Huh et al, 2003 Systems wide immuno-histochemistry Antibodies to 488 proteins applied to 3 different human cell lines and images stored and publically accessible Toward a confocal subcellular atlas of the human proteome, Barbe et /


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

start-sites ( codons ) Alternative 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 2003. LIME1 gene: LCK interacting transmembrane/ (digest) enzymes: trypsin-R: 60% (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, 2004. 39 Proteomics Informatics/


阮雪芬 National Taipei University of Technology Feb 24, 2003

as the large-scale characterization of the entire protein complement of a cell line, tissue, or organism. Goal: -To obtain a more global and/* Trypsin Protein Identification by MALDI-TOF 1. Cut protein spot 2. Protein digestion 3. Peptide purification 4. Spot onto MALDI chip 5. MALDI-TOF analysis 6. Peptide /ch/tools/findmod/ Posttranslational modification SEAQUEST http://fields.scripps.edu/sequest/ Uninterpreted MS/MS searching FASTA Search Programs http://fasta.bioch.virginia.edu/ Protein and nucleotide/


Proteomics and Bioinformatics 阮雪芬 NTU Dec 25, 2002.

large-scale characterization of the entire protein complement of a cell line, tissue, or organism. Goal: -To obtain a more global/ digestion 3. Peptide purification4. Spot onto MALDI chip 5. MALDI-TOF analysis 6. Peptide fragment fingerprint Protease Protein Identification by MALDI-TOF Ionization Sample input Analyzer Detector How /tools/findmod/Posttranslational modification SEAQUESThttp://fields.scripps.edu/sequest/Uninterpreted MS/MS searching FASTA Search Programs http://fasta.bioch.virginia.edu/Protein/


蛋白質體學 阮雪芬 Jul 18 & 25, 2003. Outline The characters of proteins Differences between protein chemistry & proteomics Why to study proteome Proteomics Introduction.

the large-scale characterization of the entire protein complement of a cell line, tissue, or organism. Goal: -To obtain a more global and/ digestion 3. Peptide purification4. Spot onto MALDI chip 5. MALDI-TOF analysis 6. Peptide fragment fingerprint Protease Protein Identification by MALDI-TOF Ionization Sample input Analyzer Detector How/tools/findmod/Posttranslational modification SEAQUESThttp://fields.scripps.edu/sequest/Uninterpreted MS/MS searching FASTA Search Programs http://fasta.bioch.virginia.edu//


Introduction : Standard methodologies for enzymatic digestions have changed little in the past 40 years. The same process for sample incubation with trypsin,

mass spectrometer (Finnigan LCQ Deca XP plus) and compared with the traditional 90minute LC/MS/MS analysis. These samples were also analyzed by MALDI-TOF to confirm the efficiency of the digestions. Methods: Standard protein digest were performed/ increased data quality, and more detailed sequencing information. HIGH THROUGHPUT PROTEIN IDENTIFICATIONS UTILIZING MICROWAVE PROTEIN DIGESTS AND OFF-LINE NANO-SPRAY CHIP TECHNOLOGY Jennifer L. Rutherford, Joe Bonapace, Mai-Loan Nguyen, Tonya Pekar, and John Pirro /


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

Single Ion Monitoring (SIM ) Ion 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 charge ratio to go through the quadrupoles / matrices & multi-component samples Single Quad Replacement Ease of use for non-MS operators Target market: Peptide ID and Metabolite ID Small molecule structural elucidation Ultimate flexibility – upgrade to MALDI, ETD, Orbitrap Target market: Peptide ID and Quan in one system Metabolite/


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

for Proteomics Mass spectrometry has been around since the turn of the century......why is MS based Proteomics so new? Ionization methods MALDI, Electrospray Protein chemistry & automation Chromatography, Gels, Computers Protein sequence databases A reference/ Identification of protein isoforms: Optimize proteomics workflow for isoform detection Identify splice variants in cancer cell-lines (MCF-7) and clinical brain tumor samples Aggressive peptide sequence enumeration dbPep for genomic annotation Open/


