Identification of Serum Protein Biomarkers for Autistic Spectrum Disorder. Melissa Butkiewicz

Save this PDF as:
 WORD  PNG  TXT  JPG

Size: px
Start display at page:

Download "Identification of Serum Protein Biomarkers for Autistic Spectrum Disorder. Melissa Butkiewicz"

Transcription

1 Identification of Serum Protein Biomarkers for Autistic Spectrum Disorder by Melissa Butkiewicz

2 Clarkson University Identification of Serum Protein Biomarkers for Autistic Spectrum Disorder A Thesis Proposal by Melissa Butkiewicz Department of Chemistry & Biomolecular Science Mentor: Dr. Costel Darie 3/12/2010

3 Abstract: Autism spectrum disorder (ASD) is a developmental disorder with no known etiology. In the United States one in 150 children are diagnosed with ASD, making ASD as prevalent as Alzheimer s disease. Identification of ASD in a child is usually performed by a child psychologist. However, so far, there are no biochemical means to identify ASD in the early stages of children. Therefore, using serum biomarkers for early detection of ASD in children will help diagnosis of ASD in its early stages, when behavioral therapy may help treat ASD. Identification of ASD serum biomarkers could be done with common proteomic analyses. In our study, we will use gel electrophoresis and mass spectrometry in a proteomics approach to identify serum biomarkers in ASD that will hopefully lead to increased early diagnosis of ASD through biochemical approaches and point to additional causes to ASD. Introduction: Proteomics is a field that combines the biochemical separation of protein samples and their identification by mass spectrometry. Classical proteomics involves separation of the protein samples by SDS-PAGE and identification of those proteins or fractions of proteins by mass spectrometry. Mass spectrometry (MS) is becoming one the leading tools in protein identification and characterization. Every mass spectrometer contains an ion source, a mass analyzer and a detector. Based on the ion source, there are two types of mass spectrometer: Matrix-Assisted Laser Desorption Ionization mass spectrometer (MALDI-MS) and electrospray ionization mass spectrometer (ESI-MS). When a liquid chromatography (LC or an HPLC) system is coupled online with a MS, the combination is LC-MS or LC-MS/MS. Although different in principle, MALDI-MS and LC-MS complement each other. The steps used to identify proteins via mass spectrometry are: 1) sample fractionation and protein digestion, 2) separation of the peptide mixture by LC-MS/MS and 3) identification of proteins upon data analysis. As previously mentioned, in the simplest case, sample fractionation involves separation of a protein mixture by SDS-PAGE; however, usually combination of more that one biochemical fractionation approaches are used in a proteomics experiment. For example, the classical 2D-PAGE involves separation of the protein sample by isoelectric focusing in the first dimension and SDS-PAGE in the second dimension. Blue Native PAGE (BN-PAGE) separates protein complexes based on external charge induced by Coomassie dye and according to their molecular mass. This method has long been used to analyze protein-protein interactions and protein complexes from organelles [6]. Separation of protein complexes from the BN-PAGE lane in a second dimension SDS-PAGE may reveal partners of a particular protein. BN-PAGE experiments may provide information about the size, number, subunit composition, stoichiometry and relative abundance of these protein complexes. Functional proteomics involves specialized proteomics or sub-proteomics such as separation and identification of the phosphorylated proteins (phospho-proteomics), glycosylated proteins

4 (glycol-proteomics) or protein-protein interactions (protein interactomics). When proteomes from two different conditions are compared (e.g. serum samples from patients with a disease or disorder and from normal subjects), the proteins that are detected in the sera of patients with a disease/disorder but that are not in the sera of normal subsets (and vice-versa) are named serum biomarkers. Successful biomarkers for diagnosis and prognosis have been identified for a wide variety of diseases, from malignant tumors such as breast prostate, ovarian, colon cancer to benign tumors. Identification of biomarkers involves use of the standard proteomics approaches mentioned above. Unfortunately, these approaches can be inconsistent, time-consuming, and expensive. Therefore, the development of alternative methods for the identification could efficiently reduce the number of people with diseases by providing early diagnosis. The need for early diagnostic tests and biomarkers for ASD is in high demand and could reduce the number of children with this disorder [5]. Our specific aim is to test a new approach for biomarker discovery. We plan to separate serum samples from normal patients and patients with ASD by BN-PAGE, cut the bands that are stained differently in each condition, digest the samples with trypsin, extract the peptides and analyze them by LC-MS/MS. Compared to previous methods used to study protein-protein interactions, there are several advantages of BN-PAGE for studying protein-protein interactions: 1) separation of protein complexes takes place under native conditions so even the transient interactions between proteins may be identified, 2) the method may simultaneously analyze association into- or dissociation form protein complexes of particular proteins as a result of disease progression, 3) by combining BN-PAGE with LC-MS/MS, both structural and functional information may be obtained (source). Combination of BN-PAGE and mass spectrometry to study protein complexes from the sera of patients with ASD also has the potential to be applied to other proteomics-based analyses of protein-protein interactions such as serum or plasma from normal patients and patients suffering with different diseases, for both diagnostic and prognostic purposes. Background: As we enter the 21 st century is it clear that biomedical research is one of the fastest growing fields in the world. Research has lead to treatments for diseases, tolerance of terminal viruses such as AIDS, and cancer treatments. Disorders such as maniac depression/bipolar disorder, obsessive compulsive disorder and the early stages of Alzheimer s disease have benefited greatly from biomedical research. Although research has answered many medical demands, one solution remains unknown. Autism Spectrum Disorder is one of the most common disorders among humans, yet so little is known about the disorder besides behavioral evidence. Approximately 1 in 110 children are diagnosed with autism [2], making the disorder as prevalent as Alzheimer s disease among the human population [1]. Autism spectrum disorder (ASD) is a disorder of brain function impairing the ability of a child to interact socially, communicate, learning languages, and imaginative play. As defined by the

