Please confirm you are human (Sign Up for free to never see this)
← Back to Search
D. Greening, R. Simpson
Published 2017 · Medicine
Save to my Library
Download PDFAnalyze on Scholarcy
Blood proteome analysis for biomarker discovery represents one of the most challenging tasks to be achieved through clinical proteomics due to the sample complexity, such as the extreme heterogeneity of proteins in very dynamic concentrations, and to the observation of proper sampling and storage conditions. Quantitative and qualitative proteomics profiling of plasma and serum could be useful both for the early detection of diseases and for the evaluation of pathological status. Two main sources of variability can affect the precision and accuracy of the quantitative experiments designed for biomarker discovery and validation. These sources are divided into two categories, pre-analytical and analytical, and are often ignored; however, they can contribute to consistent errors and misunderstanding in biomarker research. In this chapter, we review critical pre-analytical and analytical variables that can influence quantitative proteomics. According to guidelines accepted by proteomics community, we propose some recommendations and strategies for a proper proteomics analysis addressed to biomarker studies.
This paper references
Extracellular vesicle sizing and enumeration by nanoparticle tracking analysis
C. Gardiner (2013)
The applicability of a cluster of differentiation monoclonal antibody microarray to the diagnosis of human disease.
P. Ellmark (2008)
Obesity and free fatty acids.
G. Boden (2008)
The relationship of survival to staging and grading of colorectal carcinoma: A prospective study of 503 cases
R. C. Newland (1981)
Cellular origin and pathophysiology of chronic lymphocytic leukemia
M. Seifert (2012)
B cell chronic lymphocytic leukemia: lessons learned from studies of the B cell antigen receptor.
N. Chiorazzi (2003)
Solid-phase extraction and liquid chromatography--mass spectrometry for the determination of free fatty acids in shellfish.
J. Lacaze (2007)
Extensive surface protein profiles of extracellular vesicles from cancer cells may provide diagnostic signatures from blood samples
L. Belov (2016)
Microparticle-Associated Tissue Factor Activity: A Link between Cancer and Thrombosis?.
M. Tesselaar (2005)
Dendritic Cell-Derived Exosomes Express a Streptococcus pneumoniae Capsular Polysaccharide Type 14 Cross-Reactive Antigen That Induces Protective Immunoglobulin Responses against Pneumococcal Infection in Mice
J. Colino (2006)
Polyunsaturated fatty acids and their metabolites in brain function and disease
R. Bazinet (2014)
CD8α is expressed by human monocytes and enhances FcγR-dependent responses
Derrick J. Gibbings (2007)
Quantitation and standardization of lipid internal standards for mass spectroscopy.
J. D. Moore (2007)
Immunophenotyping of leukemias using a cluster of differentiation antibody microarray.
L. Belov (2001)
Genetic control of the CD4/CD8 T-cell ratio in humans
A. Amadori (1995)
Evaluation of surface chemistries for antibody microarrays.
Shannon L. Seurynck-Servoss (2007)
Differential fates of biomolecules delivered to target cells via extracellular vesicles
Masamitsu Kanada (2015)
Effect of 3.2% vs 3.8% sodium citrate concentration on routine coagulation testing.
D. Adcock (1997)
Proteomic characterisation of chronic lymphocytic leukaemia cells treated with rituximab
M. Alomari (2014)
Isotype controls in phenotyping and quantification of microparticles: a major source of error and how to evade it.
A. Trummer (2008)
Comparative proteomics evaluation of plasma exosome isolation techniques and assessment of the stability of exosomes in normal human blood plasma
Hina Kalra (2013)
Multicolor flow cytometry for evaluation of platelet surface antigens and activation markers.
Jeroen F van Velzen (2012)
Exosomes Are Unlikely Involved in Intercellular Nef Transfer
X. Luo (2015)
Multifarious roles of sialic acids in immunity
A. Varki (2012)
Isolation and Characterization of Exosomes from Cell Culture Supernatants and Biological Fluids
C. Théry (2006)
Applications of mass spectrometry for cellular lipid analysis.
C. Wang (2015)
A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language
R. Herzog (2010)
CEA serum levels in non-neoplastic disease.
A. Ruibal Morell (1992)
Colorectal cancer cell surface protein profiling using an antibody microarray and fluorescence multiplexing.
J. Zhou (2011)
Improved LC-MS method for the determination of fatty acids in red blood cells by LC-orbitrap MS.
XingNan Li (2011)
Expression of B-cell surface antigens in subpopulations of exosomes released from B-cell lymphoma cells.
