SRM assay generation and data analysis in Skyline
|
|
- Nathan Hopkins
- 5 years ago
- Views:
Transcription
1 in Skyline Preparation 1. Download the example data from (3 raw files, 1 csv file, 1 sptxt file). 2. The number formats of your computer have to be set to English (United States). Open the Control Panel Clock, Language, and Region Change Location Formats English (United States). Skyline document set-up 1. Open Skyline. 2. Go to Settings Peptide Settings and go through all tabs: a. Digestion i. Enzyme: We use trypsin, which cleaves C-terminally of lysine (K) and arginine (R), but not if these are followed by a proline (P): select Trypsin [KR P] ii. Max missed cleavages: We work with fully tryptic peptides only: select 0. iii. Background proteome: None. b. Prediction i. We do not use these settings for our case study, keep the defaults. c. Filter i. Min/Max length: We work with peptides of 7 to 25 amino acids length. ii. Exclude N-terminal AAs: Enter 0. iii. Exclude potentially ragged ends: Do not select this option. iv. Exclude peptides containing: Do not select these options. v. Auto-select all matching peptides: Do not select this option. d. Library i. Libraries containing MS2 spectral information can be downloaded from public sources or built within Skyline. We are going to import an Mtb spectral library, which has already been published. Go to and click on the 4000 QTrap link to download and unzip the spectral library in.sptxt format. ii. Edit list Add iii. Name it e.g. Mtb_Qtrap, then select the downloaded.sptxt file and confirm. iv. Select the newly generated library. v. Pick peptide matching: Library. vi. Rank peptides by: We do not need this. e. Modifications i. Structural modifications: Structural modifications concern chemical modifications of peptides. They can either be static (always present) or variable (sometimes present, sometimes not). Add here Carbamidomethyl (C) as a static modification. It comes from the cysteine reduction and alkylation step during sample preparation. ii. Max variable mods and Max neutral losses: Keep the defaults. iii. Isotope label type: Leave the default heavy. iv. Isotope modifications: We spiked-in synthetic reference peptides of which the C-terminal Arg or Lys contain 13 C and 15 N atoms. Activate these modifications: Edit list Add: 1. Label:13C(6)15N(2) (C-term K) 2. Label:13C(6)15N(4) (C-term R) v. Internal standard type: Leave the default heavy. f. Click OK to confirm all peptide settings. 1
2 3. Go to Settings Transition Settings and go through all the tabs: a. Prediction i. Precursor mass and product ion mass: We work with the monoisotopic mass. ii. Collision energy: Keep the default. iii. Declustering potential: We do not apply a customised DP. iv. Use optimisation values when present: Do not select this option. b. Filter i. Precursor charges: We work with doubly and triply charged precursors ( 2, 3 ). ii. Product ion charges: We consider singly and doubly charged product ions ( 1, 2 ). iii. Ion types: We focus on y-ions ( y ). We do not consider b-ions, because compared to y-ions they tend to be less conserved between instruments. iv. Product ions: 1. From: ion 1 and To: last ion. 2. Always add: Do not select anything here, because we are going to use the library to guide the selection of product ions. 3. Precursor m/z exclusion window: 10 Th. v. Auto-select all matching transitions: Activate this option. c. Library i. Ion match tolerance: This depends on the instrument type that was used to acquire your library. Lower values help to get a more specific peak assignment of the spectra, but if the instrument doesn t have this accuracy you will loose your peaks. Enter a mass tolerance of 1.0 Th. ii. If a library spectrum is available, pick the most intense ions: Select this option and pick the 5 most intense transitions per precursor. iii. From filtered ion charges and types: Select this option. d. Instrument i. Min/Max m/z: We typically use 300 to 1350 m/z. ii. Dynamic min product m/z: We do not use this option. iii. Match tolerance: We keep the default setting of Th iv. Firmware transition limit: Do not enter a limit. v. Firmware inclusion limit: Do not enter a limit. vi. Min/Max time: Leave these fields empty. e. Full-Scan: We do not use this. f. Click OK to confirm all transition settings. 4. Save the Skyline document: File Save as MyFile.sky SRM assay generation in Skyline With SRM assay generation we mean the selection of the most intense transitions per peptide. The selection of the optimal peptides per protein had been done before. 1. To insert the peptide list into Skyline, copy the peptide sequences together with the protein names from the file TargetPeptides.csv. Back in Skyline go to Edit Insert Peptides and paste the copied peptides and proteins here. 2. Skyline now automatically groups the peptides into proteins and selects the highest 5 transitions for each peptide from the spectral library which we specified it in the transition settings before. 3. Go through the transition list and look at the corresponding spectra. a. In the lower right corner you can see the number of proteins, peptides, precursors and transitions you have in your Skyline file. 4. This is your assay Skyline file, save it as MyFile_assays.sky. 2