5 DSM-IV classification system, ASD is diagnosed by lack of social or emotional reciprocity, inflexible adherence to specific, nonfunctional routines or rituals, delay or lack of the development of spoken language, marked impairment in the ability to initiate or sustain a conversation with others, and many other specific behavioral traits. The majority of children suffering from ASD are diagnosed between birth and 36 months of age [2]. The diagnosis of ASD proves to be a problem in our society. It is both an economical and social hardship for families that were not expecting or aware of the possibility of having an autistic child. With an estimated 1.5 million Americans suffering from ASD, it is evident that more research is needed to identify the neurological source of ASD [5]. Before a solution can be established, it is imperative that scientists can identify the disorder in forms other than observed behavior or psychological testing. Advances in biochemical research have led to identification of diseases and disorders via biomarkers. Biomarkers are indicators used in the human body to detect or measure the progress of a disease or disorder. Biomarkers have been used to detect cancer, and can help reach a better understanding of a disease or disorder. Based on previous ASD research, it has been shown that there are differences in the protein patterns in the serum samples from patients with ASD, compared with the control samples. In addition, these proteins correlate between samples from ASD patients [8]. Identifying these proteins as biomarkers can aid in the early detection of ASD in children. Therefore, combination of two dimensional gel electrophoresis (BN-PAGE and SDS-PAGE) and mass spectrometry in a proteomics approach can lead to identification of proteins that are possibly serum biomarkers for ASD. Preliminary Research: During our literature search, we identified a published paper whose authors looked for serum biomarkers in patients with ASD, using MALDI-MS. We then asked the authors if it is possible to re-analyze the same samples using our approaches. Our wish was granted and we just received the samples. In published work [8], it is evident that in the MALDI-MS spectra, there is a difference between patients with ASD, when compared with the controls (Figure 1). Figure 1: Representative example of a 1,000 12,00 Da patient MALDI-MS spectra of two ASD/ADHD(+), two ASD/ADHD(-) patients and two controls. The ASD/ADHD patients show a clear peak with a m/z ratio of kda. Additional peaks were identified with at 5.15 and 4.40 kda (data not shown).

6 The most significant difference in the MALDI-MS spectra was observed at kda, providing evidence that there is a difference in the protein pattern in the sera of patients with ASD patients, compared with the normal control subjects. The peak was observed only in the serum samples from ASD patients, but not in the normal, control subjects, suggesting that this peak contain a protein or several proteins that could be a serum biomarker or serum biomarkers for early detection of ASD. However, the peak at kda identified by MALDI-MS was not sequenced and the identity of the protein(s) that correspond to this peak is unknown. Therefore, identification of the protein(s) that is (are) responsible for this peak will help elucidating the biochemical differences between the sera from patients with ASD and their normal matched controls. The discovery of a biomarker for ASD can lead to quicker and more efficient clinical diagnoses of ASD. In our experiments, we plan to use SDS-PAGE and LC-MS/MS to specifically look for proteins with the molecular weigh between 8-12 kda, hoping to identify the differences between the serum samples from ASD patients and normal subjects, observed as a peak at kda. We also plan to combine BN-PAGE (1D) and SDS-PAGE (2D) with LC-MS/MS to search for differences between the serum samples from ASD patients and normal subjects at the protein complex level. We do have the expertise to perform the proposed experiments. We do have expertise in both analysis of protein complexes and protein-protein interactions BN-PAGE (1D) and SDS-PAGE (2D) (or only BN-PAGE 1D only), and protein identification and quantitation using LC-MS/MS. Example of the work performed in our lab show that we will be able to succeed in our proposed work. We will describe some of our results that reflect our expertise in mass spectrometry and proteomics, which will allow us to be successful in our proposal. We will also describe some results using new approaches for qualitative identification and label-free quantitation of proteins at the protein complex level. Finally, we will describe preliminary data where serum samples from patients with various forms of cancer and from normal subjects were separated by BN- PAGE. Our preliminary data using mass spectrometry and proteomics demonstrate that our lab will be able to succeed with the specific aims that we propose. Results that reflect our expertise in mass spectrometry and proteomics: 1. Peptide mass fingerprinting and protein identification using MALDI-MS and LC- MS/MS. Figure 2 shows examples of MALDI-MS and LC-MS/MS analyses of peptide mixtures that led to identification of proteins. The proteins were separated on SDS-PAGE and the gel pieces were excised and digested with trypsin, followed by extraction and concentration of the peptide mixture. The peptide mixture was then analyzed by MALDI-MS or LC-MS/MS and the results were submitted to the Mascot database for protein identification.

7 We were able to rapidly identify proteins using both MALDI-MS and LC-MS/MS systems, demonstrating that our expertise in mass spectrometry in general and proteomics in particular is more than adequate for performing the proposed work. Figure 2: A: MALDI-MS analysis of a peptide mixture. The peaks marked with letters alpha, beta or gamma correspond to peptides from three different proteins. The greater the identification of peaks that correspond to peptides from same protein, the higher the protein coverage of that identified protein and the higher the chances for correct identification. B: LC- MS/MS analysis of a peptide mixture. The LC-MS/MS experiment involves fractionation of the peptide mixture prior to MS analysis by liquid chromatography (LC), and the recorded chromatogram is named total ion current (TIC). The TIC contains many singly and multiply charged peaks that correspond to peptides, and are visible as MS mass spectra. In the MS spectra, some of the high intensity peaks are selected for fragmentation and each produces a MS/MS spectrum that contains sequence information about a protein 2. Analysis of stable and transient protein interactions using LC-MS/MS. Although we have extensive experience using MALDI-MS and LC-MS/MS, our expertise is not limited only to protein identification and analysis of their post-translational modifications (PTMs), but it also extends to analysis of both stable and transient protein-protein interactions. Examples of analysis of subunit composition (and molecular mass) of a homo-complex and a heterocomplex are shown in Figure 4. For this, we separated a mammalian cell lysate by Blue Native-PAGE (BN- PAGE; separates protein complexes under native conditions and according to their molecular weight), cut the bands according to their molecular mass in the initial gel, digested the proteins and analyzed the peptide mixture by LC-MS/MS, followed by data analysis. Once a subunit of a particular protein complex with a specified mass was identified, we looked for additional subunits in the same gel band and further compared these data with the current literature in terms of subunit composition, mass and protein interactions. In these experiments, we identified both homo- and heterocomplexes. Among putative homocomplexes, we identified Valosin-containing

