Experimental workflow
|
|
- Ferdinand Sutton
- 7 years ago
- Views:
Transcription
1 Experimental workflow Pg. 3 Lysis Protein quant Protein precipitation Pg. 4 Digest Pgs. 5&6 Label Peptides Peptide quant Ratio check Search, filter & compile data Pgs Combine Samples LC-MS3 Pg. 8 Pg. 7 Fractionate 1
2 Lysis and protein quantification 400 µl Lysis Buffer was added to each sample Lysis Buffer -50 mm Tris ph 8.5-8M Urea -1% SDS -Roche protease and phosphatase inhibitors Protein Quantification using the micro-bca assay by Pierce Sample Protein concentration (mg/ml) Total amount of protein (µg) Wt Wt Inhib Inhib Wt Wt Inhib Inhib After protein quantification lysates were immediately reduced with DTT and alkylated with iodoacetimide 2
3 Protein precipitation and digestion -170 µg of protein from each sample was precipitated using methanol/chloroform (the remaining lysate is stored at -80 o C if needed) -Digestion was performed using LysC and trypsin Protease Protease:Protein Ratio LysC 1:100 Trypsin 1:200 Protein Quantification using the micro-bca assay by Pierce Sample Peptide concentration (mg/ml) Total amount of peptide (µg) Wt Wt Inhib Inhib Wt Wt Inhib Inhib ~80 µg of each sample was labeled with TMT reagent 3
4 Tandem Mass Tags for Multiplexed Proteomics Wt-1 Wt-2 Inhib-1 Inhib-2 Wt-3 Wt-4 Inhib-3 Inhib-4 Precursor ion (MS1 scan) Reporter ion quantification (MS3 scan) Peptide Sequencing (MS2 scan) m/z m/z 4
5 Normalized Intensity Peptide labelling and ratio check (small aliquot of total peptide) ~0.2 µg of each TMT-labelled sample was mixed (1 : 1 : 1 : 1 : 1 : 1 : 1 : 1) to verify labelling success Individual normalized values The normalized intensities for each sample from the ratio check were very similar. The remainder of the labeled peptides from each sample was mixed together. Based on the ratio check no corrections were made before mixing. 5
6 AU Basic ph reverse phase (brp) sample fractionation 100 Buffer A: 5% ACN, 50 mm AmBic ph 8.0 Buffer B: 90% ACN, 50 mm AmBic ph %B Fraction size 0.37 min (~300 µl) Time, min 96-well collection plate The sample was fractionated into two sets: Set 1 consists of 12 fractions, each fraction in this set is made up of the orange numbers for an entire column, e.g., 1, 25, 49, 73. Set 2 consists of 12 fractions from the black numbers for an entire column. 6
7 Normalized intensity MS analysis One complete set (12 fractions) from HPRP was analyzed on an Orbitrap Elite mass spectrometer (one complete set is stored in the -80 o C freezer if needed) Peptides were separated using a gradient of 6 to 28% acetonitrile in 0.125% formic acid over 160 minutes. Peptides were detected (MS1) and quantified (MS3) in the Orbitrap Peptides were sequenced (MS2) in the ion trap. MS1 peptide ion chromatogram from fraction #6 Time 7
8 Results 8
9 A summary of peptide and protein numbers from 12 fractions MS2 spectra were searched using the SEQUEST algorithm against a Uniprot composite database derived from the human proteome containing its reversed complement and known contaminants. Peptide spectral matches were filtered to a 1% false discovery rate (FDR) using the target-decoy strategy combined with linear discriminant analysis. The proteins from the 12 fractions were filtered to a <1% FDR Proteins were quantified only from peptides with a summed SN threshold of >=120 Total Peptides (<1%) 107,753 Total Proteins (<1%) 9,381 Total Collapsed Proteins 7,622 Quantified Proteins 7,551 FDR percentages are shown in parentheses 9
10 7,551 quantified proteins Hierarchical clustering The normalized data was hierarchically clustered by sample and proteins 100% normalized signal 0 Proteins were normalized to the summed signal across the row. The eight samples hierarchically clustered into two distinct groups. Each group contains four samples. 10
11 Database searching, filtering and normalization I have included a spreadsheet that contains two tabs: Tab1 (Summary Data) Protein annotation, gene symbol, protein description, peptides used for quantification, averaged data and standard deviations for the two groups determined by clustering, Log 2 (ratio), p-values, Benjamini-Hochberg corrected p-values, normalized signal based on total protein intensity across all samples Tab1 (Raw Data) Protein annotation, gene symbol, protein description, peptides used for quantification, raw signal, raw standard deviation (for proteins that have more than one quantified peptide), corrected signal for each sample based on channel sum correction, normalized signal based on total protein intensity across all samples ALL data is displayed please use caution with proteins identified by one peptide only! 11