3 5. Export the transition list to feed into the instrument: File Export Transition List. a. Export an ABSciex transition list using the standard settings and a dwell time of 20 ms. b. A pop-up window asks you if you would like to use the defaults, say No. c. Save this transition list as MyFile_assays.csv. d. For the measurement we need precursor m/z, product m/z, dwell time, transition ID, declustering potential, and collision energy. How many proteins, peptides, precursors and transitions do you have in your Skyline file? For how many peptides do we have the 3+ precursor and for how many do we have the 2+ precursor in your Skyline file? Which is the predominant charge state of the fragment ions in your Skyline file? How many precursors are you left with, if you only select the 2+ precursors (change in Transition Settings)? Please change this setting back to 2+ and 3+ precursor before you continue. 3
4 SRM data analysis in Skyline After the transition list has been measured on a triple quadrupole instrument, we import the data into Skyline to check the quality of the runs and to quantify our target peptides. 1. Import SRM data: File Import Results Add single injection replicates per file OK select all raw files in the data folder Open a. Skyline will ask if you want to remove the common prefix of all files, select Do not remove to keep the complete file name. 2. To get a good overview over the data go to View Retention Times Replicate Comparison. And View Peak Areas Replicate Comparison. Then grap one of these new windows, drag them down to the little arrow pointing down, then release. Arrange all the other tabs likewise such that your Skyline looks like this: 3. This is your raw Skyline file, save it as MyFile_raw.sky. 4. Explore the SRM peak groups: a. Right click on the peak groups and play with the zoom to better see your peaks. b. You can see that the transitions have only been measured during 4 min (scheduled SRM). For time reasons we did not discuss scheduled SRM measurements in detail in this tutorial and therefore we will ignore this. But be aware that if we had measured a transition list without scheduling, we would have had for each transition a signal over the whole 30 min gradient. 5. Manually refine the peak picking: a. Make sure that the right peak is picked. If certain peaks are wrongly picked by Skyline, drag the area boundaries to what you think is the correct peak. b. The peak boundaries have to be the same for heavy and light (drag areas when you have the peptide activated, not just one precursor or a single transition). c. It is a good idea to look at the Retention Time and Peak Area windows from time to time, they help to spot problematic peaks. 6. Manually refine the transitions which should be used for quantification, i.e. remove low quality transitions by deleting them from the transition tree window. a. For correct quantification, the heavy and the light precursors need to have the same transitions. 7. This is your refined Skyline file, save it as MyFile_refined.sky. 8. To export the data to a.csv file: File Export Report 9. We will generate our own report format: Edit list Add 10. Give the newly created report a name and browse the tree view to find and select the following features: ProteinName, PeptideSequence, RatioToStandard. 4
5 11. Check the Pivot Replicate Name option, then save this report template. 12. Export and save your data in this report format: MyFile_refined.csv. Which transition of the peptide LLGSVSSGLLR is behaving weird? Does the removal of the two shouldered transitions of the peptide LPDGNGIELCR have an impact on the ratio between heavy and light? (see total ratio next to the precursor mass) Which transition of the peptide VIGPAMFAAGDVAAAR is not co-eluting with the rest and how does the dot product change if you delete it? Finalising SRM data analysis in Excel 1. Open your exported Skyline report in Excel. 2. Determine the relative changes of each peptide to the first time point. Define for the first time point the relative abundance = 1 (i.e. divide all ratios by the first ratio). 3. Average the peptide changes for each protein and plot the relative changes of the proteins over the 3 time points. 4. The highly regulated proteins prevent us to visualise the less regulated proteins. If you log-transform the y-axis (e.g. using log 2) you will see the following: a. Large changes are compressed and we can better see the less regulated proteins. b. Shifted the not regulated from 1 to 0 and rescales the down-regulated proteins such that they have the same scale as the upregulated just in negative numbers. Before, the ratios for down-regulated proteins were all squeezed between 0 and 1, while the ratios for up-regulated proteins went from 1 to. 5. The final graph should look similar to this: Ratio changes of 6 Mtb proteins during hypoxic stress Log2 (ratio to time point 0) h 6h 48h Rv2623 TB31.7 Rv3133c devr Rv0079 Rv0079 Rv2626c hrp1 Rv2027c dost Rv1812c Rv1812c Do the peptides belonging to the same protein show similar ratio changes? Discuss what could be the reason for peptides showing different regulation. 5
Tutorial 1: Setting up your Skyline document
Tutorial 1: Setting up your Skyline document Caution! For using Skyline the number formats of your computer have to be set to English (United States). Open the Control Panel Clock, Language, and Region
More informationTUTORIAL EXERCISES WITH ANSWERS