M. Oksvold (2014)
Enhanced Expression of CD13 in Vessels of Inflammatory and Neoplastic Tissues
P. D. Matteo (2011)
Induction of Exosome Release in Primary B Cells Stimulated via CD40 and the IL-4 Receptor1
Sarah C Saunderson (2008)
Conservation of unique cell-surface CD antigen mosaics in HIV-1-infected individuals.
A. Woolfson (2005)
Getting to Know Ovarian Cancer Ascites: Opportunities for Targeted Therapy-Based Translational Research
N. Ahmed (2013)
Total lymphocyte CD8 expression is not a reliable marker of cytotoxic T-cell populations in human peripheral blood following an acute bout of high-intensity exercise
J. P. Campbell (2008)
Contact printing of protein microarrays.
John Austin (2011)
Analytical methods in lipidomics and their applications.
Min Li (2014)
Analytical strategies in lipidomics and applications in disease biomarker discovery.
Chunxiu Hu (2009)
Activated platelets release two types of membrane vesicles: microvesicles by surface shedding and exosomes derived from exocytosis of multivesicular bodies and alpha-granules.
H. Heijnen (1999)
Species-specific blocking of fc-receptors in indirect immunofluorescence assays
P Sedlmayr (2001)
Proteomics Analysis of A33 Immunoaffinity-purified Exosomes Released from the Human Colon Tumor Cell Line LIM1215 Reveals a Tissue-specific Protein Signature*
S. Mathivanan (2009)
Antibody Microarrays and Multiplexing
J. Zhou (2013)
Antibody microarray analysis of cell surface antigens on CD4+ and CD8+ T cells from HIV+ individuals correlates with disease stages
Jing Qin Wu (2007)
Phenotypic protein profiling of different B cell sub-populations using antibody CD-microarrays.
P. Ellmark (2008)
Gas chromatography– mass spectrometry methods for structural analysis of fatty acids. Lipids
WW Christie (1998)
Proteolytic Potential of the MSC Exosome Proteome: Implications for an Exosome-Mediated Delivery of Therapeutic Proteasome
R. C. Lai (2012)
Analysis of human liver disease using a cluster of differentiation (CD) antibody microarray
W. Rahman (2012)
Targeted quantitative analysis of fatty acids in atherosclerotic plaques by high sensitivity liquid chromatography/tandem mass spectrometry.
Caterina Pettinella (2007)
Improved circulating microparticle analysis in acid-citrate dextrose (ACD) anticoagulant tube.
B. György (2014)
MEC1 and MEC2: two new cell lines derived from B-chronic lymphocytic leukaemia in prolymphocytoid transformation.
A. Stacchini (1999)
Optimized Normalization for Antibody Microarrays and Application to Serum-Protein Profiling*S
Darren Hamelinck (2005)
Immunohistochemical analysis of beta3 integrin (CD61): expression in pig tissues and human tumors.
A. Meroño (2002)
Differences in the Serum Nonesterified Fatty Acid Profile of Young Women Associated with a Recent History of Gestational Diabetes and Overweight/Obesity
M. Fugmann (2015)
High Levels of Exosomes Expressing CD63 and Caveolin-1 in Plasma of Melanoma Patients
M. Logozzi (2009)
Serum-free culture alters the quantity and protein composition of neuroblastoma-derived extracellular vesicles
Jinghuan Li (2015)
Human Serum IgM Glycosylation
J. N. Arnold (2005)
Elevated preoperative CEA is associated with worse survival in stage I–III rectal cancer patients
I. Tarantino (2012)
Nonspecific Immunoglobulin M Binding and Chondroitin Sulfate A Binding Are Linked Phenotypes of Plasmodium falciparum Isolates Implicated in Malaria during Pregnancy
A. Creasey (2003)
Analysis of Post-Liver Transplant Hepatitis C Virus Recurrence Using Serial Cluster of Differentiation Antibody Microarrays
W. Rahman (2015)
Sialylation of N-Linked Glycans Influences the Immunomodulatory Effects of IgM on T Cells
M. Colucci (2015)
Gender, Contraceptives and Individual Metabolic Predisposition Shape a Healthy Plasma Lipidome
S. Sales (2016)
Guidelines for the diagnosis and treatment of chronic lymphocytic leukemia: a report from the International Workshop on Chronic Lymphocytic Leukemia updating the National Cancer Institute-Working Group 1996 guidelines.
M. Hallek (2008)
Selection of internal standards for accurate quantification of complex lipid species in biological extracts by electrospray ionization mass spectrometry-What, how and why?