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

start-sites ( codons ) Alternative 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 2003. LIME1 gene: LCK interacting transmembrane/ (digest) enzymes: trypsin-R: 60% (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, 2004. 33 Proteomics Informatics/


Mass Spectrometric Peptide Identification Using MASCOT Dr. David Wishart University of Alberta, Edmonton, Canada

Identification 2D-GE + MALDI-MS –Peptide Mass Fingerprinting (PMF) 2D-GE + MS-MSMS Peptide Sequencing/Fragment Ion Searching Multidimensional LC + MS-MS –ICAT Methods (isotope labelling) –MudPIT (Multidimensional Protein Ident. Tech.) 1D-GE + LC + MS-MS De Novo Peptide Sequencing/matrixscience.com) for performing rapid, accurate, on-line MS analysis of peptides and proteins Supports 3 kinds of analyses –Peptide Mass Fingerprinting (PMF) –Sequence (tag) querying –MS/MS Ion searches Lecture 2.4(c) CGDN5 /


Establishing a new research facility: Flinders Advanced Analytical Laboratory (FAAL) Lyn Spencer Flinders University.

1) Maldi-ToF Micromass (Waters) M@ldi-ToF MS Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometer (MALDI-TOF MS) Micromass (Waters) M@ldi-ToF MS Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometer (MALDI-TOF MS) /authorised users Access Access Authorised users only Authorised users only Swipe card Swipe card Booking Booking On-line database On-line database Authorised users only Authorised users only Linked to charge, reporting summary of user charges for /


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

Spectrometry for Proteomics Mass spectrometry has been around since the turn of the century......why is MS based Proteomics so new? Ionization methods MALDI, Electrospray Protein chemistry & automation Chromatography, Gels, Computers Protein sequence databases A reference for / ESTs, mRNA sequence. Little hard 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. MCP 2003. LIME1 gene: LCK interacting /


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

MS-MS (Q- TOF, Q-TRAP)  N- and C- Terminal Sequence: MALDI-TOF ISD and EDMAN Degradation  Disulfide Bonds: HPLC-UV and HPLC-MS reductive and non-reductive  Aminoacid Modifications by HPLC-UV and HPLC-MS/MS  Glycosylation and Phosphorylation Sites by HPLC-UV, HPLC-MS/MS, ICP-MS  Glycosylation Profile by HPLC-FLD, HPLC-MS/ data processing Pharmacia PhastSystem High Speed Electrophoresis Symbiosis Pharma On line solid phase extraction system Agilent 2100 Bioanalyzer: microfluidics-based platform for/


Cancer Biology & Translation Medicine

STOP: Tumor superessor 13 Matrix Degradation —— MMPs Structural base of tumor invasion & metastasis Transformed epithelial cells Epithelial lining cells Tumor fb MMP-1, 2, 3, 11, 14 Tissue Martrix Tumor fb Transformed epithelial cells MMP-/ 2DE, 2DELC-MS Validation peptides sequence of protein MALDI-MS, SELDI-MS, LC-MSMS, ESI-MS (m/z) Analysis of the databases System Biology Approaches “-omic” Technologies (Preclinical or Clinical Utilization) MALDI-MS/MS 2D Gels- MS NMR GC-MS LC-MS FT-IR Microarray/


MICROFLUIDICS Division of Technology Transfer Licensing and Research Collaboration.

Small Volume Transport The System  A sample/wash plug is formed between immiscible liquid plugs and immiscible liquid lining the transport channel walls.  System Characteristics Immiscible carrier – e.g. fluorocarbon Distances – yards Channel walls/MS 1 Lab-built, High Throughput LC MALDI-TOF MS (2 kHz Laser). 1 Applied Biosystems AB 4700 MALDI TOF- TOF MS 1 Micromass QTOF1 QP TOF MS 2 Agilent 5973 GC-MS 1 Applied Biosystems Mariner ESI orthogonal extraction TOF-MS 1 Applied Biosystems Voyager DESTR TOF-MS/


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

sample, all the masses are measured simultaneously. So you get a spectrum. Some Pictures MALDI-RQ-Tof Micro FT-ICR LTQ-Orbitrap Each peak corresponds to a different type of /.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 to-be/ Convex 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 data /


