Using CART to Mine SELDI ProteinChip Data for Biomarkers and Disease Stratification

Size: px
Start display at page:

Download "Using CART to Mine SELDI ProteinChip Data for Biomarkers and Disease Stratification"

Transcription

1 Using CART to Mine SELDI ProteinChip Data for Biomarkers and Disease Stratification Kenna Mawk, D.V.M. Informatics Product Manager Ciphergen Biosystems, Inc.

2 Outline Introduction to ProteinChip Technology Profiling Data Analysis Identifying Biomarkers Biomarker Patterns Software 5. Case studies Summary

3 ProteinChip Technology ProteinChip Arrays for use with SELDI-TOF MS detection Surface-Enhanced Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

4 ProteinChip Array Preparation. Apply Crude Sample Proteins within the sample bind to chemical or biological docking sites on the ProteinChip surface through an affinity interaction.. Wash ProteinChip Array Proteins that bind non-specifically or buffer (salts, additives..) contaminants are washed away, eliminating sample noise. 3. Add Energy Absorbing Molecules After sample processing the chip is dried and EAM is applied to each spot to facilitate desorption and ionization in the TOF-MS.

5 SELDI-TOF-MS Detection Retained proteins are eluted from the ProteinChip Array by Laser Desorption/Ionization Ionized proteins are detected and their mass accurately determined by Time-of-Flight Mass Spectrometry Laser Intensity Detector

6 ProteinChip Arrays: Available proprietary surfaces Chemical Surfaces HO HO OH OH Si Si Si Si M y+ Cu(II) Hydrophobic Hydrophilic Ionic IMAC Biochemical Surfaces Antibody DNA Enzyme Receptor Drug

7 Protein Profiling: Multidimensional Separation Surface Interaction Potential IMAC 5(+) 5(-) 5RP Selectivity Selectivity Selectivity Selectivity Stringency

8 Disease Biomarker Discovery: Prostate Cancer Serum H H Patient Ret Map H Control Ret Map -3 Ret Map -4() GelView TM Ret Map -3() comp Difference map

9 ProteinChip Applications Clinical Research Cancer and other disease biomarker discovery Clinical research Pharmaceutical Clinical Development Toxicology Clinical trials diagnostics Protein interaction & pathway research Genome to Proteome research Target discovery Secondary screening/target validation

10 Profiling Data Analysis Identifying Biomarkers

11 Flowchart of SELDI Data Analysis Preprocess Baseline subtract Normalize Calibrate Univariate analysis Biomarker Wizard or CiphergenExpress Cluster Analysis, Detect peaks, Calculate P-values, ROC/AUC Multivariate analysis CiphergenExpress Heirarchical Clustering, PCA; Biomarker Patterns Software

12 Challenge: To convert lots of raw data to a manageable sized dataset that can be analyzed

13 What is clustering? Cluster Cluster C,.75 The peak clustering feature in Biomarker Wizard software allows grouping of similar masses across multiple spectra. To visualize the potential differences (patterns), a scatter plot is generated by plotting the intensity vs. mass-to-charge D, E, F, G, H, E,() F,() 5 5 5

14 Plotting the intensity vs. M/Z (scatter plot) allows rapid visualization of potential pattern(s) Log Normalized Intensity Non-distinctive patterns (overlapping) Potentially distinctive patterns M/Z fm 3 fm

15 Multiple Versus Single Markers Single markers often have low predictive sensitivity and specificity Multiple markers are needed for good predictive accuracy Univariate analysis may yield a long list of potential markers but does not indicate relationships Multivariate analysis more likely to identify a small panel of markers for biomarker assays

16 Effect of Patient Variability on Univariate Analysis Candidate Marker for Cancer Diagnosis Candidate Biomarker for Drug Treatment - Animal Model 5. Intensity 4 3 Intensity CANCER Sample Group NORMAL. TREATED UNTREATED P = <.

17 Combinations of Markers Improve Group Segregation Pair-wise Analysis Group A Group B

18 Multi-Markers Have Higher Specificity & Sensitivity than Single Markers Markers Cancer Sensitivity Specificity PSA Prostate 65% 35% SELDI Multi-Marker Profile Prostate 83% 97% CA5.3 Breast 3% 69% SELDI Multi-Marker Profile Breast 93% 9% CA5 Ovarian 35% 98% SELDI Multi-Marker Profile Ovarian % 95%

19 Diagnostics: a continuum Single marker Mulitiple markers Pattern

20 Biomarker Patterns Software Output: Classification trees defining patterns of multiple biomarkers Predicted Treated Control Treated Actual Control 8 9 Terminal Node N = 9 Node M44 N = 7 Node M553 N = 4 Terminal Node N = 8 Terminal Node 3 N = 3 Sensitivity: 9% Specificity: 95%

21 Biomarker Patterns Software 5. Based on CART 5. Includes feature selection tool that uses TreeNet functionality

22 Dimensionality - Feature analysis Preferred: Input data Typical: Input data A B C D E F A B C D E F G H I 3 Patients 3 Patients

23 Automatic Best Predictor Discovery

24 Discover mode allows user review and modification of predictors

25 Resultant model is created using only selected predictors

26 Case Studies

27 ProteinChip Technology Coupled with Biomarker Patterns Software for the Diagnosis of Breast Cancer Benjamin Reed Steve Cleverley William Gallagher Nathan Harris

28 Overview Breast cancer is the most common cancer in women other than skin cancer The American Cancer Society estimates that in the United States 3,5 new cases are diagnosed and about 4, women die each year from cancer originating from the breast One in 8 American women who live to 85 will develop this illness at some stage during life Appearance of a lump in the breast is not conclusive

29 Materials and Methods Serum samples were submitted for evaluation (3 control patients versus 3 patients with breast cancer) Samples set was analyzed on a ProteinChip SAX array at a ph of 9. Both single (Biomarker Wizard) and multi-marker analysis (Biomarker Patterns Software) was performed on the data

30 Single marker analysis using the Biomarker Wizard Analysis of all markers using PEAKS software stats analysis Analysis of the NNNN marker in Excel Control Breast cancer Analysis of the NNNN marker in Excel Control Breast cancer The The upregulation upregulation of of these these proteins proteins was was confirmed confirmed in in both both PEAKS PEAKS software software and and Excel Excel stats stats analysis analysis

31 Multi-marker analysis using the Biomarker Patterns Software Mass Mass Mass 4 Mass 3 The tree with the second smallest relative cost (.873) consisted of four proteins Classification: Control: 8/33 = 85% sensitivity Cancer: 7/9 = 93% specificity

32 Scientific Conclusions The power of ProteinChip technology was illustrated in picking up both single marker and multiple markers from serum Using Biomarker Patterns Software several diagnostic trees were generated that distinguished healthy and breast cancer patients with specificities ranging up to 93%