8 protein (89 kda protein), a homohexamer of 540 kda [7]. In our experiments, we identified this protein in band B4 (Figure 4; Mascot scores 1790), at a molecular mass of kda. Among the heterocomplexes identified by BN-PAGE and LC-MS/MS was proteasome (prosome). This is a hetero-28-mer (25) alpha-beta protein complex with a molecular mass of 700 kda. In our experiments, we identified five different alpha subunits: alpha 1, (Mascot score 80), alpha 3 (Mascot score 75), alpha 4 (Mascot score 56), alpha 6 (Mascot score 183) and alpha 7 (Mascot score 63) and four different beta subunits: beta 1 (Mascot score 41), beta 4 (Mascot score 123), beta 5 (Mascot score 118) and beta 6 (Mascot score 92) in a single experiment. Our experimentally determined mass of the proteasome was kda (detected in bands B1 and B2), in agreement with its calculated theoretical mass of 700 kda. Examples of MSMS spectra of identified peptides that were part of either a homocomplex (Valosin-containing protein, peak (2+), peptide EDEEESLNEVGYDDIGGCR) or a heterocomplex (Proteasome subunit alpha 6, peak (2+), peptide AINQGGLTSVAVR and Proteasome subunit beta 6, peak (2+), peptide LAAIQESGVER) are shown in Figure 3. Figure 3: Analysis of the cell lysates from unstimulated and stimulated cells by BN-PAGE and LC-MS/MS. A: The cell lysates were separated by BN-PAGE and the gel bands B1-B8 were excised, digested by trypsin, analyzed by LC-MS/MS and submitted to the Mascot search engine for protein identification. B: MS/MS spectra of peptides that were part of Proteasome alpha 6 (a) and Proteasome beta 6 (b) and Valosin-containing protein (c). These data suggest that the combination of BN-PAGE and LC-MS/MS is a powerful tool for determining the mass of a particular protein complex and the identity of its subunit composition. These data also demonstrate that our expertise in mass spectrometry is not limited only to the analysis of proteins and identification of their identity and their PTMs, but it extends to the analysis of stable (Figure 3) or transient (data not shown) protein-protein interactions.

9 We also analyzed the serum samples from patients with various types of cancer and from normal subjects by BN-PAGE. Example of such separation is shown in figure 4. Here, we separated serum samples from normal male (Figure 4A, #1-9) and female (Figure 4B, #1-9) subjects, and from male (Figure 4A, #10-19) and female (Figure 4B, #10-19) patients with cancer. Figure 4: BN-PAGE of serum samples from normal male (A, #1-9) and female (B, #1-9) subjects, and from male (A, #10-19) and female (B, #10-19) patients with cancer. The gels were stained with Coomassie Brilliant Blue. As demonstrated by our preliminary data, overall, we have the means and expertise to perform the proposed experiments and believe that we will be successful in completing our proposed work. Research Methodology: The goal of our proposed experiments is to identify proteins that specifically associate into- or dissociate from- protein complexes in sera of the patients with ASD. We will also obtain quantitative information about the relative abundances of these proteins and protein complexes. The proposed studies have been designed based on the hypothesis that protein complexes specific to ASD are formed and that deciphering the composition of these complexes will reveal significant insights about mechanisms of ASD. The main strategy for these experiments is to separate the serum samples from patients with ASD and from their matched controls by BN-PAGE or by BN-PAGE and SDS-PAGE, excise the gel bands/spots that are differently stained, digest the samples, extract the peptide mixtures, analyze them by LC-MS/MS, perform the database search, followed by data analysis. The workflow of our proposed research is summarized in Figure 5. The first step that we will perform is to optimize the running conditions for BN-PAGE (1D) and SDS-PAGE (2D) of the serum samples. Initially, we will separate serum samples from normal subjects from our tissue repository. Specifically, we will optimize the running conditions that will produce the best protein load/gel lane in both BN-PAGE (1D) and SDS-PAGE (2D). Once

10 our running conditions will be optimized, we will perform the same experiments, except that the serum samples will be depleted from immunoglobulins G (IgGs), the second most abundant protein after serum albumin. Once we will have the running conditions optimized, we will repeat these steps with serum samples from patients with ASD and from their normal matched controls. Figure 5: The workflow of our proposed experiments. The serum samples witll be separated by BN-PAGE (1D) and then SDS-PAGE (2D, not shown) and then the proteins will be digested, analized by LC- MS/MS for protein identification and quantitation, followed by data analysis. Optimization of running conditions will be performed using serum samples from normal subjects. The experiments will then be repeated, with IgG-depleted samples. Once optimized, the experiments will be repeaded in both 1D and 2D, using both undepleted and depleted serum samples from patients with ASD and their normal matched controls. Timeline: Below is the proposed outline for the proposed project. Upon completion of the research, there will be a 3 month span of time where I will be finalizing the thesis paper and preparing the oral presentation. These three months will be enough time to complete the paper and include any last minute results from the spring 2011 semester. Month Stage Goals of Each Stage 1 Initial Research 2 3 Protein Purification Complete Mass Spectrometry Training Perfect Sample Preparation Techniques Begin 2D BN-PAGE (1D) and SDS-PAGE (2D) Analysis Complete the optimization of the sample preparation, complete the 2D PAGE

