Proteomics software at MSI. Pratik Jagtap Minnesota Supercomputing institute
|
|
|
- Antony Murphy
- 6 years ago
- Views:
Transcription
1 Proteomics software at MSI. Pratik Jagtap Minnesota Supercomputing institute
2 Proteomics software at MSI. proteomics : emerging technology proteomics workflow search algorithms de novo analysis : Peaks Statistical validation of protein identification Quantitative tools Targeted proteomics Data dissemination : Tranche
3 Proteomics Fifteen Years Ago
4 Two-Dimensional gel electrophoresis pi Mw Proteins are resolved based on their isolelectric point (using isoelectric focusing) and then molecular weight (using SDS-PAGE). Gels are compared, differentially expressed proteins are excised and identified.
5 Proteomics Fifteen Years Ago Mass Spectrometry Data Extrac5on. Search algorithm Analysis So9ware that correlates the protein ID to the excised gel spot.
6 Genomics Genomics : Number of Databases for search and Shotgun analysis.
7 Multi-Dimensional Protein Identification Technology
8 mass spectrometry
9 Mass Spectrometers & data formats Thermofinnigan Xcalibur /.raw Life Technologies Analyst /.wiff ;.t2d Waters Masslynx /.raw Bruker.baf Sequest ProteinPilot X! tandem OMSSA Mascot
10 Proteomics workflow Protein Peptide Fragmentation Mass spectrum Search against database.
11 mass spectrum Intensity Mass / charge
12 Proteo-Informatics Mass Spectrometry Mass spectral data. Search algorithm De novo Tools. Sta5s5cal valida5on of pep5de and protein iden5fica5ons. Quan5ta5ve Tools. Targeted Proteomics Data Dissemina5on
13 search algorithm Mass Spectrometry Mass spectral data. Search algorithm
14 search algorithm Mass Spectrometry Mass spectral data. Search algorithm Sequest X!tandem OMSSA MaxQuant RDC : sdvlapp32 ProteinPilot CPC9 ; CGL 138. Mascot
15 Protip / TINT Raw Data from Orbitrap mzxml format Mgf format dta format X!TANDEM search OMSSA search SEQUEST search MASCOT search Scaffold Analysis Scaffold Viewer Powered by
16 performing multiple searches through Protip HUMAN DATASET MASCOT search Sequest X! tandem 441 Mascot All Together # of 462 proteins Sequest + Mascot Sequest + X! tandem X! tandem + Mascot Powered by
17 Search algorithm PROTEINPILOT
18 ProteinPilot accounts for more spectra by screening for large number of Glu >pyro Glu itraq4plex Methylthio No itraq4plex Amino(Y) Arg >GluSA(R) Deamidated(N) Deamidated(Q) Dehydrated(D) Dehydrated(E) Dehydrated(S) Dehydrated(T) Delta:H(4)C(2)(H) Dethiomethyl(M) itraq4plex(h) itraq4plex(k) itraq4plex(s) itraq4plex(t) itraq4plex(y) Methylthio(C) G A substitution Hydroxy-proline Dioxidation (W) itraq4plex(ser)
19 Search algorithm maxquant MaxQuant is an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data. MaxQuant detects peaks, isotope clusters and stable amino acid isotopelabeled (SILAC) peptide pairs as three-dimensional objects in m/z, elution time and signal intensity space. By integrating multiple mass measurements, mass accuracy in the p.p.b. range is achieved. MaxQuant quantifies several hundred thousand peptides per SILACproteome experiment.
20 De novo Tools. PEAKS Options No DB de novo Sequence but no ID Protein DB Multiple software Homologous DB Protein ID inchorus SPIDER Sequence with ID high confidence Sequence ID Sequence with putative ID data in different formats Protein ID PTM Finder PTMs Protein ID PEAKS Q quantity
21 De novo Tools. PEAKS resources at MSI PEAKS Online Get a password from Tu. Set up a search using peaklist. Monitor your search status. Links for.anz files that can be used further in PEAKS Client. PEAKS Client v4.5 PEAKS Client available at CGL : CPC7 and CPC10. Use remote access to cpc7.msi.umn.edu or cpc10.msi.umn.edu Use your.anz file (generated from Online search) for further analysis.
