Proteomic Profiling and Analytical Chemistry, Second Edition: The Crossroads PDF
Preview Proteomic Profiling and Analytical Chemistry, Second Edition: The Crossroads
PROTEOMIC PROFILING AND ANALYTICAL CHEMISTRY The Crossroads SECOND EDITION Edited by P. CIBOROWSKI University of Nebraska Medical Center, Omaha, NE, United States J. SILBERRING AGH University of Science and Technology, Krakow, Poland; Polish Academy of Sciences, Zabrze, Poland AMSTERDAM BOSTON HEIDELBERG LONDON l l l NEWYORK OXFORD PARIS SANDIEGO l l l SANFRANCISCO SINGAPORE SYDNEY TOKYO l l l Elsevier Radarweg29,POBox211,1000AEAmsterdam,Netherlands TheBoulevard,LangfordLane,Kidlington,OxfordOX51GB,UK 50HampshireStreet,5thFloor,Cambridge,MA02139,USA Copyright(cid:1)2016ElsevierB.V.Allrightsreserved. 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BritishLibraryCataloguinginPublicationData AcataloguerecordforthisbookisavailablefromtheBritishLibrary LibraryofCongressCataloging-in-PublicationData AcatalogrecordforthisbookisavailablefromtheLibraryofCongress ISBN:978-0-444-63688-1 ForinformationonallElsevierpublications visitourwebsiteathttps://www.elsevier.com/ Publisher:JohnFedor AcquisitionEditor:KathrynMorissey EditorialProjectManager:AmyClark ProductionProjectManager:PaulPrasadChandramohan Designer:GregHarris TypesetbyTNQBooksandJournals LIST OF CONTRIBUTORS J.Adamec University of Nebraska e Lincoln, Lincoln, NE, United States A. Bodzo(cid:1)n-Kułakowska AGHUniversityofScienceandTechnology,Krakow, Poland C.Boone University of Nebraska e Lincoln, Lincoln, NE, United States A. Burns University of Nebraska Medical Center, Omaha, NE, United States P.Ciborowski University of Nebraska Medical Center, Omaha, NE, United States A. Drabik AGHUniversityofScienceandTechnology,Krakow, Poland K.Frederick University of Nebraska Medical Center, Omaha, NE, United States V.Havlí(cid:3)cek InstituteofMicrobiology,AcademyofSciencesofthe Czech Republic, Prague,Czech Republic J.McMillan University of Nebraska Medical Center, Omaha, NE, United States J.Meza University of Nebraska Medical Center, Omaha, NE, United States xiii xiv LIST OFCONTRIBUTORS P.Mielczarek AGHUniversityofScienceandTechnology,Krakow, Poland P.Novák InstituteofMicrobiology,AcademyofSciencesofthe Czech Republic, Prague, Czech Republic P.Olszowy University of Nebraska Medical Center, Omaha, NE, United States; Polpharma SA Pharmaceutical Works, (cid:1) StarogardGdanski,Poland F.Qiu University of Nebraska Medical Center, Omaha, NE, United States J.Silberring AGHUniversityofScienceandTechnology,Krakow, Poland; Polish Academy of Sciences,Zabrze,Poland M. Smoluch AGHUniversityofScienceandTechnology,Krakow, Poland P.Suder AGHUniversityofScienceandTechnology,Krakow, Poland J.Wiederin University of Nebraska Medical Center, Omaha, NE, United States M. Wojtkiewicz University of Nebraska Medical Center, Omaha, NE, United States F.Yu University of Nebraska Medical Center, Omaha, NE, United States PREFACE Theterm“proteomics”wascoinedinthemid-1990s; however, the history of proteomics dates back to the mid-1950sifweconsiderthefirstscientificreporton 2-dimensional electrophoresis (“Two-dimensional electrophoresis of serum proteins.” Smithies, O. and Poulik MD. Nature. 1956, 177(4518):1033. PMID: 13322019). Many laboratories used 1- and 2-dimen- sional electrophoresis for protein analyses, and even though it was not termed “profiling,” it was very similar to what we now use in proteomic research. More recently, soft ionization and development of mass spectrometry sequencing of peptides and even intact proteins, widely opened the possibilities for globalproteinanalysis.Suddenly,wefoundourselves in the middle of something that was growing rapidly and extremely attractive to pursue scientifically. Our enthusiasmforproteomicsisstillgrowingasweenter new frontiers with the development of analytical instrumentation (mass spectrometers, Ultra High Pressure Liquid Chromatography, instruments for nano-flow, analyses, etc.) and computational capa- bilities of data analysis. We strongly believe that aholisticapproachwillrevealmuchknowledgewhich isyetnotknown.Wehavelearnedthatproteomicsis a highly interdisciplinary approach but carries a risk of false-positive results if not properly controlled at