Clinical Peptidomics: Advances in Instrumentation, Analyses, and Applications

Lin Li; Jing Wu; Christopher J. Lyon; Li Jiang; Tony Y. Hu

doi:10.34133/bmef.0019

journal article Jan 01, 2023

Clinical Peptidomics: Advances in Instrumentation, Analyses, and Applications

Lin Li

Jing Wu

Christopher J. Lyon Li Jiang

Tony Y. Hu

BME Frontiers Vol. 4 · American Association for the Advancement of Science (AAAS)

View at Publisher Save 10.34133/bmef.0019

Abstract

Extensive effort has been devoted to the discovery, development, and validation of biomarkers for early disease diagnosis and prognosis as well as rapid evaluation of the response to therapeutic interventions. Genomic and transcriptomic profiling are well-established means to identify disease-associated biomarkers. However, analysis of disease-associated peptidomes can also identify novel peptide biomarkers or signatures that provide sensitive and specific diagnostic and prognostic information for specific malignant, chronic, and infectious diseases. Growing evidence also suggests that peptidomic changes in liquid biopsies may more effectively detect changes in disease pathophysiology than other molecular methods. Knowledge gained from peptide-based diagnostic, therapeutic, and imaging approaches has led to promising new theranostic applications that can increase their bioavailability in target tissues at reduced doses to decrease side effects and improve treatment responses. However, despite major advances, multiple factors can still affect the utility of peptidomic data. This review summarizes several remaining challenges that affect peptide biomarker discovery and their use as diagnostics, with a focus on technological advances that can improve the detection, identification, and monitoring of peptide biomarkers for personalized medicine.

Topics

No keywords indexed for this article. Browse by subject →

References

143

[1]

10.1016/j.ebiom.2022.104001

[2]

Montaner J, Ramiro L, Simats A, Tiedt S, Makris K, Jickling GC, Debette S, Sanchez J-C, Bustamante A. Multilevel omics for the discovery of biomarkers and therapeutic targets for stroke. Nat Rev Neurol. 2020;16(5):247–264. 10.1038/s41582-020-0350-6

[3]

Tang Y, Chen Z, Fang Z, Zhao J, Zhou Y, Tang C. Multi-omics study on biomarker and pathway discovery of chronic obstructive pulmonary disease. J Breath Res. 2021;15(4):044001. 10.1088/1752-7163/ac15ea

[4]

Badhwar A, McFall GP, Sapkota S, Black SE, Chertkow H, Duchesne S, Masellis M, Li L, Dixon RA, Bellec P. A multiomics approach to heterogeneity in alzheimer's disease: Focused review and roadmap. Brain. 2020;143(5):1315–1331. 10.1093/brain/awz384

[5]

Pandit K, Mukhopadhyay P, Ghosh S, Chowdhury S. Natriuretic peptides: Diagnostic and therapeutic use. Indian J Endocrinol Metab. 2011;15(Suppl 4):S345–S353. 10.4103/2230-8210.86978

[6]

Conlon JM. Granin-derived peptides as diagnostic and prognostic markers for endocrine tumors. Regul Pept. 2010;165(1):5–11. 10.1016/j.regpep.2009.11.013

[7]

Schrader M, Schulz-Knappe P. Peptidomics technologies for human body fluids. Trends Biotechnol. 2001;19(10 Suppl):S55–S60. 10.1016/s0167-7799(01)01800-5

[8]

Saavedra JM, Armando I. Angiotensin ii at2 receptors contribute to regulate the sympathoadrenal and hormonal reaction to stress stimuli. Cell Mol Neurobiol. 2018;38(1):85–108. 10.1007/s10571-017-0533-x

[9]

Xu Z, Ding J, Zhang L, Feng X, Zhou J, Shen X, Lu H, Qian L, Li X. Peptidomics analysis revealed that a novel peptide vmp-19 protects against ang ii-induced injury in human umbilical vein endothelial cells. Mol Med Rep. 2021;23(4):298. 10.3892/mmr.2021.11937

[10]

Carney EF. Hypertension: New non-ras peptide modulates the vasoregulatory effects of angiotensin ii. Nat Rev Nephrol. 2015;11(6):317. 10.1038/nrneph.2015.52

[11]

diCandiaAM, deAvilaDX, Moreira GR, Villacorta H, Maisel AS. Growth differentiation factor-15, a novel systemic biomarker of oxidative stress, inflammation, and cellular aging: Potential role in cardiovascular diseases. Am Heart J Plus. 2021;9:100046.