22 Sta5s5cal valida5on of pep5de and protein iden5fica5ons.
23 Scaffold Sta5s5cal valida5on of pep5de and protein iden5fica5ons.
24 Proteomics Quantitatition
25 itraq : Isobaric Tags for Relative and Absolute Quantification. Isobaric Tag (Total mass = 145) Reporter Charged Balance Neutral loss Peptide Reactive Group Trypsin digest PRG PRG PRG PRG Mix MS -N H -N H -N H -N H MS [Reporter-Balance-Peptide] MS/MS % Intensity % Intensity Mass (m/z) QGQPIGLGEASNDTWI TTK Mass (m/z)
26 Quan5ta5ve Tool maxquant MaxQuant quantifies several hundred thousand peptides per SILAC-proteome experiment.
27 ProteinPilot supports and of itraq datasets.
28 Targeted Proteomics MRM Selectivity, Sensitivity and Dynamic Range Quantitative Proteomics Results Prediction Choose and Optimize Transistions
29 Data Dissemina5on Tranche Tranche is a free and open source file sharing tool that enables the storage of large amounts of data. Designed and built with scientists and researchers in mind, Tranche can handle very large data sets, is secure, is scalable, and all data sets are citable in scientific journals.
30 LAST WORD Sequest X! tandem OMSSA MaxQuant ProteinPilot Mascot Scaffold PEAKS TPP Tranche Trans-proteomic Pipeline Pipeline ProTIP Questions? Pratik Jagtap
Protein Grouping, FDR Analysis and Databases.
Protein Grouping, FDR Analysis and Databases. March 15th 2012 Pratik Jagtap The Minnesota http://www.mass.msi.umn.edu/ Protein Grouping, FDR Analysis and Databases Overview. Protein Grouping : Concept
Strategies for Quantitative Proteomics. Atelier "Protéomique Quantitative" La Grande Motte, France - June 26, 2007
Strategies for Quantitative Proteomics Atelier "Protéomique Quantitative", France - June 26, 2007 Bruno Domon, Ph.D. Institut of Molecular Systems Biology ETH Zurich Zürich, Switzerland OUTLINE Introduction
Spectral Counting Approaches and PEAKS
Spectral Counting Approaches and PEAKS INBRE Proteomics Workshop, April 5, 2017 Boris Zybailov Department of Biochemistry and Molecular Biology University of Arkansas for Medical Sciences 1. Introduction
Quantitative mass spec based proteomics
Quantitative mass spec based proteomics Tuula Nyman Institute of Biotechnology tuula.nyman@helsinki.fi THE PROTEOME The complete protein complement expressed by a genome or by a cell or a tissue type (M.
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 Powerful mass spectrometers like
PROTEOINFORMATICS OVERVIEW
PROTEOINFORMATICS OVERVIEW August 11th 2016 Pratik Jagtap Center for Mass Spectrometry and Proteomics http://www.cbs.umn.edu/msp Outline PROTEOMICS WORKFLOW PEAKLIST PROCESSING Search Databases Overview
High-throughput Proteomic Data Analysis. Suh-Yuen Liang ( 梁素雲 ) NRPGM Core Facilities for Proteomics and Glycomics Academia Sinica Dec.
High-throughput Proteomic Data Analysis Suh-Yuen Liang ( 梁素雲 ) NRPGM Core Facilities for Proteomics and Glycomics Academia Sinica Dec. 9, 2009 High-throughput Proteomic Data Are Information Rich and Dependent
Center for Mass Spectrometry and Proteomics Phone (612) (612)
Outline Database search types Peptide Mass Fingerprint (PMF) Precursor mass-based Sequence tag Results comparison across programs Manual inspection of results Terminology Mass tolerance MS/MS search FASTA
Mass Spectrometry Based Proteomics Data Analysis Using GalaxyP
Mass Spectrometry Based Proteomics Data Analysis Using GalaxyP GCC 2015 GalaxyP Workshop July 6th, 2015 Norwich, UK Presenters: Tim Griffin, Pratik Jagtap and James Johnson Documentation: Kevin Murray,
Innovations for Protein Research. Protein Research. Powerful workflows built on solid science
Innovations for Protein Research Protein Research Powerful workflows built on solid science Your partner in discovering innovative solutions for quantitative protein and biomarker research Applied Biosystems/MDS
Proteomics. Proteomics is the study of all proteins within organism. Challenges
Proteomics Proteomics is the study of all proteins within organism. Challenges 1. The proteome is larger than the genome due to alternative splicing and protein modification. As we have said before we
ProteinPilot Software Overview
ProteinPilot Software Overview High Quality, In-Depth Protein Identification and Protein Expression Analysis Sean L. Seymour and Christie L. Hunter SCIEX, USA As mass spectrometers for quantitative proteomics
Improving Productivity with Applied Biosystems GPS Explorer
Product Bulletin TOF MS Improving Productivity with Applied Biosystems GPS Explorer Software Purpose GPS Explorer Software is the application layer software for the Applied Biosystems 4700 Proteomics Discovery
Proteomics and some of its Mass Spectrometric Applications
Proteomics and some of its Mass Spectrometric Applications What? Large scale screening of proteins, their expression, modifications and interactions by using high-throughput approaches 2 1 Why? The number
Bioinformatic Tools. So you acquired data.. But you wanted knowledge. So Now What?