TUTORIAL EXERCISES WITH ANSWERS Tutorial 1 Settings 1. What is the exact monoisotopic mass difference for peptides carrying a 13 C (and NO additional 15 N) labelled C-terminal lysine residue? a. 6.020129
More informationSkyline Small Molecule Targets
Skyline Small Molecule Targets The Skyline Targeted Proteomics Environment provides informative visual displays of the raw mass spectrometer data you import into your Skyline documents. Originally developed
More informationTutorial 2: Analysis of DIA data in Skyline
Tutorial 2: Analysis of DIA data in Skyline In this tutorial we will learn how to use Skyline to perform targeted post-acquisition analysis for peptide and inferred protein detection and quantitation using
More informationProtein Quantitation II: Multiple Reaction Monitoring. Kelly Ruggles New York University
Protein Quantitation II: Multiple Reaction Monitoring Kelly Ruggles kelly@fenyolab.org New York University Traditional Affinity-based proteomics Use antibodies to quantify proteins Western Blot RPPA Immunohistochemistry
More informationProtein Quantitation II: Multiple Reaction Monitoring. Kelly Ruggles New York University
Protein Quantitation II: Multiple Reaction Monitoring Kelly Ruggles kelly@fenyolab.org New York University Traditional Affinity-based proteomics Use antibodies to quantify proteins Western Blot Immunohistochemistry
More informationAnalyst Software. Peptide and Protein Quantitation Tutorial
This document is provided to customers who have purchased AB Sciex equipment to use in the operation of such AB Sciex equipment. This document is copyright protected and any reproduction of this document
More informationInformation Dependent Acquisition (IDA) 1
Information Dependent Acquisition (IDA) Information Dependent Acquisition (IDA) enables on the fly acquisition of MS/MS spectra during a chromatographic run. Analyst Software IDA is optimized to generate
More informationHOWTO, example workflow and data files. (Version )
HOWTO, example workflow and data files. (Version 20 09 2017) 1 Introduction: SugarQb is a collection of software tools (Nodes) which enable the automated identification of intact glycopeptides from HCD
More informationComprehensive support for quantitation
Comprehensive support for quantitation One of the major new features in the current release of Mascot is support for quantitation. This is still work in progress. Our goal is to support all of the popular
More informationDIA-Umpire: comprehensive computational framework for data independent acquisition proteomics
DIA-Umpire: comprehensive computational framework for data independent acquisition proteomics Chih-Chiang Tsou 1,2, Dmitry Avtonomov 2, Brett Larsen 3, Monika Tucholska 3, Hyungwon Choi 4 Anne-Claude Gingras
More informationComparing whole genomes
BioNumerics Tutorial: Comparing whole genomes 1 Aim The Chromosome Comparison window in BioNumerics has been designed for large-scale comparison of sequences of unlimited length. In this tutorial you will
More informationCerno Application Note Extending the Limits of Mass Spectrometry
Creation of Accurate Mass Library for NIST Database Search Novel MS calibration has been shown to enable accurate mass and elemental composition determination on quadrupole GC/MS systems for either molecular
More information1. Prepare the MALDI sample plate by spotting an angiotensin standard and the test sample(s).
Analysis of a Peptide Sequence from a Proteolytic Digest by MALDI-TOF Post-Source Decay (PSD) and Collision-Induced Dissociation (CID) Standard Operating Procedure Purpose: The following procedure may
More informationMassHunter Software Overview
MassHunter Software Overview 1 Qualitative Analysis Workflows Workflows in Qualitative Analysis allow the user to only see and work with the areas and dialog boxes they need for their specific tasks A
More informationTOMAHAQ Method Construction
TOMAHAQ Method Construction Triggered by offset mass accurate-mass high-resolution accurate quantitation (TOMAHAQ) can be performed in the standard method editor of the instrument, without modifications
More informationTutorial 3: Building a spectral library in Skyline
SRM Curse 2013 Tutrial 3 Spectral Library Tutrial 3: Building a spectral library in Skyline Spectral libraries fr SRM methd design and fr data analysis can be either directly added t a Skyline dcument
More informationAll Ions MS/MS: Targeted Screening and Quantitation Using Agilent TOF and Q-TOF LC/MS Systems
All Ions MS/MS: Targeted Screening and Quantitation Using Agilent TOF and Q-TOF LC/MS Systems Technical Overview Introduction All Ions MS/MS is a technique that is available for Agilent high resolution
More informationMassHunter TOF/QTOF Users Meeting
MassHunter TOF/QTOF Users Meeting 1 Qualitative Analysis Workflows Workflows in Qualitative Analysis allow the user to only see and work with the areas and dialog boxes they need for their specific tasks
More informationProteomics. November 13, 2007
Proteomics November 13, 2007 Acknowledgement Slides presented here have been borrowed from presentations by : Dr. Mark A. Knepper (LKEM, NHLBI, NIH) Dr. Nathan Edwards (Center for Bioinformatics and Computational
More informationProtocol. Product Use & Liability. Contact us: InfoLine: Order per fax: www:
Protocol SpikeTides Set TAA - light SpikeTides Set TAA_L - heavy Peptide Sets for relative quantification of Tumor Associated Antigens (TAAs) in SRM and MRM Assays Contact us: InfoLine: +49-30-6392-7878