33 Developing a novel CSF-based multi-marker diagnostic test for Alzheimer s Disease Anja Hviid Simonsen Huw Davies Kaj Blennow

34 Overview Multiple forms of dementia Alzheimer s Disease most common form of dementia Complex diagnostic situation Unambiguous diagnosis is currently only possible through examination of brain pathology post-mortem Several existing CSF-based biochemical markers Differentiation of related dementias generally quite poor Post mortem data has shown -% of diagnosis on living patients incorrect

35 Clinical and commercial needs.. Increase confidence in diagnosis Earlier diagnosis of disease to improve patient treatment Shorten and improve drug development process New therapeutic leads

36 Materials and profiling methods Human CSF from 3 probable AD cases vs. 35 age-matched normal individuals AD phenotype previously assessed using MMSE scores, ApoE genotype, T-Tau, P-Tau and A-beta -4 levels Total of 3 spectra per sample

37 Data mining P-values of candidate univariate markers were calculated (Mann- Whitney) from mean peak intensity values derived from averaged duplicates. Graphing included cluster plots and box and whisker plots Discriminatory peaks with P <. were subsequently used for multivariate BPS analysis

38 NNNN m/z Biomarker P value <. AD Normal Peak intensity Peak intensity 3 3 AD AD Normal Normal AD4 AD6() AD9() AD AD5() N3() N9 N N N7()

39 NNNN m/z Biomarker.5 P value <. AD Normal Peak intensity..5.5 AD3.5 K9.5 AD8().5 N. AD Normal.5 AD8.5 N4.5 Peak intensity AD AD7().5.5 N5 N6. AD Normal

40 NNNN3 m/z Biomarker P value <. AD Normal Peak intensity Peak intensity AD Normal AD AD5 AD8 AD8() AD() N6 N6() N N() N7() AD Normal

41 Biomarker Patterns Software Model Node M77 Mass N = 65 Node M539 Mass N = 44 Terminal Node 6 AD=, N= Node 3 M7466 Mass 3 N = 9 Node 5 M3444 Mass 5 N = 5 Terminal Node AD=5, N= Node 4 M9787 Mass 4 N = 4 Terminal Node 4 AD=, N= Terminal Node 5 AD=, N=3 Terminal Node Terminal Node 3 AD=, N=9 AD=4, N= AD Normal

42 Results summary 39 peaks were found with P values <. 4 of the markers increased in Alzheimer s Disease, 5 decreased None of the peaks showed complete separation of the groups Biomarker Patterns Software Five-peak pattern of markers identified Correctly grouped all Alzheimer s Disease samples (%) and 3 out of 35 normal (9.5%)

43

44 Seeking alternates to PSA test 89, new prostate cancer cases and 3, deaths in PSA limited because of high false-positive rates up to 75% of patients with elevated serum PSA may be negative for cancer Objective of experiment: determine if serum protein profiling will discriminate between patients with prostate cancer and unaffected individuals

45 Methods Serum from 6 cancer patients and 6 controls profiled Two array types WCX: weak cation exchange IMAC3-Cu: metal affinity capture copper Pattern detection Peak detection and clustering with Biomarker Wizard Pattern detection with Biomarker Patterns Software

46 WCX Array Profiles Yes WCX 567Da<=.444 Cancer 6 Control 6 No Yes WCX 687Da<=.64 No Yes WCX 395Da<=5.378 No Cancer 4 Control Cancer Control 5 CONTROL Cancer 4 Control Yes WCX 86Da<=.57 Cancer 36 Control No CANCER Cancer 4 Control 3 Yes WCX 395Da<=3.97 Cancer 8 Control No CANCER Cancer 8 Control CONTROL Cancer 8 Control Yes WCX 337Da<=.8 Cancer 7 Control No CANCER Cancer Control Yes WCX 397Da<=.67 Cancer Control No CANCER Cancer 5 Control Accuracy=67% CANCER Cancer Control CONTROL Cancer Control

47 IMAC3-Cu Array Profiles Yes IMAC3-Cu 396Da<=8.64 Cancer 6 Control 6 No IMAC3-Cu IMAC3-Cu Yes 83Da<=.97 No Yes 4469Da<=3.945 No Cancer 59 Control 6 Cancer 3 Control Yes IMAC3-Cu 973Da<=4.345 Cancer 45 Control 3 No CONTROL Cancer 4 Control 3 CANCER Cancer 3 Control 5 CONTROL Cancer Control 5 Yes IMAC3-Cu 66Da<=3.97 Cancer 44 Control 3 No CONTROL Cancer Control CANCER Cancer 38 Control CONTROL Cancer 6 Control Accuracy=4%

48 Combined profiles Yes WCX 567Da<=.444 Cancer 6 Control 6 No WCX IMAC3-Cu Yes 687Da<=.64 No Yes 483Da<=3.37 No Cancer 4 Control Cancer Control 5 CONTROL CANCER CANCER CONTROL Cancer 4 Control Cancer 36 Control Cancer 7 Control 3 Cancer 5 Control Accuracy=85%

49 Conclusions Comparative serum proteomic profiling provides improved diagnostic potential from single protein targets in traditional blood-based diagnostics Serum profiling using SELDI-TOF-MS supplemented by bioinformatics is a viable tool for detecting prostate cancer

50 Summary ProteinChip Technology is a powerful tool for identifying biomarkers Biomarker Patterns Software provides a method for identifying diagnostic patterns of multiple biomarkers Determines multiple biomarker correlation with phenotype in clinical research studies to improve sensitivity and specificity over single marker methods Automatically and rapidly finds hidden patterns in SELDI data sets Focuses further protein characterization analysis on proteins providing the most definitive splitting rules Models can be tested with additional samples to validate or refine the models

Chapter 10apter 9. Chapter 10. Summary

Chapter 10apter 9. Chapter 10. Summary Chapter 10apter 9 Chapter 10 The field of proteomics has developed rapidly in recent years. The essence of proteomics is to characterize the behavior of a group of proteins, the system rather than the

More information

The Analysis of Proteomic Spectra from Serum Samples. Keith Baggerly Biostatistics & Applied Mathematics MD Anderson Cancer Center

The Analysis of Proteomic Spectra from Serum Samples. Keith Baggerly Biostatistics & Applied Mathematics MD Anderson Cancer Center The Analysis of Proteomic Spectra from Serum Samples Keith Baggerly Biostatistics & Applied Mathematics MD Anderson Cancer Center PROTEOMICS 1 What Are Proteomic Spectra? DNA makes RNA makes Protein Microarrays

More information

Diagnosis of Ovarian Cancer Using Decision Tree Classification of Mass Spectral Data

Diagnosis of Ovarian Cancer Using Decision Tree Classification of Mass Spectral Data Journal of Biomedicine and Biotechnology :5 () 8 PII. S7 http://jbb.hindawi.com RESEARCH ARTICLE Diagnosis of Ovarian Cancer Using Decision Tree Classification of Mass Spectral Data Antonia Vlahou,, John