Bioinformatic Tools So you acquired data.. But you wanted knowledge So Now What? We have a series of questions What the Heck is That Ion? How come my MW does not match? How do I make a DB to search against?
PTM Identification and Localization from MS Proteomics Data
05.10.17 PTM Identification and Localization from MS Proteomics Data Marc Vaudel Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway KG Jebsen Center for Diabetes
Quantitative Analysis on the Public Protein Prospector Web Site. Introduction
Quantitative Analysis on the Public Protein Prospector Web Site Peter R. Baker 1, Nicholas J. Agard 2, Alma L. Burlingame 1 and Robert J. Chalkley 1 1 Mass Spectrometry Facility, Dept. of Pharmaceutical
Mass Spectrometry and Proteomics - Lecture 6 - Matthias Trost Newcastle University
Mass Spectrometry and Proteomics - Lecture 6 - Matthias Trost Newcastle University matthias.trost@ncl.ac.uk Previously Quantitation techniques Label-free TMT SILAC Peptide identification and FDR 194 Lecture
Confident Protein ID using Spectrum Mill Software
Welcome to our E-Seminar: Confident Protein ID using Spectrum Mill Software Slide 1 Spectrum Mill Informatics Software Start with batches of raw MS data! Sp ec t ru m Mi ll Biologist-friendly answers!
基于质谱的蛋白质药物定性定量分析技术及应用
基于质谱的蛋白质药物定性定量分析技术及应用 蛋白质组学质谱数据分析 单抗全蛋白测序及鉴定 Bioinformatics Solutions Inc. Waterloo, ON, Canada 上海 中国 2017 1 3 PEAKS Studio GUI Introduction Overview of PEAKS Studio GUI Project View Tasks, running info,
Principles of Proteomic Methods
Principles of Proteomic Methods Marc Wilkins School of Biotechnology and Biomolecular Sciences What is Proteomics? - proteomics is the study of proteomes - proteomics aims to: separate, identify and characterise
Proteomics: A Challenge for Technology and Information Science. What is proteomics?
Proteomics: A Challenge for Technology and Information Science CBCB Seminar, November 21, 2005 Tim Griffin Dept. Biochemistry, Molecular Biology and Biophysics tgriffin@umn.edu What is proteomics? Proteomics
Protein Valida-on (Sta-s-cal Inference) and Protein Quan-fica-on. Center for Mass Spectrometry and Proteomics Phone (612) (612)
Protein Valida-on (Sta-s-cal Inference) and Protein Quan-fica-on Terminology Pep-de Spectrum Match Target / Decoy False discovery rate Shared pep-de Parsimony One hit wonders SPECTRUM Rela-ve Abundance
ProteinPilot Software for Protein Identification and Expression Analysis
ProteinPilot Software for Protein Identification and Expression Analysis Providing expert results for non-experts and experts alike ProteinPilot Software Overview New ProteinPilot Software transforms protein
How to view Results with Scaffold. Proteomics Shared Resource
How to view Results with Scaffold Proteomics Shared Resource Starting out Download Scaffold from http://www.proteomes oftware.com/proteom e_software_prod_sca ffold_download.html Follow installation instructions
About OMICS Group Conferences
About OMICS Group OMICS Group International is an amalgamation of Open Access publications and worldwide international science conferences and events. Established in the year 2007 with the sole aim of
Peptide and protein identification in mass spectrometry based proteomics. Yafeng Zhu, PhD student Karolinska Institutet, Scilifelab
Peptide and protein identification in mass spectrometry based proteomics Yafeng Zhu, PhD student Karolinska Institutet, Scilifelab 2017-10-12 Content How is the peptide sequence identified? What is the
Center for Mass Spectrometry and Proteomics Phone (612) (612)
Welcome to the Center for Mass Spectrometry & Proteomics Workshop Department of Biochemistry, Molecular Biology and Biophysics College of Biological Sciences University of Minnesota http://cbs.umn.edu/cmsp/
PEAKS 8 User Manual. PEAKS Team
PEAKS 8 User Manual PEAKS Team PEAKS 8 User Manual PEAKS Team Publication date 2016 Table of Contents 1. Overview... 1 1. How to Use This Manual... 1 2. What Is PEAKS?... 1 3. What Is New in PEAKS 8?...