11 analysis, start analysis using undepleted serum samples. Complete analysis of ASD serum samples Complete the MS analysis of all samples Complete data analysis Complete Rough Draft of Thesis Final Results Thesis Completion Correct Discrepancies between Data Sets Finish Thesis Paper Turn In Thesis Paper and Present Research

12 References: 1. Autism Spectrum Disorders (ASDs). [online article] 2008 October 19 [cited 2010 February 12]; Available from: 2. What is autism? [online article] 2010 [cited 2010 January 10]; Available from: 3. Darie, C., Proteomic Approach to Biomarkers. 2009, Clarkson University. 4. Dass, C., Fundamentals of contemporary mass spectrometry. Wiley-Interscience series on mass spectrometry, ed. D.M. Desiderio and N.M. Nibbering. 2007, Hoboken: John Wiley & Sons Gerlai, J. and R. Gerlai, Autism: a large unmet medical need and a complex research problem. Physiol Behav, (3): p Schagger, H. and G. von Jagow, Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form. Anal Biochem, (2): p Schmidt, W.E., et al., Valosin: isolation and characterization of a novel peptide from porcine intestine. FEBS Lett, (2): p Taurines, R., et al., Serum protein profiling and proteomics in autistic spectrum disorder using magnetic bead-assisted mass spectrometry. Eur Arch Psychiatry Clin Neurosci, 2009.

La Protéomique : Etat de l art et perspectives

La 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

Labeling Technologies for Quantitative Protein Expression Analysis

Labeling Technologies for Quantitative Protein Expression Analysis Innovative Solutions for Quantitative Protein and Biomarker Research Labeling Technologies for Quantitative Protein Expression Analysis Understanding Disease States via Quantitative Protein Expression

More information

Aiping 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 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 information

Proteomics in Practice

Proteomics 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 information

Master course KEMM03 Principles of Mass Spectrometric Protein Characterization. Exam

Master course KEMM03 Principles of Mass Spectrometric Protein Characterization. Exam Exam Master course KEMM03 Principles of Mass Spectrometric Protein Characterization 2010-10-29 kl 08.15-13.00 Use a new paper for answering each question! Write your name on each paper! Aids: Mini calculator,

More information

Introduction to Proteomics 1.0

Introduction 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 information

Using Ontologies in Proteus for Modeling Data Mining Analysis of Proteomics Experiments

Using Ontologies in Proteus for Modeling Data Mining Analysis of Proteomics Experiments Using Ontologies in Proteus for Modeling Data Mining Analysis of Proteomics Experiments Mario Cannataro, Pietro Hiram Guzzi, Tommaso Mazza, and Pierangelo Veltri University Magna Græcia of Catanzaro, 88100

More information

Biomarker Discovery through the use of Proteomics Tools. Rama Yakubu

Biomarker Discovery through the use of Proteomics Tools. Rama Yakubu Biomarker Discovery through the use of Proteomics Tools by Rama Yakubu 1 Clarkson University Biomarker Discovery through the use of Proteomics Tools A Thesis Proposal by Rama Yakubu Biomolecular Science

More information

AB 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 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 information

Introduction to Proteomics

Introduction to Proteomics Introduction to Proteomics Åsa Wheelock, Ph.D. Division of Respiratory Medicine & Karolinska Biomics Center asa.wheelock@ki.se In: Systems Biology and the Omics Cascade, Karolinska Institutet, June 9-13,

More information

Introduction to mass spectrometry (MS) based proteomics and metabolomics

Introduction 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 information

Definition of the Measurand: CRP

Definition of the Measurand: CRP A Reference Measurement System for C-reactive Protein David M. Bunk, Ph.D. Chemical Science and Technology Laboratory National Institute of Standards and Technology Definition of the Measurand: Human C-reactive

More information

In-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 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 information

Preprocessing, Management, and Analysis of Mass Spectrometry Proteomics Data

Preprocessing, Management, and Analysis of Mass Spectrometry Proteomics Data Preprocessing, Management, and Analysis of Mass Spectrometry Proteomics Data M. Cannataro, P. H. Guzzi, T. Mazza, and P. Veltri Università Magna Græcia di Catanzaro, Italy 1 Introduction Mass Spectrometry

More information

ProteinScape. Innovation with Integrity. Proteomics Data Analysis & Management. Mass Spectrometry

ProteinScape. 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 information

Pep-Miner: A Novel Technology for Mass Spectrometry-Based Proteomics

Pep-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 information

Building innovative drug discovery alliances. Evotec Munich. Quantitative Proteomics to Support the Discovery & Development of Targeted Drugs

Building innovative drug discovery alliances. Evotec Munich. Quantitative Proteomics to Support the Discovery & Development of Targeted Drugs Building innovative drug discovery alliances Evotec Munich Quantitative Proteomics to Support the Discovery & Development of Targeted Drugs Evotec AG, Evotec Munich, June 2013 About Evotec Munich A leader

More information

Microarray Technology

Microarray Technology Microarrays And Functional Genomics CPSC265 Matt Hudson Microarray Technology Relatively young technology Usually used like a Northern blot can determine the amount of mrna for a particular gene Except

More information

serum protein and A/ G ratio

serum protein and A/ G ratio serum protein and A/ G ratio Blood plasma contains at least 125 individual proteins. Serum ( as contrasted with plasma) is deficient in those coagulation protein which are consumed during the process of

More information

Analysis of proteins

Analysis of proteins Analysis of proteins Western blot Protein seperation (liqiuid chromatography) Mass spectrometry Assaying of protein in... Blood (e.g. viral infections, pregnancy test) Cells Tissue Urin (bladder infection)

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 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 information

Chapter 14. Modeling Experimental Design for Proteomics. Jan Eriksson and David Fenyö. Abstract. 1. Introduction

Chapter 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

Application 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 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 information