More information

Inter-session reproducibility measures for high-throughput data sources

Inter-session reproducibility measures for high-throughput data sources Inter-session reproducibility measures for high-throughput data sources Milos Hauskrecht, PhD, Richard Pelikan, MSc Computer Science Department, Intelligent Systems Program, Department of Biomedical Informatics,

More information

Proteomic Biomarker Discovery in Breast Cancer

Proteomic Biomarker Discovery in Breast Cancer Proteomic Biomarker Discovery in Breast Cancer Rob Baxter Laboratory for Cellular and Diagnostic Proteomics Kolling Institute, University of Sydney, Royal North Shore Hospital robert.baxter@sydney.edu.au

More information

Proteomics and Bioinformatics Approaches for Identification of Serum Biomarkers to Detect Breast Cancer

Proteomics and Bioinformatics Approaches for Identification of Serum Biomarkers to Detect Breast Cancer Clinical Chemistry 48:8 1296 1304 (2002) Cancer Diagnostics: Discovery and Clinical Applications Proteomics and Bioinformatics Approaches for Identification of Serum Biomarkers to Detect Breast Cancer

More information

Surface-Enhanced Laser Desorption/Ionization Timeof-Flight Mass Spectrometry Serum Protein Profiling to Identify Nasopharyngeal Carcinoma

Surface-Enhanced Laser Desorption/Ionization Timeof-Flight Mass Spectrometry Serum Protein Profiling to Identify Nasopharyngeal Carcinoma 99 Surface-Enhanced Laser Desorption/Ionization Timeof-Flight Mass Spectrometry Serum Protein Profiling to Identify Nasopharyngeal Carcinoma David Wing Yuen Ho, MPhil 1 Zhen Fan Yang, Ph.D. 1 Birgitta

More information

SELYMATRA: Web Application for the analysis. of mass spectra

SELYMATRA: Web Application for the analysis. of mass spectra SELYMATRA: Web Application for the analysis of mass spectra arxiv:1710.05914v1 [q-bio.qm] 15 Oct 2017 Davide Nardone, Angelo Ciaramella, Mariangela Cerreta, Salvatore Pulcrano, Gian Carlo Bellenchi, Giuseppe

More information

Tissue and Fluid Proteomics Chao-Cheng (Sam) Wang

Tissue and Fluid Proteomics Chao-Cheng (Sam) Wang Tissue and Fluid Proteomics Chao-Cheng (Sam) Wang UAB-03/09/2004 What is proteomics? A snap shot of the protein pattern!! What can proteomics do? To provide information on functional networks and/or involvement

More information

The Detection of Allergens in Food Products with LC-MS

The Detection of Allergens in Food Products with LC-MS The Detection of Allergens in Food Products with LC-MS Something for the future? Jacqueline van der Wielen Scope of Organisation Dutch Food and Consumer Product Safety Authority: Law enforcement Control

More information

Non-Traditional Approaches to MALDI- TOF Mass Spectrometry Analysis of Low Molecular Weight Polymers

Non-Traditional Approaches to MALDI- TOF Mass Spectrometry Analysis of Low Molecular Weight Polymers Non-Traditional Approaches to MALDI- TOF Mass Spectrometry Analysis of Low Molecular Weight Polymers Justin R. Engle and S. Kim R. Williams Laboratory for Advance Separation Technologies Department of

More information

Lecture 3. Tandem MS & Protein Sequencing

Lecture 3. Tandem MS & Protein Sequencing Lecture 3 Tandem MS & Protein Sequencing Nancy Allbritton, M.D., Ph.D. Department of Physiology & Biophysics 824-9137 (office) nlallbri@uci.edu Office- Rm D349 Medical Science D Bldg. Tandem MS Steps:

More information

Mass Spectrometry. - Introduction - Ion sources & sample introduction - Mass analyzers - Basics of biomolecule MS - Applications

Mass Spectrometry. - Introduction - Ion sources & sample introduction - Mass analyzers - Basics of biomolecule MS - Applications - Introduction - Ion sources & sample introduction - Mass analyzers - Basics of biomolecule MS - Applications Adapted from Mass Spectrometry in Biotechnology Gary Siuzdak,, Academic Press 1996 1 Introduction

More information

Technical Note # TN-31 Redefining MALDI-TOF/TOF Performance

Technical Note # TN-31 Redefining MALDI-TOF/TOF Performance Bruker Daltonics Technical Note # TN-31 Redefining MALDI-TOF/TOF Performance The new ultraflextreme exceeds all current expectations of MALDI-TOF/TOF technology: A proprietary khz smartbeam-ii TM MALDI

More information

INTRODUCTION TO MALDI IMAGING

INTRODUCTION TO MALDI IMAGING INTRODUCTION TO MALDI IMAGING Marten F. Snel, Emmanuelle Claude, Thérèse McKenna, and James I. Langridge Waters Corporation, Manchester, UK INT RODUCTION The last few years have seen a rapid increase in

More information

MALDI-TOF. Introduction. Schematic and Theory of MALDI

MALDI-TOF. Introduction. Schematic and Theory of MALDI MALDI-TOF Proteins and peptides have been characterized by high pressure liquid chromatography (HPLC) or SDS PAGE by generating peptide maps. These peptide maps have been used as fingerprints of protein

More information

Gene expression analysis. Roadmap. Microarray technology: how it work Applications: what can we do with it Preprocessing: Classification Clustering

Gene expression analysis. Roadmap. Microarray technology: how it work Applications: what can we do with it Preprocessing: Classification Clustering Gene expression analysis Roadmap Microarray technology: how it work Applications: what can we do with it Preprocessing: Image processing Data normalization Classification Clustering Biclustering 1 Gene

More information

AD (Leave blank) TITLE: Proteomic analyses of nipple fluid for early detection of breast cancer

AD (Leave blank) TITLE: Proteomic analyses of nipple fluid for early detection of breast cancer AD (Leave blank) Award Number: DAMD17-03-1-0575 TITLE: Proteomic analyses of nipple fluid for early detection of breast cancer PRINCIPAL INVESTIGATOR: Judy Garber CONTRACTING ORGANIZATION: Dana-Farber

More information

David M. Rocke Division of Biostatistics Department of Public Health Sciences University of California, Davis

David M. Rocke Division of Biostatistics Department of Public Health Sciences University of California, Davis David M. Rocke Division of Biostatistics Department of Public Health Sciences University of California, Davis Biomarkers Tissue (gene/protein/mirna) Invasive Only useful post-surgery/biopsy Gold standard

More information

Probability-Based Protein Identification for Post-Translational Modifications and Amino Acid Variants Using Peptide Mass Fingerprint Data