MIAPE: Mass Spectrometry Informatics
MIAPE: Mass Spectrometry Informatics Pierre-Alain Binz[1,2]*, Robert Barkovich[3], Ronald C. Beavis[4], David Creasy[5], David M. Horn[6], Randall K. Julian Jr.[7], Sean L. Seymour[8], Chris F. Taylor[9],
FACTORS THAT AFFECT PROTEIN IDENTIFICATION BY MASS SPECTROMETRY HAOFEI TIFFANY WANG. (Under the Direction of Ron Orlando) ABSTRACT
FACTORS THAT AFFECT PROTEIN IDENTIFICATION BY MASS SPECTROMETRY by HAOFEI TIFFANY WANG (Under the Direction of Ron Orlando) ABSTRACT Mass spectrometry combined with database search utilities is a valuable
N- The rank of the specified protein relative to all other proteins in the list of detected proteins.
PROTEIN SUMMARY file N- The rank of the specified protein relative to all other proteins in the list of detected proteins. Unused (ProtScore) - A measure of the protein confidence for a detected protein,
Understanding life WITH NEXT GENERATION PROTEOMICS SOLUTIONS
Innovative services and products for highly multiplexed protein discovery and quantification to help you understand the biological processes that shape life. Understanding life WITH NEXT GENERATION PROTEOMICS
Application Note TOF/MS
Application Note TOF/MS New Level of Confidence for Protein Identification: Results Dependent Analysis and Peptide Mass Fingerprinting Using the 4700 Proteomics Discovery System Purpose The Applied Biosystems
LTQ Orbitrap XL Hybrid FT Mass Spectrometer Unrivaled Performance and Flexibility
m a s s s p e c t r o m e t r y LTQ Orbitrap XL Hybrid FT Mass Spectrometer Unrivaled Performance and Flexibility Part of Thermo Fisher Scientific LTQ Orbitrap XL OFFERING OUTSTANDING MASS ACCURACY, RESOLVING
Just launched. Operated by. Karel Harant
Just launched Operated by Karel Harant 1 Rapid development of instrumentation Decline of MALDI-based instruments 2D protein electrophoresis abandoned 80% of proteomic data acquired in last two years (Somebody,
Key questions of proteomics. Bioinformatics 2. Proteomics. Foundation of proteomics. What proteins are there? Protein digestion
s s Key questions of proteomics What proteins are there? Bioinformatics 2 Lecture X roteomics How much is there of each of the proteins? - Absolute quantitation - Stoichiometry What (modification/splice)
MBios 478: Mass Spectrometry Applications [Dr. Wyrick] Slide #1. Lecture 25: Mass Spectrometry Applications
![MBios 478: Mass Spectrometry Applications [Dr. Wyrick] Slide #1. Lecture 25: Mass Spectrometry Applications](/thumbs/74/71368870.jpg "MBios 478: Mass Spectrometry Applications [Dr. Wyrick] Slide #1. Lecture 25: Mass Spectrometry Applications")
MBios 478: Mass Spectrometry Applications [Dr. Wyrick] Slide #1 Lecture 25: Mass Spectrometry Applications Measuring Protein Abundance o ICAT o DIGE Identifying Post-Translational Modifications Protein-protein
How to view Results with. Proteomics Shared Resource
How to view Results with Scaffold 3.0 Proteomics Shared Resource An overview This document is intended to walk you through Scaffold version 3.0. This is an introductory guide that goes over the basics
CCRD Proteomics facility RIH-Brown University
CCRD Proteomics facility RIH-Brown University Experimental design TO Publication Nagib Ahsan, PhD Where is the CCRD Proteomics Facility COBRE CCRD Proteomics Core Facility 1 Hoppin St, Providence, 02903
New Approaches to Quantitative Proteomics Analysis
New Approaches to Quantitative Proteomics Analysis Chris Hodgkins, Market Development Manager, SCIEX ANZ 2 nd November, 2017 Who is SCIEX? Founded by Dr. Barry French & others: University of Toronto Introduced
Mass spectrometry Proteomics and MIAPE