More informationImproved 6- Plex TMT Quantification Throughput Using a Linear Ion Trap HCD MS 3 Scan Jane M. Liu, 1,2 * Michael J. Sweredoski, 2 Sonja Hess 2 *
Improved 6- Plex TMT Quantification Throughput Using a Linear Ion Trap HCD MS 3 Scan Jane M. Liu, 1,2 * Michael J. Sweredoski, 2 Sonja Hess 2 * 1 Department of Chemistry, Pomona College, Claremont, California
More informationMnova Software for Analyzing Reaction Monitoring NMR Spectra
Mnova Software for Analyzing Reaction Monitoring NMR Spectra Version 10 Chen Peng, PhD, VP of Business Development, US & China Mestrelab Research SL San Diego, CA, USA chen.peng@mestrelab.com 858.736.4563
More informationProMass Deconvolution User Training. Novatia LLC January, 2013
ProMass Deconvolution User Training Novatia LLC January, 2013 Overview General info about ProMass Features Basics of how ProMass Deconvolution works Example Spectra Manual Deconvolution with ProMass Deconvolution
More informationAgilent MassHunter Quantitative Data Analysis
Agilent MassHunter Quantitative Data Analysis Presenters: Howard Sanford Stephen Harnos MassHunter Quantitation: Batch and Method Setup Outliers, Data Review, Reporting 1 MassHunter Quantitative Analysis
More informationTutorial 1: Library Generation from DDA data
Tutorial 1: Library Generation from DDA data 1. Introduction Before a targeted, peptide-centric DIA analysis can be performed, a spectral library containing peptide-query parameters needs to be generated.
More informationNPTEL VIDEO COURSE PROTEOMICS PROF. SANJEEVA SRIVASTAVA
LECTURE-25 Quantitative proteomics: itraq and TMT TRANSCRIPT Welcome to the proteomics course. Today we will talk about quantitative proteomics and discuss about itraq and TMT techniques. The quantitative
More informationExercises for Windows
Exercises for Windows CAChe User Interface for Windows Select tool Application window Document window (workspace) Style bar Tool palette Select entire molecule Select Similar Group Select Atom tool Rotate
More informationPeptideProphet: Validation of Peptide Assignments to MS/MS Spectra. Andrew Keller
PeptideProphet: Validation of Peptide Assignments to MS/MS Spectra Andrew Keller Outline Need to validate peptide assignments to MS/MS spectra Statistical approach to validation Running PeptideProphet
More information85. Geo Processing Mineral Liberation Data
Research Center, Pori / Pertti Lamberg 14024-ORC-J 1 (23) 85. Geo Processing Mineral Liberation Data 85.1. Introduction The Mineral Liberation Analyzer, MLA, is an automated mineral analysis system that
More informationWADA Technical Document TD2003IDCR
IDENTIFICATION CRITERIA FOR QUALITATIVE ASSAYS INCORPORATING CHROMATOGRAPHY AND MASS SPECTROMETRY The appropriate analytical characteristics must be documented for a particular assay. The Laboratory must
More informationProtein Identification Using Tandem Mass Spectrometry. Nathan Edwards Informatics Research Applied Biosystems
Protein Identification Using Tandem Mass Spectrometry Nathan Edwards Informatics Research Applied Biosystems Outline Proteomics context Tandem mass spectrometry Peptide fragmentation Peptide identification
More informationLeaf Spring (Material, Contact, geometric nonlinearity)
00 Summary Summary Nonlinear Static Analysis - Unit: N, mm - Geometric model: Leaf Spring.x_t Leaf Spring (Material, Contact, geometric nonlinearity) Nonlinear Material configuration - Stress - Strain
More informationModeling Mass Spectrometry-Based Protein Analysis
Chapter 8 Jan Eriksson and David Fenyö Abstract The success of mass spectrometry based proteomics depends on efficient methods for data analysis. These methods require a detailed understanding of the information
More information85. Geo Processing Mineral Liberation Data
Research Center, Pori / Pertti Lamberg 15023-ORC-J 1 (23) 85. Geo Processing Mineral Liberation Data 85.1. Introduction The Mineral Liberation Analyzer, MLA, is an automated mineral analysis system that
More informationLast updated: Copyright
Last updated: 2012-08-20 Copyright 2004-2012 plabel (v2.4) User s Manual by Bioinformatics Group, Institute of Computing Technology, Chinese Academy of Sciences Tel: 86-10-62601016 Email: zhangkun01@ict.ac.cn,
More informationMass spectrometry has been used a lot in biology since the late 1950 s. However it really came into play in the late 1980 s once methods were
Mass spectrometry has been used a lot in biology since the late 1950 s. However it really came into play in the late 1980 s once methods were developed to allow the analysis of large intact (bigger than
More informationAgilent All Ions MS/MS
Agilent All Ions MS/MS Workflow Overview A Determine fragment ions for LC/MS Quant method B Develop final Quant method Develop LC/MS Qualitative Analysis method Process data with Find by Formula Build
More informationHigh-Throughput Protein Quantitation Using Multiple Reaction Monitoring
High-Throughput Protein Quantitation Using Multiple Reaction Monitoring Application Note Authors Ning Tang, Christine Miller, Joe Roark, Norton Kitagawa and Keith Waddell Agilent Technologies, Inc. Santa
More informationM E R C E R W I N WA L K T H R O U G H
H E A L T H W E A L T H C A R E E R WA L K T H R O U G H C L I E N T S O L U T I O N S T E A M T A B L E O F C O N T E N T 1. Login to the Tool 2 2. Published reports... 7 3. Select Results Criteria...