theanalyticallevel.Hencewelearnedthatproteomics is still short of many standards and widely accepted quality controls. Such standards and quality control measures will be built because of our collective experience and to some extent based on “trial and error” experiments. The field of proteomics is very dynamic technologically, with new tools for sample preparation, sample analyses and data processing beingannouncedalmosteveryday.Toolsthatweuse todaymightbeeasilyreplacedtomorrowbynewand greatlyimprovedones. It is not an easy task to prepare yet another book on proteomics but we do hope that the content of xv xvi PREFACE thissecondeditionofourbookwillstimulatereaders and their interest in using a proteomics approach with care, for the benefit of expansion of our knowl- edge.Ourbookisaimedatthoseresearcherswhoare looking for a relatively compact guide that can walk them through major points of proteomic studies without greatdetailfor eachandeverystepbutwith a focus on quality control elements, frequently overlooked during daily work maintaining basic concepts and principles of proteomic studies. Therefore, Proteomic Profiling and Analytical Chem- istry: The Crossroads is written for an audience at variouslevels,technologists/technicians,undergrad- uate and graduate students, post-doctoral fellows, scientists as well as principal investigators, to high- light key points ranging from experimental design and biology of systems in question to analytical requirements andlimitations. We are indebted to all of our colleagues, coworkers, and students for their excellent contri- butions to this book. This bookcould not have been prepared without the extensive editorial work of Elsevier. Thank you all for your efforts and also for pushing us to complete materials for printing. As always, we have to say that nobody’s perfectandwe wouldbegratefulforanycommentsandsuggestions thatmayleadtotheimprovementoffutureeditions. P. Ciborowski and J. Silberring 1 INTRODUCTION J. Silberring AGHUniversityofScienceandTechnology,Krakow,Poland; PolishAcademyofSciences,Zabrze,Poland P. Ciborowski UniversityofNebraskaMedicalCenter,Omaha,NE,United States CHAPTER OUTLINE 1.1 Why Do AnalyticsMatter? 1 1.2 Expectations:Whoand What? 3 1.3 What IsNext and Where Are We Going? 4 1.1 Why Do Analytics Matter? Thesumoftheoptimalstepsintheanalyticaland proteomic analysis (process) is not equal to the optimal process in its entirety! As much as it is a trivial statement, which most of us accept to be true,ithasnotbeenfullyappreciateddespitehaving a profound impact on the success of laborious, expensive and, in many instances, lengthy projects, as proteomic studies are multistep tasks involving a variety of methods, each governed by its own strengths and limitations. The concept of a proteo- micstudycanbedepictedinmanyways.InFig.1.1, weintentionallyhighlightedanalyticalcomponents/ phases because the same rules of analytical chem- istry/biochemistry apply to discovery as well as validation experiments. The experimental design will be governed by a set of different rules, which does not include instrumentation but has biology heavily involved. As can be observed, bioinformatics analyses are not depicted in this model, as it is focused on ProteomicProfilingandAnalyticalChemistry.http://dx.doi.org/10.1016/B978-0-444-63688-1.00001-X 1 (cid:1)2016ElsevierB.V.Allrightsreserved. 2 Chapter 1 INTRODUCTION PROTEOMICS Experimental Analytical phase I Data analysis design phase phase Performance of Detection level instrumentation Bioinformatics Your question Reproducibility Sample loss New experiments Data New questions Knowledge Analytical phase II Information Validation Figure 1.1 Schematicrepresentationofaproteomicstudy. analytics.Bioinformaticswillbegovernedbyitsown set of rules which are applied to the validation of algorithms. Nevertheless, when looking at constitu- ents of a proteomic study, we realized that the scientist conducting such experiments must grasp the overview of not only how biological systems work, but also analytical boundaries for sample preparation,fractionation,andmeasurements,tools for database searches, statistics, and eventually bioinformatics tools for data analysis. Because of their complexity, proteomic studies should be