Mass spectrometry Proteomics and MIAPE Florian Breitwieser - Research Center of Molecular Medicine, Vienna, Austria Nov 18, 2010 Outline BioC-devel meeting Europe 17.-18. 11. 2010 MS-MS Proteomics Standard
Strategies in proteomics
Strategies in proteomics Systems biology - understand cellpathways, network, and complex interacting (includes Genomics, Proteomics, Metabolomics..) Biological processes - characterize protein complexes,
Current state of proteomics standardization and (C-)HPP data quality guidelines
9/6/2016 3 Department of Pharmacy Analytical Biochemistry Current state of proteomics standardization and (C-)HPP data quality guidelines DTL focus meeting on data integration, standards and fair principles
Informatics on MS-Based Proteomics
Informatics on MS-Based Proteomics Yet-Ran Chen 陳逸然 Associate Research Fellow / Associate Professor Agricultural Biotech. Research Center / Institute of Biotechnology & Genomics and Systems Biology Academia
Topics. Protein Bioinformatics ( ) Progression of Protein Analysis by Mass Spectrometry. Protein identification by mass spectrometry
Protein Bioinformatics (26.655) Lecture 15: Quantitative Proteomics Tuesday, May 5, 28 Robert N. Cole, Ph.D. Mass Spectrometry/Proteomics Facility at Johns Hopkins School of Medicine 371 Broadway Research
A New Strategy for Quantitative Proteomics Using Isotope-Coded Protein Labels
ICPL TM -Isotope Coded Label A New Strategy for Quantitative Proteomics Using Isotope-Coded Labels Alexander Schmidt Department for Max-Planck-Institute of Biochemistry Spotfire User Conference 2004, Cologne
MRMPilot Software: Accelerating MRM Assay Development for Targeted Quantitative Proteomics
Product Bulletin MRMPilot Software: Accelerating MRM Assay Development for Targeted Quantitative Proteomics With Unique QTRAP System Technology Overview Targeted peptide quantitation is a rapidly growing
A Highly Accurate Mass Profiling Approach to Protein Biomarker Discovery Using HPLC-Chip/ MS-Enabled ESI-TOF MS
Application Note PROTEOMICS METABOLOMICS GENOMICS INFORMATICS GLYILEVALCYSGLUGLNALASERLEUASPARG CYSVALLYSPROLYSPHETYRTHRLEUHISLYS A Highly Accurate Mass Profiling Approach to Protein Biomarker Discovery
Proteomics Informatics (BMSC-GA 4437)
Proteomics Informatics (BMSC-GA 4437) Instructor David Fenyö Contact information David@FenyoLab.org htt://fenyolab.org/resentations/proteomics_informatics_2013/ Learning Objectives Be able analyze a roteomics
What are proteomics? And what can they tell us about seed maturation and germination?
Danseed Symposium Kobæk Strand, Skelskør 14 March, 2017 What are proteomics? And what can they tell us about seed maturation and germination? Ian Max Møller Department of Molecular Biology and Genetics
Spectrum Mill MS Proteomics Workbench. Comprehensive tools for MS proteomics
Spectrum Mill MS Proteomics Workbench Comprehensive tools for MS proteomics Meeting the challenge of proteomics data analysis Mass spectrometry is a core technology for proteomics research, but large-scale
Combination of Isobaric Tagging Reagents and Cysteinyl Peptide Enrichment for In-Depth Quantification
Combination of Isobaric Tagging Reagents and Cysteinyl Peptide Enrichment for In-Depth Quantification Protein Expression Analysis using the TripleTOF 5600 System and itraq Reagents Vojtech Tambor 1, Christie
ichemistry SOLUTIONS Integrated chemistries to boost mass spectrometry workflows
ichemistry SOLUTIONS Integrated chemistries to boost mass spectrometry workflows ichemistry SOLUTIONS ichemistry solutions ichemistry solutions are the world s only reagents and consumables that are customdesigned
ProMass HR Applications!