Mass Spectrometry Based Proteomics

Mass 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 information

HPLC/MS/MS Analysis of Bitter Acids in Hops and Beer

HPLC/MS/MS Analysis of Bitter Acids in Hops and Beer Application Note Mass Spectrometry HPLC/MS/MS Analysis of Bitter Acids in Hops and Beer Beer represents one of the most widely consumed beverages in the world. Its annual worldwide production, measured

More information

Polyacrylamide gel formation

Polyacrylamide gel formation Part II- Protein Identification PolyAcrylamide Gel Electrophoresis (PAGE) is the best method in protein identification, MW determination, DNA sequencing, protein-protein or protein-dna interaction etc

More information

Brochure More information from http://www.researchandmarkets.com/reports/2172993/

Brochure More information from http://www.researchandmarkets.com/reports/2172993/ Brochure More information from http://www.researchandmarkets.com/reports/2172993/ Proteomics Today. Protein Assessment and Biomarkers Using Mass Spectrometry, 2D Electrophoresis,and Microarray Technology.

More information

Quantitative proteomics using TMT isobaric tags

Quantitative proteomics using TMT isobaric tags Quantitative proteomics using TMT isobaric tags Dr. Andrew Weston NIHR Biomedical Research Centre for Mental Health King's College London Proteomics Unit Institute of Psychiatry 11-13 th May 2010 Introduction

More information

Molecular Cell Biology. Prof. D. Karunagaran. Department of Biotechnology. Indian Institute of Technology Madras

Molecular Cell Biology. Prof. D. Karunagaran. Department of Biotechnology. Indian Institute of Technology Madras Molecular Cell Biology Prof. D. Karunagaran Department of Biotechnology Indian Institute of Technology Madras Module 5 Methods in Cell Biology (Methods to Manipulate Protein, DNA and RNA and Methods to

More information

Retrospective Analysis of a Host Cell Protein Perfect Storm: Identifying Immunogenic Proteins and Fixing the Problem

Retrospective Analysis of a Host Cell Protein Perfect Storm: Identifying Immunogenic Proteins and Fixing the Problem Retrospective Analysis of a Host Cell Protein Perfect Storm: Identifying Immunogenic Proteins and Fixing the Problem Kevin Van Cott, Associate Professor Dept. of Chemical and Biomolecular Engineering Nebraska

More information

ProteinPilot Report for ProteinPilot Software

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 information

Proteomics Workflows & Technologies

Proteomics Workflows & Technologies Proteomics Workflows & Technologies Proteomics "The analysis of the entire PROTEin complement expressed by a genome, or by a cell or tissue type." Wasinger VC et al, Electrophoresis 16 (1995) Proteomics

More information

FUNCTIONAL EEG ANALYZE IN AUTISM. Dr. Plamen Dimitrov

FUNCTIONAL EEG ANALYZE IN AUTISM. Dr. Plamen Dimitrov FUNCTIONAL EEG ANALYZE IN AUTISM Dr. Plamen Dimitrov Preamble Autism or Autistic Spectrum Disorders (ASD) is a mental developmental disorder, manifested in the early childhood and is characterized by qualitative

More information

Effects 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 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 information

Pesticide Analysis by Mass Spectrometry

Pesticide Analysis by Mass Spectrometry Pesticide Analysis by Mass Spectrometry Purpose: The purpose of this assignment is to introduce concepts of mass spectrometry (MS) as they pertain to the qualitative and quantitative analysis of organochlorine

More information

12/6/12. Dr. Sanjeeva Srivastava. IIT Bombay 2

12/6/12. Dr. Sanjeeva Srivastava. IIT Bombay 2 Dr. Sanjeeva Srivastava IIT Bombay Case studies 2DE: Drug treatment in malaria parasite Plasma proteome analysis of SARS An overview of DIGE technique Case study DIGE: Serum proteome analysis of prostate

More information

Laboration 1. Identifiering av proteiner med Mass Spektrometri. Klinisk Kemisk Diagnostik

Laboration 1. Identifiering av proteiner med Mass Spektrometri. Klinisk Kemisk Diagnostik Laboration 1 Identifiering av proteiner med Mass Spektrometri Klinisk Kemisk Diagnostik Sven Kjellström 2014 kjellstrom.sven@gmail.com 0702-935060 Laboration 1 Klinisk Kemisk Diagnostik Identifiering av

More information

Top-down proteomics using 2D electrophoresis

Top-down proteomics using 2D electrophoresis January 20, 2012 BMG744 Top-down proteomics using 2D electrophoresis Helen Kim 934-3880 helenkim@uab.edu Dept of Pharmacology and Toxicology McCallum Building, room 460 http://www.uab.edu/proteomics Jan

More information

Chapter 3. Protein Structure and Function

Chapter 3. Protein Structure and Function Chapter 3 Protein Structure and Function Broad functional classes So Proteins have structure and function... Fine! -Why do we care to know more???? Understanding functional architechture gives us POWER

More information

Isotopes and Mass Spectrometry

Isotopes and Mass Spectrometry PSI AP Chemistry Activity Isotopes and Mass Spectrometry Why? In this activity we will address the questions: Are all atoms of an element identical and how do we know? How can data from mass spectrometry

More information

How Mascot Integra helps run a Core Lab

How Mascot Integra helps run a Core Lab How Mascot Integra helps run a Core Lab 1 Areas where a database can help a core lab Project, experiment and sample tracking Flexibility in experiment design Role based security Automation Custom results

More information

Introduction to Proteomics

Introduction to Proteomics Introduction to Proteomics Why Proteomics? Same Genome Different Proteome Black Swallowtail - larvae and butterfly Biological Complexity Yeast - a simple proteome 6,113 proteins = 344,855 tryptic peptides

More information

MarkerView Software 1.2.1 for Metabolomic and Biomarker Profiling Analysis

MarkerView 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 information

Quantification 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 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 information