Probability-Based Protein Identification for Post-Translational Modifications and Amino Acid Variants Using Peptide Mass Fingerprint Data Probability-Based Protein Identification for Post-Translational Modifications and Amino Acid Variants Using Peptide Mass Fingerprint Data Tong WW, McComb ME, Perlman DH, Huang H, O Connor PB, Costello

More information

EARLY DETECTION OF OVARIAN CANCER USING GABOR WAVELET PHASE QUANTIZATION AND BINARY CODING

EARLY DETECTION OF OVARIAN CANCER USING GABOR WAVELET PHASE QUANTIZATION AND BINARY CODING EARLY DETECTION OF OVARIAN CANCER USING GABOR WAVELET PHASE QUANTIZATION AND BINARY CODING Stuart M. Morton Submitted to the faculty of the School of Informatics in partial fulfillment of the requirements

More information

Protein profiling as a diagnostic tool in clinical chemistry: a review

Protein profiling as a diagnostic tool in clinical chemistry: a review Clin Chem Lab Med 2005;43(12):1281 1290 2005 by Walter de Gruyter Berlin New York. DOI 10.1515/CCLM.2005.222 2005/88 Review Protein profiling as a diagnostic tool in clinical chemistry: a review Judith

More information

ABSTRACT. Objective: To establish and evaluate the fingerprint diagnostic models of cerebrospinal protein profile in glioma Using

ABSTRACT. Objective: To establish and evaluate the fingerprint diagnostic models of cerebrospinal protein profile in glioma Using Mass Spectrometric Analysis on Cerebrospinal Fluid Protein for Glioma and its Clinical Application J Liu 1, J Yu 2, H Shen 2, J Zhang 2, W Liu 2, Z Chen 2, S He 2, S Zheng 2 ABSTRACT Objective: To establish

More information

Unsupervised Identification of Isotope-Labeled Peptides

Unsupervised Identification of Isotope-Labeled Peptides Unsupervised Identification of Isotope-Labeled Peptides Joshua E Goldford 13 and Igor GL Libourel 124 1 Biotechnology institute, University of Minnesota, Saint Paul, MN 55108 2 Department of Plant Biology,

More information

J Clin Oncol 23: by American Society of Clinical Oncology INTRODUCTION

J Clin Oncol 23: by American Society of Clinical Oncology INTRODUCTION VOLUME 23 NUMBER 22 AUGUST 1 2005 JOURNAL OF CLINICAL ONCOLOGY O R I G I N A L R E P O R T Serum Proteomic Fingerprinting Discriminates Between Clinical Stages and Predicts Disease Progression in Melanoma

More information

Mass Spectrometry. Mass spectrometer MALDI-TOF ESI/MS/MS. Basic components. Ionization source Mass analyzer Detector

Mass Spectrometry. Mass spectrometer MALDI-TOF ESI/MS/MS. Basic components. Ionization source Mass analyzer Detector Mass Spectrometry MALDI-TOF ESI/MS/MS Mass spectrometer Basic components Ionization source Mass analyzer Detector 1 Principles of Mass Spectrometry Proteins are separated by mass to charge ratio (limit

More information

CNV PCA Search Tutorial

CNV PCA Search Tutorial CNV PCA Search Tutorial Release 8.1 Golden Helix, Inc. March 18, 2014 Contents 1. Data Preparation 2 A. Join Log Ratio Data with Phenotype Information.............................. 2 B. Activate only

More information

Case Studies on High Throughput Gene Expression Data Kun Huang, PhD Raghu Machiraju, PhD

Case Studies on High Throughput Gene Expression Data Kun Huang, PhD Raghu Machiraju, PhD Case Studies on High Throughput Gene Expression Data Kun Huang, PhD Raghu Machiraju, PhD Department of Biomedical Informatics Department of Computer Science and Engineering The Ohio State University Review

More information

Analysis of Uncomplexed and Copper-complexed Methanobactin with UV/Visible Spectrophotometry, Mass Spectrometry and NMR Spectrometry

Analysis of Uncomplexed and Copper-complexed Methanobactin with UV/Visible Spectrophotometry, Mass Spectrometry and NMR Spectrometry Analysis of Uncomplexed and Copper-complexed Methanobactin with UV/Visible Spectrophotometry, Mass Spectrometry and NMR Spectrometry Lee Behling, Alan DiSpirito, Scott Hartsel, Larry Masterson, Gianluigi

More information

Statistical Analysis of Single Nucleotide Polymorphism Microarrays in Cancer Studies

Statistical Analysis of Single Nucleotide Polymorphism Microarrays in Cancer Studies Statistical Analysis of Single Nucleotide Polymorphism Microarrays in Cancer Studies Stanford Biostatistics Workshop Pierre Neuvial with Henrik Bengtsson and Terry Speed Department of Statistics, UC Berkeley

More information

Ion Source. Mass Analyzer. Detector. intensity. mass/charge

Ion Source. Mass Analyzer. Detector. intensity. mass/charge Proteomics Informatics Overview of spectrometry (Week 2) Ion Source Analyzer Detector Peptide Fragmentation Ion Source Analyzer 1 Fragmentation Analyzer 2 Detector b y Liquid Chromatography (LC)-MS/MS

More information

[ APPLICATION NOTE ] High Sensitivity Intact Monoclonal Antibody (mab) HRMS Quantification APPLICATION BENEFITS INTRODUCTION WATERS SOLUTIONS KEYWORDS

[ APPLICATION NOTE ] High Sensitivity Intact Monoclonal Antibody (mab) HRMS Quantification APPLICATION BENEFITS INTRODUCTION WATERS SOLUTIONS KEYWORDS Yun Wang Alelyunas, Henry Shion, Mark Wrona Waters Corporation, Milford, MA, USA APPLICATION BENEFITS mab LC-MS method which enables users to achieve highly sensitive bioanalysis of intact trastuzumab

More information

Discrimination analysis of mass spectrometry proteomics for ovarian cancer detection 1

Discrimination analysis of mass spectrometry proteomics for ovarian cancer detection 1 Acta Pharmacol Sin 2008 Oct; 29 (10): 1240 1246 Full-length article Discrimination analysis of mass spectrometry proteomics for ovarian cancer detection 1 Yan-jun HONG 2, Xiao-dan WANG 2, David SHEN 3,

More information

Study on serum proteomic features in patients with and without recurrence or metastasis after surgical resection of esophageal carcinoma

Study on serum proteomic features in patients with and without recurrence or metastasis after surgical resection of esophageal carcinoma Study on serum proteomic features in patients with and without recurrence or metastasis after surgical resection of esophageal carcinoma G.B. Zheng, C.F. Gao, X.L. Wang, G. Zhao and D.H. Li Institute of

More information

Statistics 202: Data Mining. c Jonathan Taylor. Final review Based in part on slides from textbook, slides of Susan Holmes.