ProMass HR Applications! ProMass HR Features Ø ProMass HR includes features for high resolution data processing. Ø ProMass HR includes the standard ProMass deconvolution algorithm as well as the full Positive
Quantification of Isotope Encoded Proteins in 2D Gels
Quantification of Isotope Encoded Proteins in 2D Gels Using Surface Enhanced Resonance Raman Giselle M. Knudsen 1, Brandon M. Davis 2, Shirshendu K. Deb 1, Yvette Loethen 2, Ravindra Gudihal 1, Pradeep
Využití cílené proteomiky pro kontrolu falšování potravin: identifikace peptidových markerů v mase pomocí LC- Q Exactive MS/MS
Využití cílené proteomiky pro kontrolu falšování potravin: identifikace peptidových markerů v mase pomocí LC- Q Exactive MS/MS Michal Godula Ph.D. Thermo Fisher Scientific The world leader in serving science
De novo sequencing in the identification of mass data. Wang Quanhui Liu Siqi Beijing Institute of Genomics, CAS
De novo sequencing in the identification of mass data Wang Quanhui Liu Siqi Beijing Institute of Genomics, CAS The difficulties in mass data analysis Although the techniques of genomic sequencing are being
An Improved Approach for Glycan Structure Identification from HCD MS/MS Spectra
Introduction Method Experiments An Improved Approach for Glycan Structure Identification from HCD MS/MS Spectra Weiping Sun, Yi Liu, Gilles Lajoie, Bin Ma and Kaizhong Zhang Department of Computer Science,
Journal of Biomedical Informatics
Journal of Biomedical Informatics 42 (2009) 644 653 Contents lists available at ScienceDirect Journal of Biomedical Informatics journal homepage: www.elsevier.com/locate/yjbin Proteomic Feature Maps: A
Filter-based Protein Digestion (FPD): A Detergent-free and Scaffold-based Strategy for TMT workflows
Supporting Information Filter-based Protein Digestion (FPD): A Detergent-free and Scaffold-based Strategy for TMT workflows Ekaterina Stepanova 1, Steven P. Gygi 1, *, Joao A. Paulo 1, * 1 Department of
LC/MS/MS Solutions for Biomarker Discovery QSTAR. Elite Hybrid LC/MS/MS System. More performance, more reliability, more answers
LC/MS/MS Solutions for Biomarker Discovery QSTAR Elite Hybrid LC/MS/MS System More performance, more reliability, more answers More is better and the QSTAR Elite LC/MS/MS system has more to offer. More
Detecting Challenging Post Translational Modifications (PTMs) using CESI-MS
Detecting Challenging Post Translational Modifications (PTMs) using CESI-MS Sensitive workflow for the detection of PTMs in biological samples from small sample volumes Klaus Faserl, 1 Bettina Sarg, 1
Genomics, Transcriptomics and Proteomics
Genomics, Transcriptomics and Proteomics GENES ARNm PROTEINS Genomics Transcriptomics Proteomics (10 6 protein forms?) Maturation PTMs Partners Localisation EDyP Lab : «Exploring the Dynamics of Proteomes»
A NEW FRAMEWORK FOR QUANTITATIVE MASS SPECTROMETRY DATA ANALYSIS AND ITS APPLICATION TO DISCOVERY BASED PROTEOMICS IN C. ELEGANS
A NEW FRAMEWORK FOR QUANTITATIVE MASS SPECTROMETRY DATA ANALYSIS AND ITS APPLICATION TO DISCOVERY BASED PROTEOMICS IN C. ELEGANS by Christopher J. Mitchell A dissertation submitted to Johns Hopkins University
Basic protein and peptide science for proteomics. Henrik Johansson
Basic protein and peptide science for proteomics Henrik Johansson Proteins are the main actors in the cell Membranes Transport and storage Chemical factories DNA Building proteins Structure Proteins mediate
Appendix. Table of contents
Appendix Table of contents 1. Appendix figures 2. Legends of Appendix figures 3. References Appendix Figure S1 -Tub STIL (41) DVFFYQADDEHYIPR (55) (64) AVLLDLEPR (72) 1 451aa (1071) YLNENQLSQLSVTR (1084)
Protein Reports CPTAC Common Data Analysis Pipeline (CDAP)
Protein Reports CPTAC Common Data Analysis Pipeline (CDAP) v. 4/13/2015 Summary The purpose of this document is to describe the protein reports generated as part of the CPTAC Common Data Analysis Pipeline
RockerBox. Filtering massive Mascot search results at the.dat level
RockerBox Filtering massive Mascot search results at the.dat level Challenges Big experiments High amount of data Large raw and.dat files (> 2GB) How to handle our results?? The 2.2 peptide summary could
NPTEL
NPTEL Syllabus Proteomics: Principles and Techniques - Video course COURSE OUTLINE An introduction to proteomics: Basics of protein structure and function, An overview of systems biology, Evolution from
Modification Site Localization Scoring Integrated into a Search Engine
Modification Site Localization Scoring Integrated into a Search Engine Peter R. Baker 1, Jonathan C. Trinidad 1, Katalin F. Medzihradszky 1, Alma L. Burlingame 1 and Robert J. Chalkley 1 1 Mass Spectrometry
Faster, easier, flexible proteomics solutions
Agilent HPLC-Chip LC/MS Faster, easier, flexible proteomics solutions Our measure is your success. products applications soft ware services Phospho- Anaysis Intact Glycan & Glycoprotein Agilent s HPLC-Chip
Supplementary Tables. Note: Open-pFind is embedded as the default open search workflow of the pfind tool. Nature Biotechnology: doi: /nbt.