ProteinPilot Report for ProteinPilot Software
ProteinPilot Report for ProteinPilot Software Detailed Analysis of Protein Identification / Quantitation Results Automatically Sean L Seymour, Christie Hunter SCIEX, USA Pow erful mass spectrometers like
More informationAiping Lu. Key Laboratory of System Biology Chinese Academic Society APLV@sibs.ac.cn
Aiping Lu Key Laboratory of System Biology Chinese Academic Society APLV@sibs.ac.cn Proteome and Proteomics PROTEin complement expressed by genome Marc Wilkins Electrophoresis. 1995. 16(7):1090-4. proteomics
More informationAdvantages of the LTQ Orbitrap for Protein Identification in Complex Digests
Application Note: 386 Advantages of the LTQ Orbitrap for Protein Identification in Complex Digests Rosa Viner, Terry Zhang, Scott Peterman, and Vlad Zabrouskov, Thermo Fisher Scientific, San Jose, CA,
More informationIn-Depth Qualitative Analysis of Complex Proteomic Samples Using High Quality MS/MS at Fast Acquisition Rates
In-Depth Qualitative Analysis of Complex Proteomic Samples Using High Quality MS/MS at Fast Acquisition Rates Using the Explore Workflow on the AB SCIEX TripleTOF 5600 System A major challenge in proteomics
More informationTutorial for proteome data analysis using the Perseus software platform
Tutorial for proteome data analysis using the Perseus software platform Laboratory of Mass Spectrometry, LNBio, CNPEM Tutorial version 1.0, January 2014. Note: This tutorial was written based on the information
More informationApplication Note # LCMS-81 Introducing New Proteomics Acquisiton Strategies with the compact Towards the Universal Proteomics Acquisition Method
Application Note # LCMS-81 Introducing New Proteomics Acquisiton Strategies with the compact Towards the Universal Proteomics Acquisition Method Introduction During the last decade, the complexity of samples
More informationEffects of Intelligent Data Acquisition and Fast Laser Speed on Analysis of Complex Protein Digests
Effects of Intelligent Data Acquisition and Fast Laser Speed on Analysis of Complex Protein Digests AB SCIEX TOF/TOF 5800 System with DynamicExit Algorithm and ProteinPilot Software for Robust Protein
More informationfor mass spectrometry calibration tools Thermo Scientific Pierce Controls and Standards for Mass Spectrometry
Thermo Scientific Pierce Controls and Standards for Mass Spectrometry calibration tools for mass spectrometry Ensure confidence in instrument performance with Thermo Scientific Pierce Calibration Solutions
More informationInvestigating Biological Variation of Liver Enzymes in Human Hepatocytes
Investigating Biological Variation of Liver Enzymes in Human Hepatocytes MS/MS ALL with SWATH Acquisition on the TripleTOF Systems Xu Wang 1, Hui Zhang 2, Christie Hunter 1 1 AB SCIEX, USA, 2 Pfizer, USA
More informationThermo Scientific Mass Spectrometric Immunoassay (MSIA)
INSTRUCTIONS FOR USE OF PRODUCTS Thermo Scientific Mass Spectrometric Immunoassay (MSIA) Demonstration Protocol for Affinity Purification and Analysis of Human Insulin from Human Plasma Utilizing MSIA
More informationSpikeTides TM Peptides for relative and absolute quantification in SRM and MRM Assays
Protocol SpikeTides TM Peptides for relative and absolute quantification in SRM and MRM Assays Contact us: InfoLine: +49-30-6392-7878 Order per fax: +49-30-6392-7888 or e-mail: www: peptide@jpt.com www.jpt.com
More informationMaxQuant User s Guide Version 1.2.2.5
MaxQuant User s Guide Version 1.2.2.5 Jűrgen Cox and Matthias Mann Nature Biotechnology 26, 1367-1372 (2008) Sara ten Have 2012 http://www.lamondlab.com/ http://greproteomics.lifesci.dundee.ac.uk/ References
More informationitraq Tips and Tricks
itraq Tips and Tricks Darryl Pappin Cold Spring Harbor Laboratory Patrick Emery Matrix Science Ltd. 1 Good morning. Unfortunately Darryl Pappin is unable to attend the Matrix Science workshop and the ASMS
More informationQ-TOF User s Booklet. Enter your username and password to login. After you login, the data acquisition program will automatically start.