Statistics 202: Data Mining. c Jonathan Taylor. Final review Based in part on slides from textbook, slides of Susan Holmes. Final review Based in part on slides from textbook, slides of Susan Holmes December 5, 2012 1 / 1 Final review Overview Before Midterm General goals of data mining. Datatypes. Preprocessing & dimension

More information

Rapid identification and resistance assessment: The future is mass spectrometry

Rapid identification and resistance assessment: The future is mass spectrometry Rapid identification and resistance assessment: The future is mass spectrometry Dr Sanmarié Schlebusch Director of Microbiology Mater Pathology Brisbane Outline Introduction Plug and play Pre-prep and

More information

Research Article Protein Markers for the Differential Diagnosis of Vascular Dementia and Alzheimer s Disease

Research Article Protein Markers for the Differential Diagnosis of Vascular Dementia and Alzheimer s Disease Proteomics Volume 212, Article ID 82424, 8 pages doi:1.11/212/82424 Research Article Protein Markers for the Differential Diagnosis of Vascular Dementia and Alzheimer s Disease A. H. Simonsen, 1 N.-O.

More information

Research Article Classification of Traditional Chinese Medicine Syndromes in Patients with Chronic Hepatitis B by SELDI-Based ProteinChip Analysis

Research Article Classification of Traditional Chinese Medicine Syndromes in Patients with Chronic Hepatitis B by SELDI-Based ProteinChip Analysis Hindawi Publishing Corporation Evidence-Based Complementary and Alternative Medicine Volume, Article ID 663, pages doi:.55//663 Research Article Classification of Traditional Chinese Medicine Syndromes

More information

EpiQuik Circulating Acetyl Histone H3K18 ELISA Kit (Colorimetric)

EpiQuik Circulating Acetyl Histone H3K18 ELISA Kit (Colorimetric) EpiQuik Circulating Acetyl Histone H3K18 ELISA Kit (Colorimetric) Base Catalog # PLEASE READ THIS ENTIRE USER GUIDE BEFORE USE Uses: The EpiQuik Circulating Acetyl Histone H3K18 ELISA Kit (Colorimetric)

More information

Screening for novel oncology biomarker panels using both DNA and protein microarrays. John Anson, PhD VP Biomarker Discovery

Screening for novel oncology biomarker panels using both DNA and protein microarrays. John Anson, PhD VP Biomarker Discovery Screening for novel oncology biomarker panels using both DNA and protein microarrays John Anson, PhD VP Biomarker Discovery Outline of presentation Introduction to OGT and our approach to biomarker studies

More information

T. R. Golub, D. K. Slonim & Others 1999

T. R. Golub, D. K. Slonim & Others 1999 T. R. Golub, D. K. Slonim & Others 1999 Big Picture in 1999 The Need for Cancer Classification Cancer classification very important for advances in cancer treatment. Cancers of Identical grade can have

More information

Simple Cancer Screening Based on Urinary Metabolite Analysis

Simple Cancer Screening Based on Urinary Metabolite Analysis FEATURED ARTICLES Taking on Future Social Issues through Open Innovation Life Science for a Healthy Society with High Quality of Life Simple Cancer Screening Based on Urinary Metabolite Analysis Hitachi

More information

The Power of the Web in Cancer Drug Discovery and Clinical Trial Design: Research without a Laboratory?

The Power of the Web in Cancer Drug Discovery and Clinical Trial Design: Research without a Laboratory? Cancer Informatics C o m m e n t a r y Open Access Full open access to this and thousands of other papers at http://www.la-press.com. The Power of the Web in Cancer Drug Discovery and Clinical Trial Design:

More information

An integrated approach utilizing proteomics and bioinformatics to detect ovarian cancer *

An integrated approach utilizing proteomics and bioinformatics to detect ovarian cancer * Yu et al. / J Zhejiang Univ SCI 6B():7-31 7 Journal of Zhejiang University SCIENCE ISSN 19-39 http://www.zju.edu.cn/jzus E-mail: jzus@zju.edu.cn An integrated approach utilizing proteomics and bioinformatics

More information

An integrated approach utilizing proteomics and bioinformatics to detect ovarian cancer *

An integrated approach utilizing proteomics and bioinformatics to detect ovarian cancer * Yu et al. / J Zhejiang Univ SCI 2005 6B(4):227-231 227 Journal of Zhejiang University SCIENCE ISSN 1009-3095 http://www.zju.edu.cn/jzus E-mail: jzus@zju.edu.cn An integrated approach utilizing proteomics

More information

Metabolomic and Proteomics Solutions for Integrated Biology. Christine Miller Omics Market Manager ASMS 2015

Metabolomic and Proteomics Solutions for Integrated Biology. Christine Miller Omics Market Manager ASMS 2015 Metabolomic and Proteomics Solutions for Integrated Biology Christine Miller Omics Market Manager ASMS 2015 Integrating Biological Analysis Using Pathways Protein A R HO R Protein B Protein X Identifies

More information

Discovery Metabolomics - Quantitative Profiling of the Metabolome using TripleTOF Technology

Discovery Metabolomics - Quantitative Profiling of the Metabolome using TripleTOF Technology ANSWERS FOR SCIENCE. KNOWLEDGE FOR LIFE. Discovery Metabolomics - Quantitative Profiling of the Metabolome using TripleTOF Technology Baljit Ubhi Ph.D ASMS Baltimore, June 2014 What is Metabolomics? Also

More information

Next-Generation Immunohistochemistry: Multiplex tissue imaging with mass cytometry

Next-Generation Immunohistochemistry: Multiplex tissue imaging with mass cytometry Nat Met, April 2014 Nat Med, April 2014 Next-Generation Immunohistochemistry: Multiplex tissue imaging with mass cytometry Journal Club Timo Böge Overview Introduction Conventional Immunohistochemistry

More information

Use of proteomic patterns in serum to identify ovarian cancer

Use of proteomic patterns in serum to identify ovarian cancer Mechanisms of disease Use of proteomic patterns in serum to identify ovarian cancer Emanuel F Petricoin III, Ali M Ardekani, Ben A Hitt, Peter J Levine, Vincent A Fusaro, Seth M Steinberg, Gordon B Mills,

More information

Chapter 1. Introduction

Chapter 1. Introduction Chapter 1 Introduction 1.1 Motivation and Goals The increasing availability and decreasing cost of high-throughput (HT) technologies coupled with the availability of computational tools and data form a

More information

New Instruments and Services

New Instruments and Services New Instruments and Services http://planetorbitrap.com/orbitrap fusion Combining the best of quadrupole, Orbitrap, and ion trap mass analysis in a revolutionary Tribrid architecture, the Orbitrap Fusion