Supplementary Tables Supplementary Table 1. Detailed information for the six datasets used in this study Dataset Mass spectrometer # Raw files # MS2 scans Reference Dong-Ecoli-QE Q Exactive 5 202,452 /
Proteomics And Cancer Biomarker Discovery. Dr. Zahid Khan Institute of chemical Sciences (ICS) University of Peshawar. Overview. Cancer.
Proteomics And Cancer Biomarker Discovery Dr. Zahid Khan Institute of chemical Sciences (ICS) University of Peshawar Overview Proteomics Cancer Aims Tools Data Base search Challenges Summary 1 Overview
Investigation of a Mammalian Cellular Model for Differential Protein Expression Analysis Using 1D PAGE and Cleavable ICAT Reagents
pplication Note 1D PGE and Cleavable ICT Reagents Investigation of a Mammalian Cellular Model for Differential Protein Expression nalysis Using 1D PGE and Cleavable ICT Reagents Overview The use of two-dimensional
Supplementary Information
Identifying sources of tick blood meals using unidentified tandem mass spectral libraries Özlem Önder 1, Wenguang Shao 2, Brian Kemps 1, Henry Lam 2,3,*, Dustin Brisson 1,* 1 Department of Biology, University
Utilizing novel technology for the analysis of therapeutic antibodies and host cell protein contamination
Utilizing novel technology for the analysis of therapeutic antibodies and host cell protein contamination Kelli Jonakin, Ph.D. Senior Field Application Scientist, Seattle, WA Eric Johansen, Ph.D. Senior
Comparability Analysis of Protein Therapeutics by Bottom-Up LC-MS with Stable Isotope-Tagged Reference Standards
Comparability Analysis of Protein Therapeutics by Bottom-Up LC-MS with Stable Isotope-Tagged Reference Standards 16 September 2011 Abbott Bioresearch Center, Worcester, MA USA Manuilov, A. V., C. H. Radziejewski
Protein De novo Sequencing
Protein De novo Sequencing by Rong Wang A thesis presented to the University of Waterloo in fulfillment of the thesis requirement for the degree of Master of Mathematics in Computer Science Waterloo, Ontario,
User Rules & Regulations Core Facility for Mass Spectrometry and Proteomics (CFMP) at the Centre for Molecular Biology of Heidelberg University (ZMBH)
User Rules & Regulations Core Facility for Mass Spectrometry and Proteomics (CFMP) at the Centre for Molecular Biology of Heidelberg University (ZMBH) Accepted on 30. January 2017 1 Definition and aims
W.M. Keck Foundation Biotechnology Research Laboratory. Christopher Colangelo, Ph.D.
