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Mass Spectrometry for Biomarker Development

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General Methods in Biomarker Research and their Applications

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Abstract

Biomarkers potentially play a crucial role in early disease diagnosis, prognosis, and targeted therapy. In the past decade, mass spectrometry-based proteomics has become increasingly important in biomarker development due to large advances in technology and associated methods. This chapter mainly focuses on the application of broad (e.g., shotgun) proteomics in biomarker discovery and the utility of targeted proteomics in biomarker verification and validation. A range of mass spectrometry methodologies are discussed emphasizing their efficacy across the different stages of biomarker development, with a particular emphasis on blood-based biomarker development.

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Abbreviations

2-DE:

Two-Dimensional Gel Electrophoresis

AMT:

Accurate Mass and Time Tag

APEX:

Absolute Protein Expression

AQUA:

Absolute Quantification

CDIT:

Culture-Derived Isotope Tag

CID:

Collision-Induced Dissociation

ECD:

Electron Capture Dissociation

ELISA:

Enzyme-Linked Immunosorbent Assay

emPAI:

Exponentially Modified Protein Abundance Index

ESI:

Electrospray Ionization

ETD:

Electron Transfer Dissociation

FAIMS:

Field Asymmetric Waveform Ion Mobility Spectrometry

FDR:

False Discovery Rate

HCD:

High-Energy Collisional Dissociation

HILIC:

Hydrophilic Interaction Liquid Chromatography

iBAQ:

Intensity-Based Absolute Quantification

ICAT:

Isotope-Coded Affinity Tag

ICPL:

Isotope-Coded Protein Labeling

IEF:

Isoelectric Focusing

IMAC:

Immobilized Metal Ion Affinity Chromatography

IMS:

Ion Mobility Spectrometry

iTRAQ:

Isobaric Tag for Relative and Absolute Quantification

LC:

Liquid Chromatography

LC-MS/MS:

Liquid Chromatography-Tandem Mass Spectrometry

LOD:

Limit of Detection

LOQ:

Limit of Quantification

MALDI:

Matrix-Assisted Laser Desorption Ionization

MRM:

Multiple Reaction Monitoring

MS:

Mass Spectrometry

MS/MS:

Tandem Mass Spectrometry

MudPIT:

Multidimensional Protein Identification Technology

PAC:

Phosphoramidate Chemistry

PrEst:

Protein Epitope Signature Tag

PRISM:

High-Pressure, High-Resolution Separations Coupled with Intelligent Selection and Multiplexing

PRM:

Parallel Reaction Monitoring

PSAQ:

Protein Synthesis Absolute Quantification

PSM:

Peptide Spectrum Match

PTM:

Posttranslational Modification

QconCAT:

Quantification Concatemers

RP:

Reversed Phase

SAX:

Strong Anion Exchange

SCX:

Strong Cation Exchange

SID:

Stable Isotope Dilution

SIL:

Stable Isotope Labeling

SILAC:

Stable Isotope Labeling by Amino Acids in Cell Culture

SIN:

Spectral Index

SISCAPA:

Stable Isotope Standards and Capture by Anti-Peptide Antibodies

SPIN:

Subambient Pressure Ionization with Nano-electrospray Source

SRM:

Selected Reaction Monitoring

SRM3 :

Selected Reaction Monitoring Cubed

SWATH:

Sequential Window Acquisition of All Theoretical Fragment-Ion Spectra

TMT:

Tandem Mass Tag

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Acknowledgments

Portions of this work were supported by grants from the National Institutes of Health National Cancer Institute (U24 CA160019 and Interagency Agreement ACN12003-001-00000) and National Institute of General Medical Sciences (P41 GM103493). The research was performed at the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy (DOE) Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory, which is operated by Battelle Memorial Institute for the DOE under Contract DE-AC05-76RL0 1830.

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  1. Environmental Molecular Sciences Laboratory, and Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, MSIN K8-98, 999, Richland, WA, 99352, USA

    Chaochao Wu, Tao Liu, Erin S. Baker, Karin D. Rodland & Richard D. Smith

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  1. Chaochao Wu
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  2. Tao Liu
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  3. Erin S. Baker
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  4. Karin D. Rodland
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  5. Richard D. Smith
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Correspondence to Richard D. Smith .

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Editors and Affiliations

  1. Department of Nutrition and Dietetics, Division of Diabetes & Nutritional Sciences, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom

    Victor R. Preedy

  2. Faculty of Science & Technology, Department of Biomedical Sciences, University of Westminster, London, United Kingdom

    Vinood B. Patel

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Wu, C., Liu, T., Baker, E.S., Rodland, K.D., Smith, R.D. (2015). Mass Spectrometry for Biomarker Development. In: Preedy, V., Patel, V. (eds) General Methods in Biomarker Research and their Applications. Biomarkers in Disease: Methods, Discoveries and Applications. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7696-8_21

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