Mass Spectra Alignments and their Significance

Mass Spectra Alignments and their Significance Mass Spectra Alignments and their Significance Sebastian Böcker 1, Hans-Michael altenbach 2 1 Technische Fakultät, Universität Bielefeld 2 NRW Int l Graduate School in Bioinformatics and Genome Research,

More information

Spectrum Quality Assessment in Mass Spectrometry Proteomics

Spectrum Quality Assessment in Mass Spectrometry Proteomics Spectrum Quality Assessment in Mass Spectrometry Proteomics 1. Background Rheanna Mainzer Supervised by Dr. Luke Prendergast La Trobe University An important research problem in mass spectrometry is in

More information

Integrated Data Mining Strategy for Effective Metabolomic Data Analysis

Integrated Data Mining Strategy for Effective Metabolomic Data Analysis The First International Symposium on Optimization and Systems Biology (OSB 07) Beijing, China, August 8 10, 2007 Copyright 2007 ORSC & APORC pp. 45 51 Integrated Data Mining Strategy for Effective Metabolomic

More information

Error Tolerant Searching of Uninterpreted MS/MS Data

Error Tolerant Searching of Uninterpreted MS/MS Data Error Tolerant Searching of Uninterpreted MS/MS Data 1 In any search of a large LC-MS/MS dataset 2 There are always a number of spectra which get poor scores, or even no match at all. 3 Sometimes, this

More information

CHROMOSOMES Dr. Fern Tsien, Dept. of Genetics, LSUHSC, NO, LA

CHROMOSOMES Dr. Fern Tsien, Dept. of Genetics, LSUHSC, NO, LA CHROMOSOMES Dr. Fern Tsien, Dept. of Genetics, LSUHSC, NO, LA Cytogenetics is the study of chromosomes and their structure, inheritance, and abnormalities. Chromosome abnormalities occur in approximately:

More information

MASCOT Search Results Interpretation

MASCOT 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 information

Global and Discovery Proteomics Lecture Agenda

Global 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 information

Protein Prospector and Ways of Calculating Expectation Values

Protein Prospector and Ways of Calculating Expectation Values Protein Prospector and Ways of Calculating Expectation Values 1/16 Aenoch J. Lynn; Robert J. Chalkley; Peter R. Baker; Mark R. Segal; and Alma L. Burlingame University of California, San Francisco, San

More information

Advantages of the LTQ Orbitrap for Protein Identification in Complex Digests

Advantages 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 information

Register of Students with Severe Disabilities

Register of Students with Severe Disabilities Department of Education Learners first, connected and inspired Register of Students with Severe Disabilities Department of Education Register of Students with Severe Disabilities 1. Eligibility Criteria

More information

Increasing the Multiplexing of High Resolution Targeted Peptide Quantification Assays

Increasing 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 information

Tutorial for Proteomics Data Submission. Katalin F. Medzihradszky Robert J. Chalkley UCSF

Tutorial 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 information

Study of serum protein electrophoresis in suspected cases of Multiple Myeloma.

Study of serum protein electrophoresis in suspected cases of Multiple Myeloma. Journal homepage: http://www.journalijar.com INTERNATIONAL JOURNAL OF ADVANCED RESEARCH RESEARCH ARTICLE Study of serum protein electrophoresis in suspected cases of Multiple Myeloma. Dr. Dharmishtha N.

More information

Unique Software Tools to Enable Quick Screening and Identification of Residues and Contaminants in Food Samples using Accurate Mass LC-MS/MS

Unique Software Tools to Enable Quick Screening and Identification of Residues and Contaminants in Food Samples using Accurate Mass LC-MS/MS Unique Software Tools to Enable Quick Screening and Identification of Residues and Contaminants in Food Samples using Accurate Mass LC-MS/MS Using PeakView Software with the XIC Manager to Get the Answers

More information

MultiQuant Software 2.0 for Targeted Protein / Peptide Quantification

MultiQuant 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 information

Principles and Applications of Proteomics

Principles and Applications of Proteomics Principles and Applications of Proteomics Why Proteomics? 2-DE Overview Sample preparation 1 st & 2 nd dimension seperation Data Analysis Sample preparation for Mass Spectrometry Mass Spectrometry MALDI-TOF,

More information

The 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 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 information

Interpretation A molecular mass spectrum

Interpretation A molecular mass spectrum Interpretation Mass spectral interpretation is not a trivial process. Presented below are some basic terms and examples designed to provide a background on which to build further knowledge through additional

More information

Introduction to Mass Spectrometry. W.M. Keck Biomedical Mass Spectrometry Lab

Introduction to Mass Spectrometry. W.M. Keck Biomedical Mass Spectrometry Lab Introduction to Mass Spectrometry W.M. Keck Biomedical Mass Spectrometry Lab Moore Health Sciences Library Rooms 1335 & 1337 May 18, 2010 The Keck Mass Spectrometry Lab of the Biomolecular Resource Facility

More information

Identification of Novel Biomarkers of Brain Injury by Integrating Bioinformatics and Mass Spectrometry-based Proteomics

Identification of Novel Biomarkers of Brain Injury by Integrating Bioinformatics and Mass Spectrometry-based Proteomics Identification of Novel Biomarkers of Brain Injury by Integrating Bioinformatics and Mass Spectrometry-based Proteomics Collaborative Study 2 Introduction Brain injury: 1. Non-traumatic Infection Stroke

More information

Methods for Protein Analysis

Methods for Protein Analysis Methods for Protein Analysis 1. Protein Separation Methods The following is a quick review of some common methods used for protein separation: SDS-PAGE (SDS-polyacrylamide gel electrophoresis) separates

More information

Week 9: MS in Space and Proteomics

Week 9: MS in Space and Proteomics Week 9: MS in Space and Proteomics 1 Last Time Detectors Small Molecule Applications, Environmental: (e.g. TWQC) 2 Mass Spectrometry in Space Possibly the coolest application of small molecule MS is in

