Biomarker Discovery and Clinical Proteomics

Overview

Journal Trends Analyt Chem

Specialty Chemistry

Date 2010 Feb 23

PMID 20174458

Citations 32

Authors

Jerzy Silberring

Pawel Ciborowski

Affiliations

Soon will be listed here.

Abstract

New biomarkers are urgently needed to accelerate efforts in developing new drugs and treatments of known diseases. New clinical and translational proteomics studies emerge almost every day. However, discovery of new diagnostic biomarkers lags behind because of variability at every step in proteomics studies (e.g., assembly of a cohort of patients, sample preparation and the nature of body fluids, selection of a profiling method and uniform protocols for data analysis).Quite often, the validation step that follows the discovery phase does not reach desired levels of sensitivity and specificity or reproducibility between laboratories. Mass spectrometry and gel-based methods do not provide enough throughput for screening thousands of clinical samples. Further development of protein arrays may address this issue.Despite many obstacles, proteomics delivers vast amounts of information useful for understanding the molecular mechanisms underlying diseases.

Citing Articles

Ultrasensitive, Multiplexed Buoyant Sensor for Monitoring Cytokines in Biofluids.

Guo H, Gupta R, Sharma D, Zhanov E, Malone C, Jada R Nano Lett. 2023; 23(22):10171-10178.

PMID: 37922456 PMC: 10863391. DOI: 10.1021/acs.nanolett.3c02516.

Biomarkers as Biomedical Bioindicators: Approaches and Techniques for the Detection, Analysis, and Validation of Novel Biomarkers of Diseases.

Ahmad A, Imran M, Ahsan H Pharmaceutics. 2023; 15(6).

PMID: 37376078 PMC: 10303887. DOI: 10.3390/pharmaceutics15061630.

Effects of filtration and alpha-amylase depletion on salivary biochemical composition measurements.

Franco-Martinez L, Ceron J, Martinez-Subiela S, Tvarijonaviciute A PLoS One. 2023; 18(5):e0286092.

PMID: 37235564 PMC: 10218723. DOI: 10.1371/journal.pone.0286092.

Label-Free Quantification from Direct Infusion Shotgun Proteome Analysis (DISPA-LFQ) with CsoDIAq Software.

Jiang Y, Hutton A, Cranney C, Meyer J Anal Chem. 2022; 95(2):677-685.

PMID: 36527718 PMC: 9850400. DOI: 10.1021/acs.analchem.2c02249.

Adjunctive Techniques and Diagnostic Aids in the Early Detection of Oral Premalignant Disorders and Cancer: An Update for the General Dental Practitioners.

Krishnan Pandarathodiyil A, Vijayan S, Milanes D, Chopra V, Anil S J Pharm Bioallied Sci. 2022; 14(Suppl 1):S28-S33.

PMID: 36110790 PMC: 9469411. DOI: 10.4103/jpbs.jpbs_635_21.

References

Huang H, Stasyk T, Morandell S, Mogg M, Schreiber M, Feuerstein I . Enrichment of low-abundant serum proteins by albumin/immunoglobulin G immunoaffinity depletion under partly denaturing conditions. Electrophoresis. 2005; 26(14):2843-9. DOI: 10.1002/elps.200500167. View

Dawood S, Leyland-Jones B . Pharmacology and pharmacogenetics of chemotherapeutic agents. Cancer Invest. 2009; 27(5):482-8. DOI: 10.1080/07357900802574660. View

Hsu H, Wittemann S, Joos T . Miniaturized parallelized sandwich immunoassays. Methods Mol Biol. 2008; 428:247-61. DOI: 10.1007/978-1-59745-117-8_14. View

Service R . Proteomics. Proteomics ponders prime time. Science. 2008; 321(5897):1758-61. DOI: 10.1126/science.321.5897.1758. View

Pruvost A, BECHER F, Bardouille P, Guerrero C, Creminon C, Delfraissy J . Direct determination of phosphorylated intracellular anabolites of stavudine (d4T) by liquid chromatography/tandem mass spectrometry. Rapid Commun Mass Spectrom. 2001; 15(16):1401-8. DOI: 10.1002/rcm.384. View