More informationOECD QSAR Toolbox v.3.3. Step-by-step example of how to build a userdefined
OECD QSAR Toolbox v.3.3 Step-by-step example of how to build a userdefined QSAR Background Objectives The exercise Workflow of the exercise Outlook 2 Background This is a step-by-step presentation designed
More informationAgilent MassHunter Quantitative Data Analysis
Agilent MassHunter Quantitative Data Analysis Presenters: Howard Sanford Stephen Harnos MassHunter Quantitation: Batch Table, Compound Information Setup, Calibration Curve and Globals Settings 1 MassHunter
More informationApplication Note. U. Heat of Formation of Ethyl Alcohol and Dimethyl Ether. Introduction
Application Note U. Introduction The molecular builder (Molecular Builder) is part of the MEDEA standard suite of building tools. This tutorial provides an overview of the Molecular Builder s basic functionality.
More informationGAS CHROMATOGRAPHY MASS SPECTROMETRY. Pre-Lab Questions
GAS CHROMATOGRAPHY MASS SPECTROMETRY Pre-Lab Questions Questions to be answered before doing the experiment. The answers are due at the beginning of each experiment without exception (the questions are
More informationProtocol. Product Use & Liability. Contact us: InfoLine: Order per fax: www:
Protocol SpikeTides Sets SpikeTides Sets_L heavy SpikeMix SpikeMix_L heavy Peptide Sets for relative quantification of Proteins in Mass Spectrometry Based Assays Contact us: InfoLine: +49-30-6392-7878
More informationSpectronaut Pulsar. User Manual
Spectronaut Pulsar User Manual 1 General Information... 6 1.1 Computer System Requirements... 6 1.2 Scope of Spectronaut Software... 6 1.3 Spectronaut Pulsar... 6 1.4 Spectronaut Release Features... 7
More informationDownloading GPS Waypoints
Downloading Data with DNR- GPS & Importing to ArcMap and Google Earth Written by Patrick Florance & Carolyn Talmadge, updated on 4/10/17 DOWNLOADING GPS WAYPOINTS... 1 VIEWING YOUR POINTS IN GOOGLE EARTH...
More informationSite-specific Identification of Lysine Acetylation Stoichiometries in Mammalian Cells
Supplementary Information Site-specific Identification of Lysine Acetylation Stoichiometries in Mammalian Cells Tong Zhou 1, 2, Ying-hua Chung 1, 2, Jianji Chen 1, Yue Chen 1 1. Department of Biochemistry,
More informationWorkflow concept. Data goes through the workflow. A Node contains an operation An edge represents data flow The results are brought together in tables
PROTEOME DISCOVERER Workflow concept Data goes through the workflow Spectra Peptides Quantitation A Node contains an operation An edge represents data flow The results are brought together in tables Protein
More informationOECD QSAR Toolbox v.4.1. Step-by-step example for building QSAR model
OECD QSAR Toolbox v.4.1 Step-by-step example for building QSAR model Background Objectives The exercise Workflow of the exercise Outlook 2 Background This is a step-by-step presentation designed to take
More informationLECTURE-13. Peptide Mass Fingerprinting HANDOUT. Mass spectrometry is an indispensable tool for qualitative and quantitative analysis of
LECTURE-13 Peptide Mass Fingerprinting HANDOUT PREAMBLE Mass spectrometry is an indispensable tool for qualitative and quantitative analysis of proteins, drugs and many biological moieties to elucidate
More informationNature Methods: doi: /nmeth Supplementary Figure 1. Fragment indexing allows efficient spectra similarity comparisons.