Bioinformatics Core (B) Progress and Future Goals www.functionalglycomics.org.

files (1826) Mouse Phenotyping (G) 16 KO Strains (11) 266 Experiments (149) 3116 data files (1100) Glycotechnology (C) Mouse: 11 tissues, 8 KO strains, 92 MALDI-MS spectra Human: 11 Tissues 108 MALDI- MS spectra Cell Lines: 12 Cell Lines 27 Spectra GBP-Glycan (H) 247 Samples (143) CFG Scientific Core Data CFG Scientific Core Data Enhanced dissemination interfaces Navigation and downloading of CFG Data – Gene/


Chapter 3 Exploring Proteins and Proteomes. A collective name for the genes existed in an organism C. elegance (roundworm) : 97 million bases, 19,000.

the use of these antibodies. Monoclonal Antibody Monoclonal hybridoma cell lines can generate large amount of homogeneous antibodies. Monoclonal antibodies can serve/ : Insoluble Matrix (Polystyrene Beads), HF : Hydrofluoric Acid MALDI-TOF Mass Spectrometry MALDI : Matrix-Assisted Laser Desorption-Ionization TOF : Time of Flight/ + Peptide can be sequenced by MS Individual proteins can be identified by MS Protein cleavage, followed by chromatographic separation and MS NMR (Nuclear Magnetic Resonance) Basis /


Quantitative proteomics - SILAC Harini Chandra a The identification and quantitation of complex protein mixtures have been facilitated by mass spectrometric.

m2 First show all the components of the instrument – the syringe, four rods, cube, blue rectangle, gray square with the dotted lines & the detector. Next show appearance of the coloured circles. Only the red one must move through the rods and after entering the /1.2 Da 0.2 Quantitation Trypsin Chymotrypsin Peptidase # C 13 Data format Instrument Precursor Start search… MALDI-TOF ESI-Q-TOF MALDI-TOF-TOF ESI-Q-TOF MASCOT LC-MS/MS data analysis iTRAQ 4plex SILAC ICAT D8 SILAC 5 3 2 4 1 Master Layout (Part 2) /


Chapter Clinical Laboratory Chemistry Copyright ©2011 by Pearson Education, Inc. All rights reserved. Clinical Laboratory Chemistry Sunheimer Graves Instrumentation.

Pearson Education, Inc. All rights reserved. Clinical Laboratory Chemistry Sunheimer Graves Figure 2-29 Mass spectrograph showing discrete lines representing the abundance of species based on their mass-to-charge ratio. Copyright ©2011 by Pearson Education, Inc./Inc. All rights reserved. Clinical Laboratory Chemistry Sunheimer Graves m/z The mass spectrograph shown below is a typical MALDI-TOF MS spectra of an in-gel tryptic digest acquired in reflectron mode. Copyright ©2011 by Pearson Education, Inc. All/


Affinity Chromatography and Ion Exchange Chromatography Shannon E. Spence.

are coated with liquid stationary phase b) support-coated open tubular (SCOT). the inner wall of the capillary is lined with a thin layer of support material such as diatomaceous earth, which the stationary phase has been adsorbed. SCOT columns/ all of the analyzers listed above can be used in conjunction with electrospray ionization, whereas MALDI is not usually coupled to a quadrupole analyzer. Analyzers Tandem (MS-MS) mass spectrometers are instruments that have more than one analyzer and so can be used/


Chapter 3 Despair Inc.. POLYMERIZATION KINETICS REVIEW.

plotted against the volume fraction of polystyrene. The molecular weight of each fraction is given. The dashed lines show the predictions of the Flory-Huggins theory for two of the fractions. Practical Use of Polymer TDs/change of the thermistor) and related to solution molality : heat of vaporization per gram (solvent) m : molarity Mass Spectrometry MALDI-MS (MALDI-TOF) MALDI-MS (matrix-assisted laser desorption ionization mass spectrometry) (TOF - time-of-flight) ● Imbeds polymer in a matrix of low/


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