Proteomics in Systems Biology: Methods and Protocols

327 Pages·2016·13.094 MB·English

by  Jörg Reinders

Methods in
Molecular Biology 1394
Jörg Reinders Editor
Proteomics
in Systems
Biology
Methods and Protocols
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB , UK
For further volumes:
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Proteomics in Systems Biology
Methods and Protocols
Edited by
Jörg Reinders
Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
Editor
Jörg R einders
Institute of Functional Genomics
University of Regensburg
Regensburg, G ermany
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-3339-6 ISBN 978-1-4939-3341-9 (eBook)
DOI 10.1007/978-1-4939-3341-9
Library of Congress Control Number: 2015957400
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Prefa ce
Proteomics techniques have constantly been developed further through the last decade and
have been applied successfully for all kinds of samples and biological or medical questions.
Nowadays, they are established methods in many research labs, and proteomic studies can
be accomplished with good reliability and coverage on a routine basis. Therefore,
proteomics can be used as a powerful tool in functional genomics and systems biology
studies. Current challenges are thus the implementation of proteomic analyses in these
comprehensive studies. This applies for both sample generation and preparation to ensure
consistency over several levels of analyses like genomics, transcriptomics, and metabolomics
and integration of the multilevel data to generate biological knowledge. This book gives an
overview of contemporary quantitative proteomics methods and data interpretation
approaches and also gives examples of how to implement proteomics into systems biology.
Regensburg, Germany J örg Reinders
v

Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i x
1 Multiplexed Quantitative Proteomics for High-Throughput
Comprehensive Proteome Comparisons of Human Cell Lines. . . . . . . . . . . . . 1
Amanda Edwards and W ilhelm H aas
2 S ample Preparation Approaches for iTRAQ Labeling and Quantitative
Proteomic Analyses in Systems Biology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Christos Spanos and J. B ernadette M oore
3 T wo Birds with One Stone: Parallel Quantification of Proteome
and Phosphoproteome Using iTRAQ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 5
Fiorella A. Solari , Laxmikanth K ollipara , A lbert Sickmann ,
and René P. Zahedi
4 Selected Reaction Monitoring to Measure Proteins of Interest
in Complex Samples: A Practical Guide. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Yuehan F eng and P aola P icotti
5 M onitoring PPARG-Induced Changes in Glycolysis by Selected Reaction
Monitoring Mass Spectrometry. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Andreas Hentschel and R obert A hrends
6 A Targeted MRM Approach for Tempo-Spatial Proteomics Analyses. . . . . . . . 7 5
Annie Moradian , T anya R . P orras-Yakushi , M ichael J. Sweredoski ,
and Sonja H ess
7 T argeted Phosphoproteome Analysis Using Selected/Multiple Reaction
Monitoring (SRM/MRM) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 7
Jun Adachi , R yohei N arumi , and Takeshi T omonaga
8 T esting Suitability of Cell Cultures for SILAC-Experiments
Using SWATH-Mass Spectrometry. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Yvonne R einders , Daniel Völler , A nja-K. B osserhoff , P eter J. O efner ,
and Jörg R einders
9 Combining Amine-Reactive Cross-Linkers and Photo-R eactive Amino Acids
for 3D-Structure Analysis of Proteins and Protein Complexes . . . . . . . . . . . . . 109
Philip L össl and Andrea S inz
10 T issue MALDI Mass Spectrometry Imaging (MALDI MSI) of Peptides . . . . . 1 29
Birte B eine , Hanna C . Diehl , Helmut E . M eyer , and Corinna H enkel
11 E thyl Esterification for MALDI-MS Analysis of Protein Glycosylation. . . . . . . 1 51
Karli R. Reiding , Emanuela L onardi , A gnes L . H ipgrave Ederveen ,
and Manfred W uhrer
12 Characterization of Protein N-Glycosylation by Analysis
of ZIC-HILIC-Enriched Intact Proteolytic Glycopeptides. . . . . . . . . . . . . . . . 163
Gottfried Pohlentz , K ristina M arx , and Michael Mormann
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viii Contents
13 Simple and Effective Affinity Purification Procedures for Mass
Spectrometry-Based Identification of Protein- Protein Interactions
in Cell Signaling Pathways. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
Julian H. M. Kwan and Andrew Emili
14 A Systems Approach to Understand Antigen Presentation
and the Immune Response . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 89
Nadine L. D udek , N athan P . C roft , R alf B. Schittenhelm ,
Sri H . Ramarathinam , and Anthony W . Purcell
15 P rofiling of Small Molecules by Chemical Proteomics . . . . . . . . . . . . . . . . . . . 2 11
Kilian V.M. H uber and Giulio S uperti-Furga
16 G enerating Sample-Specific Databases for Mass Spectrometry-Based
Proteomic Analysis by Using RNA Sequencing . . . . . . . . . . . . . . . . . . . . . . . . 2 19
Toni Luge and S ascha S auer
17 A Proteomic Workflow Using High-Throughput De Novo Sequencing
Towards Complementation of Genome Information for Improved
Comparative Crop Science . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 33
R einhard Turetschek , David Lyon , Getinet Desalegn , H ans-Peter Kaul ,
and Stefanie W ienkoop
18 From Phosphoproteome to Modeling of Plant Signaling Pathways . . . . . . . . . 2 45
Maksim Z akhartsev , Heidi P ertl-Obermeyer , and Waltraud X . S chulze
19 I nterpretation of Quantitative Shotgun Proteomic Data . . . . . . . . . . . . . . . . . 2 61
Elise Aasebø , F rode S . B erven , Frode Selheim , H arald Barsnes ,
and Marc V audel
20 A Simple Workflow for Large Scale Shotgun Glycoproteomics. . . . . . . . . . . . . 2 75
Astrid Guldbrandsen , H arald B arsnes , A nn Cathrine K roksveen ,
Frode S . B erven , and M arc Vaudel
21 S ystemic Analysis of Regulated Functional Networks. . . . . . . . . . . . . . . . . . . . 2 87
Luis Francisco Hernández Sánchez , Elise Aasebø , F rode S elheim ,
Frode S . B erven , H elge R æde , H arald B arsnes , and Marc Vaudel
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 11
Contributors
ELISE A ASEBØ • Proteomics Unit, Department of Biomedicine , U niversity of Bergen ,
Bergen, N orway
JUN ADACHI • Laboratory of Proteome Research, N ational Institute of Biomedical
Innovation , Health and Nutrition, Osaka, Japan
ROBERT AHRENDS • Leibniz-Institut für Analytische Wissenschaften—ISAS—e.V. ,
Dortmund, G ermany
HARALD BARSNES • Proteomics Unit, Department of Biomedicine , U niversity of Bergen ,
Bergen , N orway ; KG Jebsen Center for Diabetes Research, Department of Clinical
Science, U niversity of Bergen , B ergen , N orway
BIRTE BEINE • Leibniz-Institut für Analytische Wissenschaften—ISAS—e.V. , Dortmund,
Germany
FRODE S. BERVEN • Proteomics Unit, Department of Biomedicine , U niversity of Bergen ,
Bergen, N orway ; KG Jebsen Centre for Multiple Sclerosis Research, Department of
Clinical Medicine, University of Bergen , B ergen, N orway ; N orwegian Multiple Sclerosis
Competence Centre, Department of Neurology , Haukeland University Hospital ,
Bergen, N orway
ANJA-K. B OSSERHOFF • Institute of Pathology, University of Regensburg , Regensburg,
Germany ; Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University
Erlangen-Nürnberg , Erlangen, Germany
NATHAN P . C ROFT • Department of Biochemistry and Molecular Biology, School of Biomedical
Sciences, M onash University , C layton, V IC, Australia
GETINET DESALEGN • Department of Crop Sciences, U niversity of Natural Resources
and Life Sciences , Vienna, Austria
HANNA C . D IEHL • Clinical Proteomics, Medizinisches Proteome-Center, Ruhr-U niversity ,
Bochum , G ermany
NADINE L . D UDEK • Department of Biochemistry and Molecular Biology, School of Biomedical
Sciences, Monash University , Clayton , VIC, Australia
AMANDA E DWARDS • Center for Cancer Research, Massachusetts General Hospital, Charlestown,
MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
ANDREW E MILI • Department of Molecular Genetics, Donnelly Centre for Cellular
and Biomolecular Research , University of Toronto , Toronto , ON, C anada
YUEHAN F ENG • Department of Biology, Institute of Biochemistry , E TH Zurich , Z urich,
Switzerland
ASTRID GULDBRANDSEN • Proteomics Unit, Department of Biomedicine , U niversity
of Bergen , B ergen, Norway ; KG Jebsen Centre for Multiple Sclerosis Research,
Department of Clinical Medicine, U niversity of Bergen , B ergen , N orway
WILHELM H AAS • Center for Cancer Research, Massachusetts General Hospital, Charlestown,
MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
CORINNA H ENKEL • Leibniz-Institut für Analytische Wissenschaften—ISAS—e.V. ,
Dortmund, G ermany
ANDREAS HENTSCHEL • Leibniz-Institut für Analytische Wissenschaften—ISAS—e.V. ,
Dortmund, G ermany
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