Supplementary Figure 1 Fragment indexing allows efficient spectra similarity comparisons. The cost and efficiency of spectra similarity calculations can be approximated by the number of fragment comparisons
More informationQuantitation of High Resolution MS Data Using UNIFI: Acquiring and Processing Full Scan or Tof-MRM (Targeted HRMS) Datasets for Quantitative Assays
: Acquiring and Processing Full Scan or Tof-MRM (Targeted HRMS) Datasets for Quantitative Assays Mark Wrona, Jayne Kirk, and Yun Alelyunas Waters Corporation, Milford, MA, USA APPLICATION BENEFITS Ability
More information41. Sim Reactions Example
HSC Chemistry 7.0 41-1(6) 41. Sim Reactions Example Figure 1: Sim Reactions Example, Run mode view after calculations. General This example contains instruction how to create a simple model. The example
More informationImproved Throughput and Reproducibility for Targeted Protein Quantification Using a New High-Performance Triple Quadrupole Mass Spectrometer
Improved Throughput and Reproducibility for Targeted Protein Quantification Using a New High-Performance Triple Quadrupole Mass Spectrometer Reiko Kiyonami, Mary Blackburn, Andreas FR Hühme: Thermo Fisher
More informationQuantitation of a target protein in crude samples using targeted peptide quantification by Mass Spectrometry
Quantitation of a target protein in crude samples using targeted peptide quantification by Mass Spectrometry Jon Hao, Rong Ye, and Mason Tao Poochon Scientific, Frederick, Maryland 21701 Abstract Background:
More informationFigure S1. Interaction of PcTS with αsyn. (a) 1 H- 15 N HSQC NMR spectra of 100 µm αsyn in the absence (0:1, black) and increasing equivalent
Figure S1. Interaction of PcTS with αsyn. (a) 1 H- 15 N HSQC NMR spectra of 100 µm αsyn in the absence (0:1, black) and increasing equivalent concentrations of PcTS (100 µm, blue; 500 µm, green; 1.5 mm,
More informationElectric Fields and Equipotentials
OBJECTIVE Electric Fields and Equipotentials To study and describe the two-dimensional electric field. To map the location of the equipotential surfaces around charged electrodes. To study the relationship
More informationComputer simulation of radioactive decay
Computer simulation of radioactive decay y now you should have worked your way through the introduction to Maple, as well as the introduction to data analysis using Excel Now we will explore radioactive
More informationIncuCyte ZOOM NeuroTrack Fluorescent Processing
IncuCyte ZOOM NeuroTrack Fluorescent Processing The NeuroTrack TM Software Module (Cat No 9600-0011) is used to measure the processes of neurons in monoculture or with fluorescent labeling in co-culture.
More informationPeptide Mass Fingerprinting (PMF) Data Acquisition Using the Voyager DE- PRO Database Search with PMF Data using Ms-Fit
Peptide Mass Fingerprinting (PMF) Data Acquisition Using the Voyager DE- PRO Introduction page 1 Sample preparation (ZipTip) page 1 Data acquisition using the Voyager DE Pro page 5 Resolution and mass
More informationTutorial. Getting started. Sample to Insight. March 31, 2016
Getting started March 31, 2016 Sample to Insight CLC bio, a QIAGEN Company Silkeborgvej 2 Prismet 8000 Aarhus C Denmark Telephone: +45 70 22 32 44 www.clcbio.com support-clcbio@qiagen.com Getting started
More informationX!TandemPipeline (Myosine Anabolisée) validating, filtering and grouping MSMS identifications
X!TandemPipeline 3.3.3 (Myosine Anabolisée) validating, filtering and grouping MSMS identifications Olivier Langella and Benoit Valot langella@moulon.inra.fr; valot@moulon.inra.fr PAPPSO - http://pappso.inra.fr/
More informationAnalyst Software. Automatic Optimization Tutorial
This document is provided to customers who have purchased AB Sciex equipment to use in the operation of such AB Sciex equipment. This document is copyright protected and any reproduction of this document
More informationLigand Scout Tutorials
Ligand Scout Tutorials Step : Creating a pharmacophore from a protein-ligand complex. Type ke6 in the upper right area of the screen and press the button Download *+. The protein will be downloaded and
More informationGeodatabases and ArcCatalog
Geodatabases and ArcCatalog Prepared by Francisco Olivera, Ph.D. and Srikanth Koka Department of Civil Engineering Texas A&M University February 2004 Contents Brief Overview of Geodatabases Goals of the
More informationHR/AM Targeted Peptide Quantification on a Q Exactive MS: A Unique Combination of High Selectivity, High Sensitivity, and High Throughput
HR/AM Targeted Peptide Quantification on a Q Exactive MS: A Unique Combination of High Selectivity, High Sensitivity, and High Throughput Yi Zhang 1, Zhiqi Hao 1, Markus Kellmann 2 and Andreas FR. Huhmer
More informationYou w i ll f ol l ow these st eps : Before opening files, the S c e n e panel is active.