More information

Unique Software Tools to Enable Quick Screening and Identification of Residues and Contaminants in Food Samples using Accurate Mass LC-MS/MS

Unique Software Tools to Enable Quick Screening and Identification of Residues and Contaminants in Food Samples using Accurate Mass LC-MS/MS Unique Software Tools to Enable Quick Screening and Identification of Residues and Contaminants in Food Samples using Accurate Mass LC-MS/MS Using PeakView Software with the XIC Manager to Get the Answers

More information

Challenges in Computational Analysis of Mass Spectrometry Data for Proteomics

Challenges 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 information

Support vector machine evaluation of peptide identification via mass spectrometry

Support vector machine evaluation of peptide identification via mass spectrometry Support vector machine evaluation of peptide identification via mass spectrometry William Stafford Noble Department of Genome Sciences Department of Computer Science and Engineering University of Washington

More information

Application Note # MT-90 MALDI-TDS: A Coherent MALDI Top-Down-Sequencing Approach Applied to the ABRF-Protein Research Group Study 2008

Application 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 information

TWO DIMENSIONAL DIFFERENTIAL IN-GEL ELECTROPHORESIS- BASED PROTEOMICS OF MALE GAMETES IN RELATION TO

TWO DIMENSIONAL DIFFERENTIAL IN-GEL ELECTROPHORESIS- BASED PROTEOMICS OF MALE GAMETES IN RELATION TO TWO DIMENSIONAL DIFFERENTIAL IN-GEL ELECTROPHORESIS- BASED PROTEOMICS OF MALE GAMETES IN RELATION TO OXIDATIVE STRESS Alaa Hamada, MD., Rakesh Sharma, PhD., Stefan S Du Plessis, PhD., Belinda Willard,

More information

Biopharmaceutical Glycosylation Analysis

Biopharmaceutical 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 information

Functional Data Analysis of MALDI TOF Protein Spectra

Functional Data Analysis of MALDI TOF Protein Spectra Functional Data Analysis of MALDI TOF Protein Spectra Dean Billheimer dean.billheimer@vanderbilt.edu. Department of Biostatistics Vanderbilt University Vanderbilt Ingram Cancer Center FDA for MALDI TOF

More information

FINDING PROTEINS THAT HIT THE MARK PROVEN TRACK-RECORD OF PROTEOMICS EXPERTISE

FINDING PROTEINS THAT HIT THE MARK PROVEN TRACK-RECORD OF PROTEOMICS EXPERTISE FINDING PROTEINS THAT HIT THE MARK PROVEN TRACK-RECORD OF PROTEOMICS EXPERTISE Bioanalytical Services Fit-for-Purpose Assays Biomarker Discovery and Development Proven track-record of proteomics expertise

More information

Statistical Analysis Strategies for Shotgun Proteomics Data

Statistical 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 information

BBSRC TECHNOLOGY STRATEGY: TECHNOLOGIES NEEDED BY RESEARCH KNOWLEDGE PROVIDERS

BBSRC TECHNOLOGY STRATEGY: TECHNOLOGIES NEEDED BY RESEARCH KNOWLEDGE PROVIDERS BBSRC TECHNOLOGY STRATEGY: TECHNOLOGIES NEEDED BY RESEARCH KNOWLEDGE PROVIDERS 1. The Technology Strategy sets out six areas where technological developments are required to push the frontiers of knowledge

More information

Unique Software Tools to Enable Quick Screening and Identification of Residues and Contaminants in Food Samples using Accurate Mass LC-MS/MS

Unique Software Tools to Enable Quick Screening and Identification of Residues and Contaminants in Food Samples using Accurate Mass LC-MS/MS Unique Software Tools to Enable Quick Screening and Identification of Residues and Contaminants in Food Samples using Accurate Mass LC-MS/MS Using PeakView Software with the XIC Manager to Get the Answers

More information

Electrospray Ion Trap Mass Spectrometry. Introduction

Electrospray Ion Trap Mass Spectrometry. Introduction Electrospray Ion Source Electrospray Ion Trap Mass Spectrometry Introduction The key to using MS for solutions is the ability to transfer your analytes into the vacuum of the mass spectrometer as ionic

More information

MRMPilot Software: Accelerating MRM Assay Development for Targeted Quantitative Proteomics

MRMPilot 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 information

SUMMARY. Key words: in-gel digestion, filter plate, LC-MSMS, proteomics.

SUMMARY. Key words: in-gel digestion, filter plate, LC-MSMS, proteomics. J Electrophoresis 2005 ; 49 : 71 [Short Communication] Assessment of filter plates for multi-well in-gel digestion of proteins separated by polyacrylamide gel electrophoresis to identify them with LC-ESI/MSMS

More information

From Kanalstrahlen to Top Down Identification of Biomolecules

From Kanalstrahlen to Top Down Identification of Biomolecules LC-MS: From history to the future From Kanalstrahlen to Top Down Identification of Biomolecules Gunnar Stenhagen Stenhagen Analyslab AB one of the main reasons for writing this book was the hope that it

More information

Milk protein analysis with the Agilent 2100 Bioanalyzer and the Agilent Protein 80 kit

Milk protein analysis with the Agilent 2100 Bioanalyzer and the Agilent Protein 80 kit Milk protein analysis with the Agilent 21 Bioanalyzer and the Agilent Protein 8 kit Application Note Food Analysis Author Rainer Nitsche Agilent Technologies, Inc. Waldbronn, Germany Abstract Protein content

More information

PeptidomicsDB: a new platform for sharing MS/MS data.

PeptidomicsDB: 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 information

prime Innovation with Integrity The multidimensional path to the Proteome Mass Spectrometry

prime Innovation with Integrity The multidimensional path to the Proteome Mass Spectrometry prime The multidimensional path to the Proteome Innovation with Integrity Mass Spectrometry Reach for the Full Potential of Proteomics. Open Your Eyes to PRIME The Proteome is far more complex than was

More information

The Knowledge and Awareness of Autism Spectrum Disorders within the Hispanic Community.