Yl Yale University Ui it School Sh of fmdii Medicine W.M. Keck Foundation Biotechnology Research Laboratory Christopher Colangelo, Ph.D. Quantitative Protein Profiling & Targeted Protein Expression NIDA
BIOINFORMATICS ORIGINAL PAPER
BIOINFORMATICS ORIGINAL PAPER Vol 25 no 22 29, pages 2969 2974 doi:93/bioinformatics/btp5 Data and text mining Improving peptide identification with single-stage mass spectrum peaks Zengyou He and Weichuan
Advances in analytical biochemistry and systems biology: Proteomics
Advances in analytical biochemistry and systems biology: Proteomics Brett Boghigian Department of Chemical & Biological Engineering Tufts University July 29, 2005 Proteomics The basics History Current
Protein Identification & Protein Profiling in the Neuroproteome Kathy Stone
Protein Identification & Protein Profiling in the Neuroproteome Kathy Stone Overview of the Neuroproteomics Cores Synergy Protein Profiling and Identification, Biophysics, and Phosphoinositide Analysis
Absolute quantitation of seed allergens using tandem mass spectrometry
Absolute quantitation of seed allergens using tandem mass spectrometry Severin E. Stevenson AEIC spring meeting April 18 th, 2012 Hotel Indigo Research Triangle Park, NC Overview Quantitative proteomics
Agilent Software Tools for Mass Spectrometry Based Multi-omics Studies
Agilent Software Tools for Mass Spectrometry Based Multi-omics Studies Technical Overview Introduction The central dogma for biological information flow is expressed as a series of chemical conversions
ENCODE DCC Antibody Validation Document
ENCODE DCC Antibody Validation Document Date of Submission 09/12/12 Name: Trupti Kawli Email: trupti@stanford.edu Lab Snyder Antibody Name: SREBP1 (sc-8984) Target: SREBP1 Company/ Source: Santa Cruz Biotechnology
Proteomics and Cancer
Proteomics and Cancer Japan Society for the Promotion of Science (JSPS) Science Dialogue Program at Niitsu Senior High School Niitsu, Niigata September 4th 2006 Vladimir Valera, M.D, PhD JSPS Postdoctoral
See More, Much More Clearly
TRIPLETOF 6600 SYSTEM WITH SWATH ACQUISITION 2.0 See More, Much More Clearly NEXT-GENERATION PROTEOMICS PLATFORM Every Peak. Every Run. Every Time. The Next-generation Proteomics Platform is here: The
Glycomics Project Overview
Wright State University CORE Scholar Kno.e.sis Publications The Ohio Center of Excellence in Knowledge- Enabled Computing (Kno.e.sis) 2007 Glycomics Project Overview Satya S. Sahoo Wright State University
Supporting Information for
Supporting Information for CharmeRT: Boosting peptide identifications by chimeric spectra identification and retention time prediction Viktoria Dorfer*,,a, Sergey Maltsev,b, Stephan Winkler a, Karl Mechtler*,b,c.
Computing with large data sets
Computing with large data sets Richard Bonneau, spring 2009 Lecture 14 (week 8): genomics 1 Central dogma Gene expression DNA RNA Protein v22.0480: computing with data, Richard Bonneau Lecture 14 places
PRIDE Inspector: a tool to visualize and validate MS proteomics data
! PRIDE Inspector: a tool to visualize and validate MS proteomics data Rui Wang, Antonio Fabregat, Daniel Ríos, David Ovelleiro, Joseph M. Foster, Richard G. Côté, Johannes Griss, Attila Csordas, Yasset
Supplemental Materials
Supplemental Materials MSGFDB Parameters For all MSGFDB searches, the following parameters were used: 30 ppm precursor mass tolerance, enable target-decoy search, enzyme specific scoring (for Arg-C, Asp-N,
Nature Biotechnology: doi: /nbt Supplementary Figure 1. The workflow of Open-pFind.
Supplementary Figure 1 The workflow of Open-pFind. The MS data are first preprocessed by pparse, and then the MS/MS data are searched by the open search module. Next, the MS/MS data are re-searched by
Publishing Proteomics Data: How to Win Reviewers and Influence Editors
Publishing Proteomics Data: How to Win Reviewers and Influence Editors Susan T. Weintraub, Ph.D. University of Texas Health Science Center at San Antonio St. Louis - ASMS 2015 San Antonio - ASMS 2016 Why
timstof Pro powered by PASEF and the Evosep One for high speed and sensitive shotgun proteomics
timstof Pro powered by PASEF and the Evosep One for high speed and sensitive shotgun proteomics The Parallel Accumulation Serial Fragmentation (PASEF) method for trapped ion mobility spectrometry (TIMS)
Overview. Tools for Protein Sample Preparation, 2-D Electrophoresis, and Imaging and Analysis
Expression Proteomics // Tools for Protein Separation and Analysis www.expressionproteomics.com 1 2 3 4 Overview Tools for Protein Sample Preparation, 2-D Electrophoresis, and Imaging and Analysis overview
Metabolite Identification Workflows: A Flexible Approach to Data Analysis and Reporting
Metabolite Identification Workflows: A Flexible Approach to Data Analysis and Reporting Stephen McDonald and Mark D. Wrona Waters Corporation, Milford, MA, USA A P P L I C AT ION B E N E F I T S The flexibility
BST 226 Statistical Methods for Bioinformatics David M. Rocke. February 10, 2014 BST 226 Statistical Methods for Bioinformatics 1
BST 226 Statistical Methods for Bioinformatics David M. Rocke February 10, 2014 BST 226 Statistical Methods for Bioinformatics 1 Proteomics by LS/MS/MS Proteins are digested with trypsin or other proteases