Q-TOF User s Booklet Enter your username and password to login. After you login, the data acquisition program will automatically start. ~ 1 ~ This data acquisition window will come up after the program
More informationProteinScape. Innovation with Integrity. Proteomics Data Analysis & Management. Mass Spectrometry
ProteinScape Proteomics Data Analysis & Management Innovation with Integrity Mass Spectrometry ProteinScape a Virtual Environment for Successful Proteomics To overcome the growing complexity of proteomics
More informationThe Scheduled MRM Algorithm Enables Intelligent Use of Retention Time During Multiple Reaction Monitoring
The Scheduled MRM Algorithm Enables Intelligent Use of Retention Time During Multiple Reaction Monitoring Delivering up to 2500 MRM Transitions per LC Run Christie Hunter 1, Brigitte Simons 2 1 AB SCIEX,
More informationusing ms based proteomics
quantification using ms based proteomics lennart martens Computational Omics and Systems Biology Group Department of Medical Protein Research, VIB Department of Biochemistry, Ghent University Ghent, Belgium
More informationIncreasing the Multiplexing of High Resolution Targeted Peptide Quantification Assays
Increasing the Multiplexing of High Resolution Targeted Peptide Quantification Assays Scheduled MRM HR Workflow on the TripleTOF Systems Jenny Albanese, Christie Hunter AB SCIEX, USA Targeted quantitative
More informationProteomic data analysis for Orbitrap datasets using Resources available at MSI. September 28 th 2011 Pratik Jagtap
Proteomic data analysis for Orbitrap datasets using Resources available at MSI. September 28 th 2011 Pratik Jagtap The Minnesota http://www.mass.msi.umn.edu/ Proteomics workflow Trypsin Protein Peptides
More informationProSightPC 3.0 Quick Start Guide
ProSightPC 3.0 Quick Start Guide The Thermo ProSightPC 3.0 application is the only proteomics software suite that effectively supports high-mass-accuracy MS/MS experiments performed on LTQ FT and LTQ Orbitrap
More informationProteomics in Practice
Reiner Westermeier, Torn Naven Hans-Rudolf Höpker Proteomics in Practice A Guide to Successful Experimental Design 2008 Wiley-VCH Verlag- Weinheim 978-3-527-31941-1 Preface Foreword XI XIII Abbreviations,
More informationGlobal and Discovery Proteomics Lecture Agenda
Global and Discovery Proteomics Christine A. Jelinek, Ph.D. Johns Hopkins University School of Medicine Department of Pharmacology and Molecular Sciences Middle Atlantic Mass Spectrometry Laboratory Global
More informationTutorial for Proteomics Data Submission. Katalin F. Medzihradszky Robert J. Chalkley UCSF
Tutorial for Proteomics Data Submission Katalin F. Medzihradszky Robert J. Chalkley UCSF Why Have Guidelines? Large-scale proteomics studies create huge amounts of data. It is impossible/impractical to
More informationSession 1. Course Presentation: Mass spectrometry-based proteomics for molecular and cellular biologists
Program Overview Session 1. Course Presentation: Mass spectrometry-based proteomics for molecular and cellular biologists Session 2. Principles of Mass Spectrometry Session 3. Mass spectrometry based proteomics
More informationQuantitative proteomics background
Proteomics data analysis seminar Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post transcriptional regulation of key cellular processes de Groot, M., Daran
More informationMarkerView Software 1.2.1 for Metabolomic and Biomarker Profiling Analysis
MarkerView Software 1.2.1 for Metabolomic and Biomarker Profiling Analysis Overview MarkerView software is a novel program designed for metabolomics applications and biomarker profiling workflows 1. Using
More informationLa Protéomique : Etat de l art et perspectives
La Protéomique : Etat de l art et perspectives Odile Schiltz Institut de Pharmacologie et de Biologie Structurale CNRS, Université de Toulouse, Odile.Schiltz@ipbs.fr Protéomique et Spectrométrie de Masse
More information泛 用 蛋 白 質 體 學 之 質 譜 儀 資 料 分 析 平 台 的 建 立 與 應 用 Universal Mass Spectrometry Data Analysis Platform for Quantitative and Qualitative Proteomics
泛 用 蛋 白 質 體 學 之 質 譜 儀 資 料 分 析 平 台 的 建 立 與 應 用 Universal Mass Spectrometry Data Analysis Platform for Quantitative and Qualitative Proteomics 2014 Training Course Wei-Hung Chang ( 張 瑋 宏 ) ABRC, Academia
More informationAn In-Gel Digestion Protocol
An In-Gel Digestion Protocol This protocol describes the digestion of a protein present in an SDS-PAGE gel band with trypsin. The band can be taken from either a 1D or 2D electrophoresis gel. Reagents
More informationShotgun Proteomic Analysis. Department of Cell Biology The Scripps Research Institute
Shotgun Proteomic Analysis Department of Cell Biology The Scripps Research Institute Biological/Functional Resolution of Experiments Organelle Multiprotein Complex Cells/Tissues Function Expression Analysis
More informationMass Spectrometry Based Proteomics
Mass Spectrometry Based Proteomics Proteomics Shared Research Oregon Health & Science University Portland, Oregon This document is designed to give a brief overview of Mass Spectrometry Based Proteomics
More informationLearning Objectives:
Proteomics Methodology for LC-MS/MS Data Analysis Methodology for LC-MS/MS Data Analysis Peptide mass spectrum data of individual protein obtained from LC-MS/MS has to be analyzed for identification of
More informationChoices, choices, choices... Which sequence database? Which modifications? What mass tolerance?