The Knowledge and Awareness of Autism Spectrum Disorders within the Hispanic Community. East Tennessee State University Digital Commons @ East Tennessee State University Undergraduate Honors Theses 5-2012 The Knowledge and Awareness of Autism Spectrum Disorders within the Hispanic Community.

More information

Absolute quantification of low abundance proteins by shotgun proteomics

Absolute quantification of low abundance proteins by shotgun proteomics Absolute quantification of low abundance proteins by shotgun proteomics Dr. Stefanie Wienkoop www.proteomefactory.com In cooperation with: Max-Planck-Institut für Molekulare Pflanzenphysiologie Stable

More information

Mass Spectrometry Signal Calibration for Protein Quantitation

Mass 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 information

The Open2Dprot Proteomics Project for n-dimensional Protein Expression Data Analysis

The Open2Dprot Proteomics Project for n-dimensional Protein Expression Data Analysis The Open2Dprot Proteomics Project for n-dimensional Protein Expression Data Analysis http://open2dprot.sourceforge.net/ Revised 2-05-2006 * (cf. 2D-LC) Introduction There is a need for integrated proteomics

More information

Session 1. Course Presentation: Mass spectrometry-based proteomics for molecular and cellular biologists

Session 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 information

Highly Selective Analysis of Steroid Biomarkers using SelexION Ion Mobility Technology

Highly Selective Analysis of Steroid Biomarkers using SelexION Ion Mobility Technology Highly Selective Analysis of Steroid Biomarkers using SelexION Ion Mobility Technology Hua-Fen Liu, Witold Woroniecki, Doina Caraiman, and Yves LeBlanc AB SCIEX, Foster City, USA One of the most challenging

More information

Mass Spectrometry for Chemists and Biochemists

Mass Spectrometry for Chemists and Biochemists Erasmus Intensive Program SYNAPS Univ. of Crete - Summer 2007 Mass Spectrometry for Chemists and Biochemists Spiros A. Pergantis Assistant Professor of Analytical Chemistry Department of Chemistry University

More information

Industry 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 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 information

Protein Purification and Analysis

Protein Purification and Analysis Protein Purification and Analysis Numbers of genes: Humans ~40,000 genes Yeast ~6000 genes Bacteria ~3000 genes Solubility of proteins important for purification: 60-80% soluble, 20-40% membrane Some proteins

More information

LABORATÓRIUMI GYAKORLAT SILLABUSZ SYLLABUS OF A PRACTICAL DEMONSTRATION. financed by the program

LABORATÓRIUMI GYAKORLAT SILLABUSZ SYLLABUS OF A PRACTICAL DEMONSTRATION. financed by the program TÁMOP-4.1.1.C-13/1/KONV-2014-0001 projekt Az élettudományi-klinikai felsőoktatás gyakorlatorientált és hallgatóbarát korszerűsítése a vidéki képzőhelyek nemzetközi versenyképességének erősítésére program

More information

European Scientific Journal March 2016 edition vol.12, No.7 ISSN: 1857 7881 (Print) e - ISSN 1857-7431

European Scientific Journal March 2016 edition vol.12, No.7 ISSN: 1857 7881 (Print) e - ISSN 1857-7431 Applicability Degree of Autism Spectrum Disorder Diagnostic Criteria of Diagnostic and Statistical Manual of Mental Disorders the 5 the Edition (DSM V) on Children Enrolled in Autism Centers in Jordan

More information

CONTENTS. PART I INSTRUMENTATION 1 1 DEFINITIONS AND EXPLANATIONS 3 Ann Westman-Brinkmalm and Gunnar Brinkmalm References 13

CONTENTS. PART I INSTRUMENTATION 1 1 DEFINITIONS AND EXPLANATIONS 3 Ann Westman-Brinkmalm and Gunnar Brinkmalm References 13 CONTENTS FOREWORD CONTRIBUTORS xiii xv PART I INSTRUMENTATION 1 1 DEFINITIONS AND EXPLANATIONS 3 Ann Westman-Brinkmalm and Gunnar Brinkmalm References 13 2 A MASS SPECTROMETER S BUILDING BLOCKS 15 Ann

More information

LECTURE-14. Gel-based electrophoresis. Two-dimensional electrophoresis workflow: Staining and image analysis TRANSCRIPT

LECTURE-14. Gel-based electrophoresis. Two-dimensional electrophoresis workflow: Staining and image analysis TRANSCRIPT LECTURE-14 Gel-based electrophoresis Two-dimensional electrophoresis workflow: Staining and image analysis TRANSCRIPT So welcome to the proteomics course. In the last lecture we discussed about the gel

More information

Evaluation of LC-MS data for the absolute quantitative analysis of marker proteins

Evaluation of LC-MS data for the absolute quantitative analysis of marker proteins Evaluation of LC-MS data for the absolute quantitative analysis of marker proteins Nathanaël Delmotte 1, Bettina Mayr 1, Andreas Leinenbach 1, Knut Reinert 2, Oliver Kohlbacher 3, Christoph Klein 4, and

More information

Shop! VWRBiosciences,more than just a helping hand

Shop! VWRBiosciences,more than just a helping hand section line 2 BioSciences section line 1 VWRBiosciences,more than just a helping hand Proteomics round-up What can we offer? In today s world of discovery, technology is critical to a better understanding

More information

Proteomic fingerprinting initiatives. Dr Dan Agranoff Imperial College, London Hammersmith Hospitals NHS Trust

Proteomic fingerprinting initiatives. Dr Dan Agranoff Imperial College, London Hammersmith Hospitals NHS Trust Proteomic fingerprinting initiatives Dr Dan Agranoff Imperial College, London Hammersmith Hospitals NHS Trust Overview Biomarkers Proteomic fingerprints Serum proteome Mass spectrometry Pattern recognition

More information