con- ductedbyateamofexperts.Astheproteomicsfield evolves,thecollectiveexperiencefromanincreasing number of studies inevitably leads to widely accepted quality criteria. Although significant prog- resshas been made,many questions about uniform qualitycontrolcriteriaremaintobeanswered.Such answers will result from systematic studies con- ducted across many laboratories, platforms, and biological systems (models). Therefore, in this book we attempt to highlight in a short, yet comprehen- sive manner, the impact of the basic principles of analytical chemistry/biochemistry on the final success of a proteomic experiment. We hope that this point of view will help both biologists and chemists to better understand all components of complex proteomic study. Chapter1 INTRODUCTION 3 1.2 Expectations: Who and What? If two scientists, a biologist and chemist, sit at atableanddiscussproteomicmethodology,theywill likely emphasize different aspects of the same study, which in each viewpoint is critical for a successful outcome.Moreover,theyquiteoftenspeakintechnical languagethatisnotfullyunderstoodbytheother.This is because chemists are focused on sensitivity and accuracyofanalyticalmeasurements,whilebiologists pay attention to explaining biological/pathological effectsandarelessconcernedwithexactquantitation ofanalytes.ThisresemblesthefamouspoembyJohn G.Saxe,“TheBlindMenandtheElephant,”inwhich everyonetriestoidentifytheparttheyaretouching(ie, biologist/chemist) but nobody can get a sense of the whole system (ie, proteomic study). Biologists are willingtoacceptahighrangeofresponses,resultingin high standard deviations showing or indicating “trends”indatabehaviorthatsupporttheirhypothesis. Chemists, on the other hand, expect data to be expressed by numerical values with high precision, accuracy,reproducibility,andlowstandarddeviation. Indeed, as much as precision of analytical measure- mentsisimportant,inmanyinstances,sucheffortswill notimprovetheoveralloutputdiscriminatingbetween true and false. This is mostly because, very often, an exact correlation between quantitative change and biological effect is not defined. For example, how importantisittomeasureadifferencebetweenlevels ofproteinexpression above10-foldchangewhenthe response of biological system is already saturated bythe5-foldchangeofthisprotein?Asimilarquestion mayarisefromenzymology,wherethemostimportant factor is enzymatic activity and not the protein expressionmeasuredbyatypicalproteomicapproach, whichwillalsomeasureinactiveenzymes.Ifwebring statisticiansandbioinformaticianstothesametableas the biologist and chemist, which veryoften happens, the discussion becomes even more complicated. As illustratedinFig.1.2,ourquestioniswhatdoweseeon theothersideofourofficewallswhenwelookforthe expertiseofourfellowcolleagues?Itiscriticalforeach ofus to peeroutside ofthe wallsthat confine us and beholdtheworldofthosewhosurroundus. 4 Chapter 1 INTRODUCTION BIOLOGISTS Biostatisticians and Chemists and Bioinformaticians Mass Spectrometrists Figure1.2 Whatweseeontheothersideofthewallofourofficewhenwelookintotheoffice spaceofourfellowcolleagueswiththeirexpertise. 1.3 What Is Next and Where Are We Going? Sinceproteomicsmovedfromqualitativetoquan- titativeprofilingusingliquid-phase-basedmethodsof sample fractionation, it fully entered the domain of analytical chemistry. As much as it is beneficial for proteomics to have a wide range of well-established analytical methods, the complexity of proteomic profiling creates multipletechnical issues. First,clas- sical analytical chemistry focuses on high accuracy measurementsofsingleorfewcompoundsatthesame time.Itallowsadjustingmethods ofsampleprepara- tion and analytical parameters with specific objec- tive(s)scarifyingmeasurementsofothercompounds, whicharecontaminants,ratherthananalytes.Impor- tantly, analytical chemistry exploits specific charac- teristics of analyzed compounds and this concept fulfillsitspurpose.Incontrast,proteomicsattemptsto measurehundredsandthousandsofmoleculesatthe same time which can have a wide range of chemical characteristics (eg, posttranslational modifications of proteinsandpeptides)andthathaveawidedynamic rangeofconcentrations,suchasthecircumstancewith
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