M. Wang (2017)
Lipidomic profiling before and after Roux-en-Y gastric bypass in obese patients with diabetes
J. Graessler (2014)
Mechanisms linking obesity to insulin resistance and type 2 diabetes
S. Kahn (2006)
Identity of the elusive IgM Fc receptor (FcμR) in humans
H. Kubagawa (2009)
Liquid chromatography-high resolution mass spectrometry analysis of fatty acid metabolism.
J. Kamphorst (2011)
Treatment of older patients with chronic lymphocytic leukemia: key questions and current answers.
T. Shanafelt (2013)
Association between Plasma Nonesterified Fatty Acids Species and Adipose Tissue Fatty Acid Composition
C. Hellmuth (2013)
Disease-specific complications of chronic lymphocytic leukemia.
C. Dearden (2008)
Optimizing the lipidomics workflow for clinical studies—practical considerations
T. Hyötyläinen (2015)
Phenotyping of Leukocytes and Leukocyte-Derived Extracellular Vesicles
L. H. Pugholm (2016)
Nonesterified fatty acid determination for functional lipidomics: comprehensive ultrahigh performance liquid chromatography-tandem mass spectrometry quantitation, qualification, and parameter prediction.
C. Hellmuth (2012)
Tetraspanins in Extracellular Vesicle Formation and Function
Zoraida Andreu (2014)
Differentiating chronic lymphocytic leukemia from monoclonal B-lymphocytosis according to clinical outcome: on behalf of the GIMEMA chronic lymphoproliferative diseases working group
S. Molica (2011)
Staging of colorectal cancer
N. Davis (1984)
Circulating microvesicles in B-cell chronic lymphocytic leukemia can stimulate marrow stromal cells: implications for disease progression.
A. Ghosh (2010)
Importance of exosome depletion protocols to eliminate functional and RNA-containing extracellular vesicles from fetal bovine serum
G. Shelke (2014)
Profiles of surface mosaics on chronic lymphocytic leukemias distinguish stable and progressive subtypes.
Pauline Y. Huang (2013)
Minimal experimental requirements for definition of extracellular vesicles and their functions: a position statement from the International Society for Extracellular Vesicles
J. Lötvall (2014)
Exosomes and HIV Gag bud from endosome-like domains of the T cell plasma membrane
A. Booth (2006)
CD20 levels determine the in vitro susceptibility to rituximab and complement of B-cell chronic lymphocytic leukemia: further regulation by CD55 and CD59.
J. Golay (2001)
Higher-Order Oligomerization Targets Plasma Membrane Proteins and HIV Gag to Exosomes
Y. Fang (2007)
Shotgun lipidomics on a LTQ Orbitrap mass spectrometer by successive switching between acquisition polarity modes.
K. Schuhmann (2012)
Free fatty acids regulate gut incretin glucagon-like peptide-1 secretion through GPR120
A. Hirasawa (2005)
Distinct RNA profiles in subpopulations of extracellular vesicles: apoptotic bodies, microvesicles and exosomes
Rossella Crescitelli (2013)
Prognostic impact of epithelial cell adhesion molecule in ovarian cancer patients
M. Lee (2014)
Longitudinal microarray analysis of cell surface antigens on peripheral blood mononuclear cells from HIV+ individuals on highly active antiretroviral therapy
Jing Qin Wu (2007)
Stable and unstable angina: Identifying novel markers on circulating leukocytes
A. Brown (2008)
This paper is referenced by
Biofluid-Based Circulating Tumor Molecules as Diagnostic Tools for Use in Personalized Medicine
Yutian Li (2013)
Proteomics in Schizophrenia: A Gateway to Discover Potential Biomarkers of Psychoneuroimmune Pathways
D. Rodrigues-Amorim (2019)
Integrative Analysis of Novel Metabolic Subtypes in Pancreatic Cancer Fosters New Prognostic Biomarkers
Laura Follia (2019)
Enabling quantification of protein concentration in human serum biopsies using attenuated total reflectance – Fourier transform infrared (ATR-FTIR) spectroscopy
K. Spalding (2018)
Advances in liquid biopsy on-chip for cancer management: Technologies, biomarkers, and clinical analysis
Amogha Tadimety (2018)
Plasma glutathione status as indicator of pre-analytical centrifugation delay
Tamara Tomin (2020)
High-dimensionality Data Analysis of Pharmacological Systems Associated with Complex Diseases
Jhana O Hendrickx (2020)