Optimization 1 Choices, choices, choices... Which sequence database? Which modifications? What mass tolerance? Where to begin? 2 Sequence Databases Swiss-prot MSDB, NCBI nr dbest Species specific ORFS
More informationTutorial 9: SWATH data analysis in Skyline
Tutorial 9: SWATH data analysis in Skyline In this tutorial we will learn how to perform targeted post-acquisition analysis for protein identification and quantitation using a data-independent dataset
More informationPep-Miner: A Novel Technology for Mass Spectrometry-Based Proteomics
Pep-Miner: A Novel Technology for Mass Spectrometry-Based Proteomics Ilan Beer Haifa Research Lab Dec 10, 2002 Pep-Miner s Location in the Life Sciences World The post-genome era - the age of proteome
More informationSub menu of functions to give the user overall information about the data in the file
Visualize The Multitool for Proteomics! File Open Opens an.ez2 file to be examined. Import from TPP Imports data from files created by Trans Proteomic Pipeline. User chooses mzxml, pepxml and FASTA files
More informationSimultaneous qualitative and quantitative analysis using the Agilent 6540 Accurate-Mass Q-TOF
Simultaneous qualitative and quantitative analysis using the Agilent 654 Accurate-Mass Q-TOF Technical Overview Authors Pat Perkins Anabel Fandino Lester Taylor Agilent Technologies, Inc. Santa Clara,
More informationFrequently Asked Questions Next Generation Sequencing
Frequently Asked Questions Next Generation Sequencing Import These Frequently Asked Questions for Next Generation Sequencing are some of the more common questions our customers ask. Questions are divided
More informationA Streamlined Workflow for Untargeted Metabolomics
A Streamlined Workflow for Untargeted Metabolomics Employing XCMS plus, a Simultaneous Data Processing and Metabolite Identification Software Package for Rapid Untargeted Metabolite Screening Baljit K.