More information

MALDI-IMS (MATRIX-ASSISTED LASER DESORPTION/IONIZATION

MALDI-IMS (MATRIX-ASSISTED LASER DESORPTION/IONIZATION MALDI-IMS (MATRIX-ASSISTED LASER DESORPTION/IONIZATION IMAGING MASS SPECTROMETER) IN TISSUE STUDY YANXIAN CHEN MARCH 8 TH, WEDNESDAY. SEMINAR FOCUSING ON What is MALDI imaging mass spectrometer? How does

More information

Exercises: Differential Methylation

Exercises: Differential Methylation Exercises: Differential Methylation Version 2018-04 Exercises: Differential Methylation 2 Licence This manual is 2014-18, Simon Andrews. This manual is distributed under the creative commons Attribution-Non-Commercial-Share

More information

The use of random projections for the analysis of mass spectrometry imaging data Palmer, Andrew; Bunch, Josephine; Styles, Iain

The use of random projections for the analysis of mass spectrometry imaging data Palmer, Andrew; Bunch, Josephine; Styles, Iain The use of random projections for the analysis of mass spectrometry imaging data Palmer, Andrew; Bunch, Josephine; Styles, Iain DOI: 10.1007/s13361-014-1024-7 Citation for published version (Harvard):

More information

IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 11, NO. X, XXXXX IEEE 2 DATA SETS

IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 11, NO. X, XXXXX IEEE 2 DATA SETS /ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 11, NO. X, XXXXX 2014 1 Q1 Biomarker Signature Discovery from Mass Spectrometry Data Ao Kong, Chinmaya Gupta, Mauro Ferrari, Marco Agostini,

More information

Mass Spectrometry Course Árpád Somogyi Chemistry and Biochemistry MassSpectrometry Facility) University of Debrecen, April 12-23, 2010

Mass Spectrometry Course Árpád Somogyi Chemistry and Biochemistry MassSpectrometry Facility) University of Debrecen, April 12-23, 2010 Mass Spectrometry Course Árpád Somogyi Chemistry and Biochemistry MassSpectrometry Facility) University of Debrecen, April 12-23, 2010 Introduction, Ionization Methods Mass Analyzers, Ion Activation Methods

More information

Biological Mass Spectrometry. April 30, 2014

Biological Mass Spectrometry. April 30, 2014 Biological Mass Spectrometry April 30, 2014 Mass Spectrometry Has become the method of choice for precise protein and nucleic acid mass determination in a very wide mass range peptide and nucleotide sequencing

More information

From single studies to an EBM based assessment some central issues

From single studies to an EBM based assessment some central issues From single studies to an EBM based assessment some central issues Doug Altman Centre for Statistics in Medicine, Oxford, UK Prognosis Prognosis commonly relates to the probability or risk of an individual

More information

Int J Clin Exp Med 2015;8(2): /ISSN: /IJCEM

Int J Clin Exp Med 2015;8(2): /ISSN: /IJCEM Int J Clin Exp Med 2015;8(2):2077-2085 www.ijcem.com /ISSN:1940-5901/IJCEM0003180 Original Article Comparative proteomic analysis of serum diagnosis patterns of sputum smear-positive pulmonary tuberculosis

More information

Alzheimer s disease. The future of clinical trials: big problem, Big Data, big solution?

Alzheimer s disease. The future of clinical trials: big problem, Big Data, big solution? Alzheimer s disease The future of clinical trials: big problem, Big Data, big solution? The Problem More than 36m people with dementia Consumes 1% global GDP Serial trials failure Targets for therapy Nothing

More information

National Surgical Adjuvant Breast and Bowel Project (NSABP) Foundation Annual Progress Report: 2008 Formula Grant

National Surgical Adjuvant Breast and Bowel Project (NSABP) Foundation Annual Progress Report: 2008 Formula Grant National Surgical Adjuvant Breast and Bowel Project (NSABP) Foundation Annual Progress Report: 2008 Formula Grant Reporting Period July 1, 2011 December 31, 2011 Formula Grant Overview The National Surgical

More information

OVERVIEW OF CURRENT IDENTIFICATION SYSTEMS AND DATABASES

OVERVIEW OF CURRENT IDENTIFICATION SYSTEMS AND DATABASES OVERVIEW OF CURRENT IDENTIFICATION SYSTEMS AND DATABASES EVERY STEP OF THE WAY 1 EVERY STEP OF THE WAY MICROBIAL IDENTIFICATION METHODS DNA RNA Genotypic Sequencing of ribosomal RNA regions of bacteria

More information

Evaluating Classifiers for Disease Gene Discovery

Evaluating Classifiers for Disease Gene Discovery Evaluating Classifiers for Disease Gene Discovery Kino Coursey Lon Turnbull khc0021@unt.edu lt0013@unt.edu Abstract Identification of genes involved in human hereditary disease is an important bioinfomatics

More information

MICROARRAYS AND OTHER NEW TECHNOLOGIES. Diagnosis of Gastric Cancer by Serum Proteomic Fingerprinting

MICROARRAYS AND OTHER NEW TECHNOLOGIES. Diagnosis of Gastric Cancer by Serum Proteomic Fingerprinting GASTROENTEROLOGY 2006;130:1858 1864 MICROARRAYS AND OTHER NEW TECHNOLOGIES Diagnosis of Gastric Cancer by Serum Proteomic Fingerprinting TERENCE C. W. POON, JOSEPH J. Y. SUNG, SHUK M. CHOW, ENDERS K. W.

More information

Assessing Functional Neural Connectivity as an Indicator of Cognitive Performance *

Assessing Functional Neural Connectivity as an Indicator of Cognitive Performance * Assessing Functional Neural Connectivity as an Indicator of Cognitive Performance * Brian S. Helfer 1, James R. Williamson 1, Benjamin A. Miller 1, Joseph Perricone 1, Thomas F. Quatieri 1 MIT Lincoln

More information

Proteomics of body liquids as a source for potential methods for medical diagnostics Prof. Dr. Evgeny Nikolaev

Proteomics of body liquids as a source for potential methods for medical diagnostics Prof. Dr. Evgeny Nikolaev Proteomics of body liquids as a source for potential methods for medical diagnostics Prof. Dr. Evgeny Nikolaev Institute for Biochemical Physics, Rus. Acad. Sci., Moscow, Russia. Institute for Energy Problems

More information

Predicting Breast Cancer Survivability Rates

Predicting Breast Cancer Survivability Rates Predicting Breast Cancer Survivability Rates For data collected from Saudi Arabia Registries Ghofran Othoum 1 and Wadee Al-Halabi 2 1 Computer Science, Effat University, Jeddah, Saudi Arabia 2 Computer

More information

Application Note # MT-111 Concise Interpretation of MALDI Imaging Data by Probabilistic Latent Semantic Analysis (plsa)