You w i ll f ol l ow these st eps : A. O pen a n i m a g e s t a c k. B. Tr a c e t h e d e n d r i t e w i t h t h e user-guided m ode. C. D e t e c t t h e s p i n e s a u t o m a t i c a l l y. D. C
More informationPC235: 2008 Lecture 5: Quantitation. Arnold Falick
PC235: 2008 Lecture 5: Quantitation Arnold Falick falickam@berkeley.edu Summary What you will learn from this lecture: There are many methods to perform quantitation using mass spectrometry (any method
More informationSIERRA ANALYTICS, INC. Version Polymerix Software User Manual
SIERRA ANALYTICS, INC. Version 3.0.0 Polymerix Software User Manual V E R S I O N 3.0.0 M A R C H 2013 Polymerix Software User Manual Copyright 2010 to 2013 Sierra Analytics, Inc. 5815 Stoddard Road, Suite
More informationMAGNETITE OXIDATION EXAMPLE
HSC Chemistry 7.0 1 MAGNETITE OXIDATION EXAMPLE Pelletized magnetite (Fe 3 O 4 ) ore may be oxidized to hematite (Fe 2 O 3 ) in shaft furnace. Typical magnetite content in ore is some 95%. Oxidation is
More informationSpectrum-to-Spectrum Searching Using a. Proteome-wide Spectral Library
MCP Papers in Press. Published on April 30, 2011 as Manuscript M111.007666 Spectrum-to-Spectrum Searching Using a Proteome-wide Spectral Library Chia-Yu Yen, Stephane Houel, Natalie G. Ahn, and William
More informationMERGING (MERGE / MOSAIC) GEOSPATIAL DATA
This help guide describes how to merge two or more feature classes (vector) or rasters into one single feature class or raster dataset. The Merge Tool The Merge Tool combines input features from input
More informationBioanalytical Chem: 4590: LC-MSMS of analgesics LC-MS Experiment Liquid Chromatography Mass Spectrometry (LC/MS)
Liquid Chromatography Mass Spectrometry (LC/MS) Prelab Questions: Questions to be answered before doing the experiment. The answers are due at the beginning of each experiment without exception (the questions
More informationCreate Satellite Image, Draw Maps
Create Satellite Image, Draw Maps 1. The goal Using Google Earth, we want to create and import a background file into our Adviser program. From there, we will be creating paddock boundaries. The accuracy
More informationLearning ArcGIS: Introduction to ArcCatalog 10.1
Learning ArcGIS: Introduction to ArcCatalog 10.1 Estimated Time: 1 Hour Information systems help us to manage what we know by making it easier to organize, access, manipulate, and apply knowledge to the
More informationData Structures & Database Queries in GIS
Data Structures & Database Queries in GIS Objective In this lab we will show you how to use ArcGIS for analysis of digital elevation models (DEM s), in relationship to Rocky Mountain bighorn sheep (Ovis
More informationPhysical Chemistry II Laboratory
Kuwata Spring 2003 Physical Chemistry II Laboratory The Rovibrational Spectra of H 35 Cl and H 37 Cl Using FTIR Write-Up Due Date: Thursday, April 17 (You may record spectra and write your reports in teams
More informationChemical Labeling Strategy for Generation of Internal Standards for Targeted Quantitative Proteomics
Chemical Labeling Strategy for Generation of Internal Standards for Targeted Quantitative Proteomics mtraq Reagents Triplex Christie Hunter, Brian Williamson, Marjorie Minkoff AB SCIEX, USA The utility
More informationAgilent MassHunter Profinder: Solving the Challenge of Isotopologue Extraction for Qualitative Flux Analysis
Agilent MassHunter Profinder: Solving the Challenge of Isotopologue Extraction for Qualitative Flux Analysis Technical Overview Introduction Metabolomics studies measure the relative abundance of metabolites
More informationThe Quantizing functions
The Quantizing functions What is quantizing? Quantizing in its fundamental form is a function that automatically moves recorded notes, positioning them on exact note values: For example, if you record
More informationThe Agilent 6495 Triple Quadrupole LC/MS: Peptide Quantitation Performance
The Agilent 495 Triple Quadrupole LC/MS: Peptide Quantitation Performance Technical Overview Introduction Sample complexity and the low concentration of certain biomarkers are the major challenges encountered
More informationHEC-HMS Lab 2 Using Thiessen Polygon and Inverse Distance Weighting
HEC-HMS Lab 2 Using Thiessen Polygon and Inverse Distance Weighting Created by Venkatesh Merwade (vmerwade@purdue.edu) Learning outcomes The objective of this lab is to learn how to input data from multiple
More informationISIS/Draw "Quick Start"
ISIS/Draw "Quick Start" Click to print, or click Drawing Molecules * Basic Strategy 5.1 * Drawing Structures with Template tools and template pages 5.2 * Drawing bonds and chains 5.3 * Drawing atoms 5.4