More information# LCMS-35 esquire series. Application of LC/APCI Ion Trap Tandem Mass Spectrometry for the Multiresidue Analysis of Pesticides in Water
Application Notes # LCMS-35 esquire series Application of LC/APCI Ion Trap Tandem Mass Spectrometry for the Multiresidue Analysis of Pesticides in Water An LC-APCI-MS/MS method using an ion trap system
More informationMultiQuant Software 2.0 for Targeted Protein / Peptide Quantification
MultiQuant Software 2.0 for Targeted Protein / Peptide Quantification Gold Standard for Quantitative Data Processing Because of the sensitivity, selectivity, speed and throughput at which MRM assays can
More informationSimultaneous Metabolite Identification and Quantitation with UV Data Integration Using LightSight Software Version 2.2
Technical ote Simultaneous Metabolite Identification and Quantitation with UV Data Integration Using LightSight Software Version 2.2 Alek. Dooley, Carmai Seto, esham Ghobarah, and Elliott B. Jones verview:
More informationAgilent G2721AA/G2733AA Spectrum Mill MS Proteomics Workbench
Agilent G2721AA/G2733AA Spectrum Mill MS Proteomics Workbench Application Guide Agilent Technologies Notices Agilent Technologies, Inc. 2012 No part of this manual may be reproduced in any form or by any
More informationMASCOT Search Results Interpretation
The Mascot protein identification program (Matrix Science, Ltd.) uses statistical methods to assess the validity of a match. MS/MS data is not ideal. That is, there are unassignable peaks (noise) and usually
More informationResearch-grade Targeted Proteomics Assay Development: PRMs for PTM Studies with Skyline or, How I learned to ditch the triple quad and love the QE
Research-grade Targeted Proteomics Assay Development: PRMs for PTM Studies with Skyline or, How I learned to ditch the triple quad and love the QE Jacob D. Jaffe Skyline Webinar July 2015 Proteomics and
More informationSTANFORD UNIVERSITY MASS SPECTROMETRY 333 CAMPUS DR., MUDD 175 STANFORD, CA 94305-5080
Training on the ZQ Open access MS Questions? Contact Dr. Allis Chien allis@stanford.edu 650-723-0710 0710 STANFORD UNIVERSITY MASS SPECTROMETRY STANFORD UNIVERSITY MASS SPECTROMETRY 333 CAMPUS DR., MUDD
More informationStatistical Analysis Strategies for Shotgun Proteomics Data
Statistical Analysis Strategies for Shotgun Proteomics Data Ming Li, Ph.D. Cancer Biostatistics Center Vanderbilt University Medical Center Ayers Institute Biomarker Pipeline normal shotgun proteome analysis
More informationMass Spectrometry Signal Calibration for Protein Quantitation
Cambridge Isotope Laboratories, Inc. www.isotope.com Proteomics Mass Spectrometry Signal Calibration for Protein Quantitation Michael J. MacCoss, PhD Associate Professor of Genome Sciences University of
More informationHigh-Resolution Targeted Quantitation: Biomarker Discovery in a Mouse Transgenic Model of Myopathy
pplication Note: 555 High-Resolution Targeted Quantitation: iomarker Discovery in a Mouse Transgenic Model of Myopathy Claire Dauly 1, Manuel Fréret 2, Laurent Drouot 2, Jenny T.C. Ho 3, Pascal Cosette
More informationTECHNICAL BULLETIN. HIS-Select Nickel Affinity Gel. Catalog Number P6611 Storage Temperature 2 8 C
HIS-Select Nickel Affinity Gel Catalog Number P6611 Storage Temperature 2 8 C TECHNICAL BULLETIN Product Description HIS-Select Nickel Affinity Gel is an immobilized metalion affinity chromatography (IMAC)
More informationApplication Note. Authors. Abstract. Automated Peptide Sample Preparation for LC/MS
Workflow Automation for LC/MS: In Solution Protein Digestion, Peptide Cleanup, and Strong Cation-Exchange Fractionation of Peptides Enabled by AssayMAP Technology Application Note Automated Peptide Sample
More informationThermo Scientific SIEVE Software for Differential Expression Analysis
m a s s s p e c t r o m e t r y Thermo Scientific SIEVE Software for Differential Expression Analysis Automated, label-free, semi-quantitative analysis of proteins, peptides, and metabolites based on comparisons
More informationPeak intensity Trypsin. Protein Sequence Before trypsin digestion After digestion with trypsin for 24 h digestion
Supplemental table 1. The completeness of trypsin digestion of the signature peptides with native flanking sequence. The signature peptides with native flanking sequence were digested with trypsin as described
More informationMRMPilot Software: Accelerating MRM Assay Development for Targeted Quantitative Proteomics
MRMPilot Software: Accelerating MRM Assay Development for Targeted Quantitative Proteomics With Unique QTRAP and TripleTOF 5600 System Technology Targeted peptide quantification is a rapidly growing application
More informationHigh-Throughput 3-D Chromatography Through Ion Exchange SPE
High-Throughput 3-D Chromatography Through Ion Exchange SPE Application Note 205 Luke Roenneburg and Alan Hamstra (Gilson, Inc.) Introduction 2-dimensional (2-D) separation is the separation of a sample
More informationUbiquitin Interact Kit
Ubiquitin Interact Kit Item No. 15978 Customer Service 800.364.9897 * Technical Support 888.526.5351 www.caymanchem.com TABLE OF CONTENTS GENERAL INFORMATION 3 Materials Supplied 3 Precautions 4 If You
More informationChallenges in Computational Analysis of Mass Spectrometry Data for Proteomics
Ma B. Challenges in computational analysis of mass spectrometry data for proteomics. SCIENCE AND TECHNOLOGY 25(1): 1 Jan. 2010 JOURNAL OF COMPUTER Challenges in Computational Analysis of Mass Spectrometry
More informationOverview. Purpose. Methods. Results
A ovel Approach to Quantify Unbound Cisplatin, Carboplatin, and xaliplatin in Human Plasma Ultrafiltrate by Measuring Platinum-DDTC Complex Using LC/M/M Min Meng, Ryan Kuntz, Al Fontanet, and Patrick K.