Application Note # MT-111 Concise Interpretation of MALDI Imaging Data by Probabilistic Latent Semantic Analysis (plsa) Application Note # MT-111 Concise Interpretation of MALDI Imaging Data by Probabilistic Latent Semantic Analysis (plsa) MALDI imaging datasets can be very information-rich, containing hundreds of mass

More information

Feature selection methods for early predictive biomarker discovery using untargeted metabolomic data

Feature selection methods for early predictive biomarker discovery using untargeted metabolomic data Feature selection methods for early predictive biomarker discovery using untargeted metabolomic data Dhouha Grissa, Mélanie Pétéra, Marion Brandolini, Amedeo Napoli, Blandine Comte and Estelle Pujos-Guillot

More information

Using Hydrophilic Interaction Chromatography (HILIC) for the Retention of Highly Polar Analytes

Using Hydrophilic Interaction Chromatography (HILIC) for the Retention of Highly Polar Analytes Using Hydrophilic Interaction Chromatography (HILIC) for the Retention of Highly Polar Analytes Eric S. Grumbach,, Diane M. Diehl and Jeffrey R. Mazzeo 2003 Waters Corp. Outline Introduction HILIC Definition

More information

Abstract. Background. Objective

Abstract. Background. Objective Molecular epidemiology of clinical tissues with multi-parameter IHC Poster 237 J Ruan 1, T Hope 1, J Rheinhardt 2, D Wang 2, R Levenson 1, T Nielsen 3, H Gardner 2, C Hoyt 1 1 CRi, Woburn, Massachusetts,

More information

Dan Koller, Ph.D. Medical and Molecular Genetics

Dan Koller, Ph.D. Medical and Molecular Genetics Design of Genetic Studies Dan Koller, Ph.D. Research Assistant Professor Medical and Molecular Genetics Genetics and Medicine Over the past decade, advances from genetics have permeated medicine Identification

More information

Denoising Tandem Mass Spectrometry Data

Denoising Tandem Mass Spectrometry Data East Tennessee State University Digital Commons @ East Tennessee State University Electronic Theses and Dissertations 5-2017 Denoising Tandem Mass Spectrometry Data Felix Offei East Tennessee State Universtiy

More information

Introduction to Discrimination in Microarray Data Analysis

Introduction to Discrimination in Microarray Data Analysis Introduction to Discrimination in Microarray Data Analysis Jane Fridlyand CBMB University of California, San Francisco Genentech Hall Auditorium, Mission Bay, UCSF October 23, 2004 1 Case Study: Van t

More information

Biost 590: Statistical Consulting

Biost 590: Statistical Consulting Biost 590: Statistical Consulting Statistical Classification of Scientific Questions October 3, 2008 Scott S. Emerson, M.D., Ph.D. Professor of Biostatistics, University of Washington 2000, Scott S. Emerson,

More information

Characterization of an Unknown Compound Using the LTQ Orbitrap

Characterization of an Unknown Compound Using the LTQ Orbitrap Characterization of an Unknown Compound Using the LTQ rbitrap Donald Daley, Russell Scammell, Argenta Discovery Limited, 8/9 Spire Green Centre, Flex Meadow, Harlow, Essex, CM19 5TR, UK bjectives unknown

More information

LECTURE-15. itraq Clinical Applications HANDOUT. Isobaric Tagging for Relative and Absolute quantitation (itraq) is a quantitative MS

LECTURE-15. itraq Clinical Applications HANDOUT. Isobaric Tagging for Relative and Absolute quantitation (itraq) is a quantitative MS LECTURE-15 itraq Clinical Applications HANDOUT PREAMBLE Isobaric Tagging for Relative and Absolute quantitation (itraq) is a quantitative MS based method for quantifying proteins subject to various different

More information

Analyzing Trace-Level Impurities of a Pharmaceutical Intermediate Using an LCQ Fleet Ion Trap Mass Spectrometer and the Mass Frontier Software Package

Analyzing Trace-Level Impurities of a Pharmaceutical Intermediate Using an LCQ Fleet Ion Trap Mass Spectrometer and the Mass Frontier Software Package Analyzing Trace-Level Impurities of a Pharmaceutical Intermediate Using an LCQ Fleet Ion Trap Mass Spectrometer and the Mass Frontier Software Package Chromatography and Mass Spectrometry Application Note

More information

Alterations in the serum proteome profile during the development of ovarian cancer

Alterations in the serum proteome profile during the development of ovarian cancer INTERNATIONAL JOURNAL OF ONCOLOGY 45: 2495-2501, 2014 Alterations in the serum proteome profile during the development of ovarian cancer Liping Sun 1,2, Li Li 1, Zhao Li 1,2, Shuhui Hong 3, Qifeng Yang

More information

Spectral Analysis and Quantitation in MALDI-MS Imaging.

Spectral Analysis and Quantitation in MALDI-MS Imaging. Tina Memo No. 2016-017 Internal, Second Year Reoort. Spectral Analysis and Quantitation in MALDI-MS Imaging. Somrudee Deepaisarn. Last updated 2 /12 / 2016 Imaging Science and Biomedical Engineering Division,

More information

LC/MS/MS SOLUTIONS FOR LIPIDOMICS. Biomarker and Omics Solutions FOR DISCOVERY AND TARGETED LIPIDOMICS

LC/MS/MS SOLUTIONS FOR LIPIDOMICS. Biomarker and Omics Solutions FOR DISCOVERY AND TARGETED LIPIDOMICS LC/MS/MS SOLUTIONS FOR LIPIDOMICS Biomarker and Omics Solutions FOR DISCOVERY AND TARGETED LIPIDOMICS Lipids play a key role in many biological processes, such as the formation of cell membranes and signaling

More information

An Improved Algorithm To Predict Recurrence Of Breast Cancer

An Improved Algorithm To Predict Recurrence Of Breast Cancer An Improved Algorithm To Predict Recurrence Of Breast Cancer Umang Agrawal 1, Ass. Prof. Ishan K Rajani 2 1 M.E Computer Engineer, Silver Oak College of Engineering & Technology, Gujarat, India. 2 Assistant

More information

Matrix Assisted Laser Desorption Ionization Time-of-flight Mass Spectrometry

Matrix Assisted Laser Desorption Ionization Time-of-flight Mass Spectrometry Matrix Assisted Laser Desorption Ionization Time-of-flight Mass Spectrometry Time-of-Flight Mass Spectrometry. Basic principles An attractive feature of the time-of-flight (TOF) mass spectrometer is its

More information

Integrated Analysis of Copy Number and Gene Expression

Integrated Analysis of Copy Number and Gene Expression Integrated Analysis of Copy Number and Gene Expression Nexus Copy Number provides user-friendly interface and functionalities to integrate copy number analysis with gene expression results for the purpose

More information

Analysis of microdissected prostate tissue with ProteinChip arrays - a way to new insights into carcinogenesis and to diagnostic tools