More informationv WMS Tutorials GIS Module Importing, displaying, and converting shapefiles Required Components Time minutes
v. 11.0 WMS 11.0 Tutorial Importing, displaying, and converting shapefiles Objectives This tutorial demonstrates how to import GIS data, visualize it, and convert it into WMS coverage data that could be
More informationOECD QSAR Toolbox v.4.1
OECD QSAR Toolbox v.4.1 Step-by-step example on how to predict the skin sensitisation potential approach of a chemical by read-across based on an analogue approach Outlook Background Objectives Specific
More informationLab 1 Uniform Motion - Graphing and Analyzing Motion
Lab 1 Uniform Motion - Graphing and Analyzing Motion Objectives: < To observe the distance-time relation for motion at constant velocity. < To make a straight line fit to the distance-time data. < To interpret
More informationmzmatch Excel Template Tutorial
mzmatch Excel Template Tutorial Installation & Requirements Installation The template may be used to process mzmatch output text files without additional installations or add-ins. Microsoft Excel 2007
More informationDISCLAIMER. Some General Comments on this Workbook. How to Use This Workbook. Peptide-MS-Calc.xls 1
Peptide-MS-Calc.xls 1 DISCLAIMER This workbook was written using Excel X on Mac S X. Whilst it will probably work on recent versions of Excel for windows, you may experience some problems. If you benefit
More informationInstructions for Mapping 2011 Census Data
Instructions for Mapping 2011 Census Data To map 2011 census data, you must download the census boundary files and the census data separately, then join the two files in ArcMap. In this guide, we will
More informationGeodatabases and ArcCatalog
Geodatabases and ArcCatalog Francisco Olivera, Ph.D., P.E. Srikanth Koka Lauren Walker Aishwarya Vijaykumar Keri Clary Department of Civil Engineering April 21, 2014 Contents Geodatabases and ArcCatalog...
More informationIntroduction to Spark
1 As you become familiar or continue to explore the Cresset technology and software applications, we encourage you to look through the user manual. This is accessible from the Help menu. However, don t
More informationProtein Deconvolution Version 2.0
Thermo Protein Deconvolution Version 2.0 User Guide XCALI-97414 Revision A August 2012 2012 Thermo Fisher Scientific Inc. All rights reserved. ReSpect is a trademark of Positive Probability Ltd. Xcalibur
More informationv Prerequisite Tutorials GSSHA WMS Basics Watershed Delineation using DEMs and 2D Grid Generation Time minutes
v. 10.1 WMS 10.1 Tutorial GSSHA WMS Basics Creating Feature Objects and Mapping Attributes to the 2D Grid Populate hydrologic parameters in a GSSHA model using land use and soil data Objectives This tutorial
More informationOECD QSAR Toolbox v.3.3. Step-by-step example of how to build and evaluate a category based on mechanism of action with protein and DNA binding
OECD QSAR Toolbox v.3.3 Step-by-step example of how to build and evaluate a category based on mechanism of action with protein and DNA binding Outlook Background Objectives Specific Aims The exercise Workflow
More informationWMS 9.0 Tutorial GSSHA Modeling Basics Infiltration Learn how to add infiltration to your GSSHA model
v. 9.0 WMS 9.0 Tutorial GSSHA Modeling Basics Infiltration Learn how to add infiltration to your GSSHA model Objectives This workshop builds on the model developed in the previous workshop and shows you
More informationTandem MS = MS / MS. ESI-MS give information on the mass of a molecule but none on the structure
Tandem MS = MS / MS ESI-MS give information on the mass of a molecule but none on the structure In tandem MS (MSMS) (pseudo-)molecular ions are selected in MS1 and fragmented by collision with gas. collision
More informationLab 1: Dynamic Simulation Using Simulink and Matlab
Lab 1: Dynamic Simulation Using Simulink and Matlab Objectives In this lab you will learn how to use a program called Simulink to simulate dynamic systems. Simulink runs under Matlab and uses block diagrams
More informationOECD QSAR Toolbox v.3.3
OECD QSAR Toolbox v.3.3 Step-by-step example on how to predict the skin sensitisation potential of a chemical by read-across based on an analogue approach Outlook Background Objectives Specific Aims Read
More informationPurdue-UAB Botanicals Center for Age- Related Disease
Purdue-UAB Botanicals Center for Age- Related Disease MALDI-TOF Mass Spectrometry Fingerprinting Technique Landon Wilson MALDI-TOF mass spectrometry is an advanced technique for rapid protein identification
More information