More informationMethod Development of LC-MS/MS Analysis of Aminoglycoside Drugs: Challenges and Solutions
Method Development of LC-MS/MS Analysis of Aminoglycoside Drugs: Challenges and Solutions authors Angela (Qi) Shen, Ling Morgan, Marcele L. Barroso, and Xin Zhang; Tandem Labs Tuyen Nguyen; Sepracor Inc.
More informationReal-time PCR: Understanding C t
APPLICATION NOTE Real-Time PCR Real-time PCR: Understanding C t Real-time PCR, also called quantitative PCR or qpcr, can provide a simple and elegant method for determining the amount of a target sequence
More informationMascot Search Results FAQ
Mascot Search Results FAQ 1 We had a presentation with this same title at our 2005 user meeting. So much has changed in the last 6 years that it seemed like a good idea to re-visit the topic. Just about
More informationAlready said. Already said. Outlook. Look at LC-MS data. A look at data for quantitative analysis using MSight and Phenyx. What data for quantitation?
A look at data for quantitative analysis using MSight and Phenyx Pierre-Alain Binz Institut Suisse de Bioinformatique GeneBio SA Atelier Protéomique Quantitative 25-27 Juin 2007 La Grande Motte Already
More informationIntroduction to mass spectrometry (MS) based proteomics and metabolomics
Introduction to mass spectrometry (MS) based proteomics and metabolomics Tianwei Yu Department of Biostatistics and Bioinformatics Rollins School of Public Health Emory University September 10, 2015 Background
More informationAlignment and Preprocessing for Data Analysis
Alignment and Preprocessing for Data Analysis Preprocessing tools for chromatography Basics of alignment GC FID (D) data and issues PCA F Ratios GC MS (D) data and issues PCA F Ratios PARAFAC Piecewise
More informationFast and Automatic Mapping of Disulfide Bonds in a Monoclonal Antibody using SYNAPT G2 HDMS and BiopharmaLynx 1.3
Fast and Automatic Mapping of Disulfide Bonds in a Monoclonal Antibody using SYNAPT G2 HDMS and BiopharmaLynx 1.3 Hongwei Xie and Weibin Chen Waters Corporation, Milford, MA, U.S. A P P L I C AT ION B
More informationPeptidomicsDB: a new platform for sharing MS/MS data.
PeptidomicsDB: a new platform for sharing MS/MS data. Federica Viti, Ivan Merelli, Dario Di Silvestre, Pietro Brunetti, Luciano Milanesi, Pierluigi Mauri NETTAB2010 Napoli, 01/12/2010 Mass Spectrometry
More informationAB SCIEX TOF/TOF 4800 PLUS SYSTEM. Cost effective flexibility for your core needs
AB SCIEX TOF/TOF 4800 PLUS SYSTEM Cost effective flexibility for your core needs AB SCIEX TOF/TOF 4800 PLUS SYSTEM It s just what you expect from the industry leader. The AB SCIEX 4800 Plus MALDI TOF/TOF
More informationProteomic Analysis using Accurate Mass Tags. Gordon Anderson PNNL January 4-5, 2005
Proteomic Analysis using Accurate Mass Tags Gordon Anderson PNNL January 4-5, 2005 Outline Accurate Mass and Time Tag (AMT) based proteomics Instrumentation Data analysis Data management Challenges 2 Approach
More informationApplication Note # MT-90 MALDI-TDS: A Coherent MALDI Top-Down-Sequencing Approach Applied to the ABRF-Protein Research Group Study 2008
Bruker Daltonics Application Note # MT-90 MALDI-TDS: A Coherent MALDI Top-Down-Sequencing Approach Applied to the ABRF-Protein Research Group Study 2008 In the ABRF-PRG study 2008 [*] the ability to characterize
More informationPinpointing phosphorylation sites using Selected Reaction Monitoring and Skyline
Pinpointing phosphorylation sites using Selected Reaction Monitoring and Skyline Christina Ludwig group of Ruedi Aebersold, ETH Zürich The challenge of phosphosite assignment Peptides Phosphopeptides MS/MS
More informationLC-MS/MS Method for the Determination of Docetaxel in Human Serum for Clinical Research
LC-MS/MS Method for the Determination of Docetaxel in Human Serum for Clinical Research J. Jones, J. Denbigh, Thermo Fisher Scientific, Runcorn, Cheshire, UK Application Note 20581 Key Words SPE, SOLA,
More informationProtease Peptide Microarrays Ready-to-use microarrays for protease profiling
Protocol Protease Peptide Microarrays Ready-to-use microarrays for protease profiling Contact us: InfoLine: +49-30-97893-117 Order per fax: +49-30-97893-299 Or e-mail: peptide@jpt.com www: www.jpt.com
More informationClassic Immunoprecipitation
292PR 01 G-Biosciences 1-800-628-7730 1-314-991-6034 technical@gbiosciences.com A Geno Technology, Inc. (USA) brand name Classic Immunoprecipitation Utilizes Protein A/G Agarose for Antibody Binding (Cat.