Analysis of microdissected prostate tissue with ProteinChip arrays - a way to new insights into carcinogenesis and to diagnostic tools INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE 9: 341-347, 2002 341 Analysis of microdissected prostate tissue with ProteinChip arrays - a way to new insights into carcinogenesis and to diagnostic tools AXEL

More information

Large-scale identity-by-descent mapping discovers rare haplotypes of large effect. Suyash Shringarpure 23andMe, Inc. ASHG 2017

Large-scale identity-by-descent mapping discovers rare haplotypes of large effect. Suyash Shringarpure 23andMe, Inc. ASHG 2017 Large-scale identity-by-descent mapping discovers rare haplotypes of large effect Suyash Shringarpure 23andMe, Inc. ASHG 2017 1 Why care about rare variants of large effect? Months from randomization 2

More information

Solving practical problems. Maria Kuhtinskaja

Solving practical problems. Maria Kuhtinskaja Solving practical problems Maria Kuhtinskaja What does a mass spectrometer do? It measures mass better than any other technique. It can give information about chemical structures. What are mass measurements

More information

Analysis of Triglycerides in Cooking Oils Using MALDI-TOF Mass Spectrometry and Principal Component Analysis

Analysis of Triglycerides in Cooking Oils Using MALDI-TOF Mass Spectrometry and Principal Component Analysis Analysis of Triglycerides in Cooking Oils Using MALDI-TOF Mass Spectrometry and Principal Component Analysis Kevin Cooley Chemistry Supervisor: Kingsley Donkor 1. Abstract Triglycerides are composed of

More information

MALDI Imaging Mass Spectrometry

MALDI Imaging Mass Spectrometry MALDI Imaging Mass Spectrometry Nan Kleinholz Mass Spectrometry and Proteomics Facility The Ohio State University Mass Spectrometry and Proteomics Workshop What is MALDI Imaging? MALDI: Matrix Assisted

More information

General Single Ion Calibration. Pete 14-May-09

General Single Ion Calibration. Pete 14-May-09 General Single Ion Calibration Pete 14-May-09 Purpose of SI calibration Measure the instrument response of a single ion. Necessary for understanding of error in instrument (counting statistics) Calculation

More information

Aliccia Bollig-Fischer, PhD Department of Oncology, Wayne State University Associate Director Genomics Core Molecular Therapeutics Program Karmanos

Aliccia Bollig-Fischer, PhD Department of Oncology, Wayne State University Associate Director Genomics Core Molecular Therapeutics Program Karmanos Aliccia Bollig-Fischer, PhD Department of Oncology, Wayne State University Associate Director Genomics Core Molecular Therapeutics Program Karmanos Cancer Institute Development of a multiplexed assay to

More information

Analysis of Peptides via Capillary HPLC and Fraction Collection Directly onto a MALDI Plate for Off-line Analysis by MALDI-TOF

Analysis of Peptides via Capillary HPLC and Fraction Collection Directly onto a MALDI Plate for Off-line Analysis by MALDI-TOF Analysis of Peptides via Capillary HPLC and Fraction Collection Directly onto a MALDI Plate for Off-line Analysis by MALDI-TOF Application Note 219 Joan Stevens, PhD; Luke Roenneburg; Kevin Fawcett (Gilson,

More information

Phosphorylation of proteins Steve Barnes Feb 19th, 2002 in some cases, proteins are found in a stable, hyperphosphorylated state, e.g.

Phosphorylation of proteins Steve Barnes Feb 19th, 2002 in some cases, proteins are found in a stable, hyperphosphorylated state, e.g. Phosphorylation of proteins Steve Barnes Feb 19th, 2002 in some cases, proteins are found in a stable, hyperphosphorylated state, e.g., casein more interestingly, in most other cases, it is a transient

More information

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry and Proteomics: A New Era in Anaerobic Microbiology

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry and Proteomics: A New Era in Anaerobic Microbiology SUPPLEMENT ARTICLE Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry and Proteomics: A New Era in Anaerobic Microbiology Haroun N. Shah, Carrina J. Keys, Oliver Schmid, and Saheer

More information

The vapour of imidazolium based ionic liquids: a mass spectrometry study

The vapour of imidazolium based ionic liquids: a mass spectrometry study The vapour of imidazolium based ionic liquids: a mass spectrometry study A. Deyko, K. R. J. Lovelock*, P. Licence, R. G. Jones School of Chemistry The University of Nottingham University Park Nottingham

More information

Three Biomarkers Identified from Serum Proteomic Analysis for the Detection of Early Stage Ovarian Cancer

Three Biomarkers Identified from Serum Proteomic Analysis for the Detection of Early Stage Ovarian Cancer [CANCER RESEARCH 64, 5882 5890, August 15, 2004] Three Biomarkers Identified from Serum Proteomic Analysis for the Detection of Early Stage Ovarian Cancer Zhen Zhang, 1 Robert C. Bast, Jr., 2 Yinhua Yu,

More information

New developments in pathogenesis, gastric cancer. Matthias Ebert. II. Medizinische Klinik Klinikum rechts der Isar TU München

New developments in pathogenesis, gastric cancer. Matthias Ebert. II. Medizinische Klinik Klinikum rechts der Isar TU München New developments in pathogenesis, diagnosis, therapy and prevention of gastric cancer Matthias Ebert II. Medizinische Klinik Klinikum rechts der Isar TU München Gastric Cancer Pathogenesis Diagnosis Treatment

More information

Summary. Correspondence Edward W. Cowen. Accepted for publication 24 May 2007

Summary. Correspondence Edward W. Cowen.   Accepted for publication 24 May 2007 CLINICAL AND LABORATORY INVESTIGATIONS DOI 10.1111/j.1365-2133.2007.08185.x Differentiation of tumour-stage mycosis fungoides, psoriasis vulgaris and normal controls in a pilot study using serum proteomic

More information

MS/MS to Targeted Proteomics (MRM)

MS/MS to Targeted Proteomics (MRM) MS/MS to Targeted Proteomics (MRM) How it worked on the Human Lens Proteome Jayson Falkner PhD jay@singleorganism.com Genes Show Limited Value in Predicting Diseases With only a few exceptions, what the

More information

Hiroya Hidaka *1), Masaki Takiwaki 2), Mine Yamashita 2), Shinya Otsuki 1), Kenji Kawasaki 3), Mitsutoshi Sugano 3) and Takayuki Honda 4)

Hiroya Hidaka *1), Masaki Takiwaki 2), Mine Yamashita 2), Shinya Otsuki 1), Kenji Kawasaki 3), Mitsutoshi Sugano 3) and Takayuki Honda 4) Mild acid hydrolysis of sphingolipids yields lysosphingolipids: a matrix-assisted laser desorption and ionization time-of-flight mass spectrometry study Hiroya Hidaka *1), Masaki Takiwaki 2), Mine Yamashita

More information