Jebrail M, Luk V, Shih S, Fobel R, Ng A, Yang H . Digital microfluidics for automated proteomic processing. J Vis Exp. 2009; (33). PMC: 3157851. DOI: 10.3791/1603. View

INGALLS A, DICKIE M, Snell G . Obese, a new mutation in the house mouse. J Hered. 1950; 41(12):317-8. DOI: 10.1093/oxfordjournals.jhered.a106073. View

Yan L, Tonack S, Smith R, Dodd S, Jenkins R, Kitteringham N . Confounding effect of obstructive jaundice in the interpretation of proteomic plasma profiling data for pancreatic cancer. J Proteome Res. 2008; 8(1):142-8. DOI: 10.1021/pr800451h. View

Rozek W, Horning J, Anderson J, Ciborowski P . Sera proteomic biomarker profiling in HIV-1 infected subjects with cognitive impairment. Proteomics Clin Appl. 2010; 2(10-11):1498-507. PMC: 3406605. DOI: 10.1002/prca.200780114. View

10.

Ramachandran N, Raphael J, Hainsworth E, Demirkan G, Fuentes M, Rolfs A . Next-generation high-density self-assembling functional protein arrays. Nat Methods. 2008; 5(6):535-8. PMC: 3070491. DOI: 10.1038/nmeth.1210. View

11.

Aebersold R . A stress test for mass spectrometry-based proteomics. Nat Methods. 2009; 6(6):411-2. DOI: 10.1038/nmeth.f.255. View

12.

Kornblau S, Tibes R, Qiu Y, Chen W, Kantarjian H, Andreeff M . Functional proteomic profiling of AML predicts response and survival. Blood. 2008; 113(1):154-64. PMC: 2951831. DOI: 10.1182/blood-2007-10-119438. View

13.

Westman-Brinkmalm A, Ruetschi U, Portelius E, Andreasson U, Brinkmalm G, Karlsson G . Proteomics/peptidomics tools to find CSF biomarkers for neurodegenerative diseases. Front Biosci (Landmark Ed). 2009; 14(5):1793-806. DOI: 10.2741/3341. View

14.

Iliopoulos D, Malizos K, Oikonomou P, Tsezou A . Integrative microRNA and proteomic approaches identify novel osteoarthritis genes and their collaborative metabolic and inflammatory networks. PLoS One. 2008; 3(11):e3740. PMC: 2582945. DOI: 10.1371/journal.pone.0003740. View

15.

Templin M, Stoll D, Schwenk J, Potz O, Kramer S, Joos T . Protein microarrays: promising tools for proteomic research. Proteomics. 2003; 3(11):2155-66. DOI: 10.1002/pmic.200300600. View

16.

Anderson N, Anderson N . The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics. 2002; 1(11):845-67. DOI: 10.1074/mcp.r200007-mcp200. View

17.

Hattori S, Iida N, Kosako H . Identification of protein kinase substrates by proteomic approaches. Expert Rev Proteomics. 2008; 5(3):497-505. DOI: 10.1586/14789450.5.3.497. View

18.

Cox D, Zhong F, Du M, Duchoslav E, Sakuma T, McDermott J . Multiple reaction monitoring as a method for identifying protein posttranslational modifications. J Biomol Tech. 2005; 16(2):83-90. PMC: 2291721. View

19.

Suder P, Bodzon-Kulakowska A, Mak P, Bierczynska-Krzysik A, Daszykowski M, Walczak B . The proteomic analysis of primary cortical astrocyte cell culture after morphine administration. J Proteome Res. 2009; 8(10):4633-40. DOI: 10.1021/pr900443r. View

20.

Fenner B, Scannell M, Prehn J . Identification of polyubiquitin binding proteins involved in NF-kappaB signaling using protein arrays. Biochim Biophys Acta. 2009; 1794(7):1010-6. DOI: 10.1016/j.bbapap.2009.02.013. View