More informationOverview. Triple quadrupole (MS/MS) systems provide in comparison to single quadrupole (MS) systems: Introduction
Advantages of Using Triple Quadrupole over Single Quadrupole Mass Spectrometry to Quantify and Identify the Presence of Pesticides in Water and Soil Samples André Schreiber AB SCIEX Concord, Ontario (Canada)
More informationIncreased Power for the Analysis of Label-Free LC- MS/MS Proteomic Data by Combining Spectral Counts and Peptide Peak Attributes
Increased Power for the Analysis of Label-Free LC- MS/MS Proteomic Data by Combining Spectral Counts and Peptide Peak Attributes Lee Dicker, Xihong Lin, & Alexander R. Ivanov Corresponding author: email,
More informationSignal to Noise Instrumental Excel Assignment
Signal to Noise Instrumental Excel Assignment Instrumental methods, as all techniques involved in physical measurements, are limited by both the precision and accuracy. The precision and accuracy of a
More informationSoftware for protein identification and quantitative analysis of mass spectrometry data used for protein characterization and proteomics Version 5.
Release Notes ProteinPilot Software for protein identification and quantitative analysis of mass spectrometry data used for protein characterization and proteomics Version 5.0 Introduction Thank you for
More informationMethod development for analysis of formaldehyde in foodsimulant. melamine-ware by GC-MS and LC-MS/MS. Internal Technical Report
of melamine-ware by GC-MS and LC-MS/MS Page 1 of 15 Method development for analysis of formaldehyde in foodsimulant extracts of melamine-ware by GC-MS and LC-MS/MS December 2012 Contact Point: Chris Hopley
More informationDatabase Searching Tutorial/Exercises Jimmy Eng
Database Searching Tutorial/Exercises Jimmy Eng Use the PETUNIA interface to run a search and generate a pepxml file that is analyzed through the PepXML Viewer. This tutorial will walk you through the
More informationMonoclonal Antibody Fragment Separation and Characterization Using Size Exclusion Chromatography Coupled with Mass Spectrometry
Monoclonal ntibody Fragment Separation and haracterization Using Size Exclusion hromatography oupled with Mass Spectrometry uthors Haiying hen Katherine McLaughlin Sepax Technologies, Inc. 5 Innovation
More informationBiopharmaceutical Glycosylation Analysis
Biopharmaceutical Glycosylation Analysis Glycosylation Analysis: Product Offering Molecular model of erythropoietin with complex N-linked glycans. Courtesy of M.R Wormald and R.A Dwek, Oxford Glycobioloy
More informationProtein quantification and detection methods
Protein quantification and detection methods 1) Spectroscopic procedures 2) Measurement of the total protein content by colorimetry 3) Amino acid analysis 4) Other methods, eg. radiolabelling of proteins,
More informationDesigning Assays for the TaqMan Protein Assay
Designing Assays for the TaqMan Protein Assay Antibody Selection...2 Assay Design...2 Antibody Search...3 Biotinylated Antibodies...3 Working with pre-biotinylated antibodies...4 Working with non-biotinylated
More informationAnalysis of Liquid Samples on the Agilent GC-MS
Analysis of Liquid Samples on the Agilent GC-MS I. Sample Preparation A. Solvent selection. 1. Boiling point. Low boiling solvents (i.e. b.p. < 30 o C) may be problematic. High boiling solvents (b.p. >
More informationCPAS Overview. Josh Eckels LabKey Software jeckels@labkey.com
CPAS Overview Josh Eckels LabKey Software jeckels@labkey.com CPAS Web-based system for processing, storing, and analyzing results of MS/MS experiments Key goals: Provide a great analysis front-end for
More informationHRMS in Clinical Research: from Targeted Quantification to Metabolomics
A sponsored whitepaper. HRMS in Clinical Research: from Targeted Quantification to Metabolomics By: Bertrand Rochat Ph. D., Research Project Leader, Faculté de Biologie et de Médecine of the Centre Hospitalier
More informationIndustry Perspective: Advantages of Open Access and Walkup LC/ MS Supporting Protein Drug Discovery and Development
Industry Perspective: Advantages of Open Access and Walkup LC/ MS Supporting Protein Drug Discovery and Development Dawn Stickle, Agilent Technologies Originally presented by Eric Fang, Novartis Overview
More informationIntroduction to Proteomics 1.0
Introduction to Proteomics 1.0 CMSP Workshop Tim Griffin Associate Professor, BMBB Faculty Director, CMSP Objectives Why are we here? For participants: Learn basics of MS-based proteomics Learn what s
More informationA Generic Kit-Based Approach for Quantifying Monoclonal Antibody Drugs Through Direct Digestion of Discovery Study Samples
A Generic Kit-Based Approach for Quantifying Monoclonal Antibody Drugs Through Direct Digestion of Discovery Study Samples Mary Lame, Hua Yang, Sherri Naughton, and Erin Chambers Waters Corporation, Milford,
More informationAppendix 5 Overview of requirements in English
Appendix 5 Overview of requirements in English This document is a translation of Appendix 4 (Bilag 4) section 2. This translation is meant as a service for the bidder and in case of any differences between
More informationProtein Hit1, a novel box C/D snornp assembly factor, controls cellular concentration of protein Rsa1p by direct interaction
Supplementary data Protein Hit1, a novel box C/D snornp assembly factor, controls cellular concentration of protein Rsa1p by direct interaction Benjamin Rothé, Jean-Michel Saliou, Marc Quinternet, Régis
More informationQuantification of Multiple Therapeutic mabs in Serum Using microlc-esi-q-tof Mass Spectrometry
Quantification of Multiple Therapeutic mabs in Serum Using microlc-esi-q-tof Mass Spectrometry Paula Ladwig, David Barnidge, Mindy Kohlhagen, John Mills, Maria Willrich, Melissa R. Snyder and David Murray
More informationMass Frontier Version 7.0
Mass Frontier Version 7.0 User Guide XCALI-97349 Revision A February 2011 2011 Thermo Fisher Scientific Inc. All rights reserved. Mass Frontier, Mass Frontier Server Manager, Fragmentation Library, Spectral
More informationHierarchical Clustering Analysis
Hierarchical Clustering Analysis What is Hierarchical Clustering? Hierarchical clustering is used to group similar objects into clusters. In the beginning, each row and/or column is considered a cluster.
More informationTechnical Report. Automatic Identification and Semi-quantitative Analysis of Psychotropic Drugs in Serum Using GC/MS Forensic Toxicological Database
C146-E175A Technical Report Automatic Identification and Semi-quantitative Analysis of Psychotropic Drugs in Serum Using GC/MS Forensic Toxicological Database Hitoshi Tsuchihashi 1 Abstract: A sample consisting
More informationApplication Note # LCMS-92 Interlaboratory Tests Demonstrate the Robustness and Transferability of the Toxtyper Workflow
Application Note # LCMS-92 Interlaboratory Tests Demonstrate the Robustness and Transferability of the Toxtyper Workflow Abstract There is high demand in clinical research and forensic toxicology for comprehensive,
More informationQuantitative mass spectrometry in proteomics: a critical review
Anal Bioanal Chem (2007) 389:1017 1031 DOI 10.1007/s00216-007-1486-6 REVIEW Quantitative mass spectrometry in proteomics: a critical review Marcus Bantscheff & Markus Schirle & Gavain Sweetman & Jens Rick
More informationSupplementary Materials and Methods (Metabolomics analysis)
Supplementary Materials and Methods (Metabolomics analysis) Metabolite extraction and mass spectrometry analysis. 12 Vldlr-/- knock out and 12 wild type (WT) retinas were separately frozen at -80 ºC in
More informationChapter 14. Modeling Experimental Design for Proteomics. Jan Eriksson and David Fenyö. Abstract. 1. Introduction
Chapter Modeling Experimental Design for Proteomics Jan Eriksson and David Fenyö Abstract The complexity of proteomes makes good experimental design essential for their successful investigation. Here,
More information