[12]

10.1016/j.cej.2021.130428

[13]

Wei W, Liu S, Song J, Feng T, Yang R, Cheng Y, Li H, Hao L. Mgf-19e peptide promoted proliferation, differentiation and mineralization of mc3t3-e1 cell and promoted bone defect healing. Gene. 2020;749:144703. 10.1016/j.gene.2020.144703

[14]

10.1016/j.stem.2010.06.017

[15]

Soltaninejad H, Zare-Zardini H, Ordooei M, Ghelmani Y, Ghadiri-Anari A, Mojahedi S, Hamidieh AA. Antimicrobial peptides from amphibian innate immune system as potent antidiabetic agents: A literature review and bioinformatics analysis. J Diabetes Res. 2021;2021:2894722. 10.1155/2021/2894722

[16]

10.1038/s41596-021-00566-6

[17]

Schulte I Tammen H Selle H Zucht H-D Schulz-Knappe P. Clinical peptidomics: Peptide-biomarker discovery in blood. In: Marko-Varga G editor. Comprehensive analytical chemistry . Amsterdam (Netherlands): Elsevier; 2005. p. 385–409. 10.1016/s0166-526x(05)46007-9

[18]

10.1021/acs.jproteome.1c00295

[19]

Cunningham R, Ma D, Li L. Mass spectrometry-based proteomics and peptidomics for systems biology and biomarker discovery. Front Biol. 2012;7(4):313–335. 10.1007/s11515-012-1218-y

[20]

Perpetuo L, Klein J, Ferreira R, Guedes S, Amado F, Leite-Moreira A, Silva AMS, Thongboonkerd V, Vitorino R. How can artificial intelligence be used for peptidomics?Expert Rev Proteomics. 2021;18(7):527–556. 10.1080/14789450.2021.1962303

[21]

Balchen M, Lund H, Reubsaet L, Pedersen-Bjergaard S. Fast, selective, and sensitive analysis of low-abundance peptides in human plasma by electromembrane extraction. Anal Chim Acta. 2012;716:16–23. 10.1016/j.aca.2011.02.058

[22]

Schrader M. Origins technological development and applications of peptidomics. In: Fricker L Schrader M editors. Peptidomics: Methods and strategies. New York (NK): Springer; 2018. p. 3–39. 10.1007/978-1-4939-7537-2_1

[23]

Bay M, Kirk V, Parner J, Hassager C, Nielsen H, Krogsgaard K, Trawinski J, Boesgaard S, Aldershvile J. Nt-probnp: A new diagnostic screening tool to differentiate between patients with normal and reduced left ventricular systolic function. Heart. 2003;89(2):150–154. 10.1136/heart.89.2.150

[24]

10.3390/ijms22031030

[25]

10.1038/nature04533

[26]

Okusaka T, Eguchi K, Kasai T, Kurata T, Yamamoto N, Ohe Y, Tamura T, Shinkai T, Saijo N. Serum levels of pro-gastrin-releasing peptide for follow-up of patients with small cell lung cancer. Clin Cancer Res. 1997;3(1):123–127.

[27]

Ebeling PR, Peterson JM, Riggs BL. Utility of type i procollagen propeptide assays for assessing abnormalities in metabolic bone diseases. J Bone Miner Res. 1992;7(11):1243–1250. 10.1002/jbmr.5650071118

[28]

Copp DH, Cheney B. Calcitonin-a hormone from the parathyroid which lowers the calcium-level of the blood. Nature. 1962;193:381–382. 10.1038/193381a0

[29]

Clark JL, Cho S, Rubenstein AH, Steiner DF. Isolation of a proinsulin connecting peptide fragment (c-peptide) from bovine and human pancreas. Biochem Biophys Res Commun. 1969;35(4):456–461. 10.1016/0006-291x(69)90367-2

[30]

Rehfeld JF, Stadil F, Vikelsoe J. Immunoreactive gastrin components in human serum. Gut. 1974;15(2):102–111. 10.1136/gut.15.2.102

[31]

Price PA, Parthemore JG, Deftos LJ. New biochemical marker for bone metabolism. Measurement by radioimmunoassay of bone gla protein in the plasma of normal subjects and patients with bone disease. J Clin Invest. 1980;66(5):878–883. 10.1172/jci109954

[32]

Mussap M, Dalla VestraM, Fioretto P, Saller A, Varagnolo M, Nosadini R, Plebani M. Cystatin c is a more sensitive marker than creatinine for the estimation of GFR in type 2 diabetic patients. Kidney Int. 2002;61(4):1453–1461. 10.1046/j.1523-1755.2002.00253.x

[33]

Genest J, Cantin M. Atrial natriuretic factor. Circulation. 1987;75(1 Pt 2):I118–I124.

[34]

Finoulst I, Pinkse M, Van DongenW, Verhaert P. Sample preparation techniques for the untargeted LC-MS-based discovery of peptides in complex biological matrices. J Biomed Biotechnol. 2011;2011:245291. 10.1155/2011/245291

[35]

Fernández-Puente P, González-Rodríguez L, Calamia V, Picchi F, Lourido L, Camacho-Encina M, Oreiro N, Rocha B, Paz-González R, Marina A, et al.Analysis of endogenous peptides released from osteoarthritic cartilage unravels novel pathogenic markers. Mol Cell Proteomics. 2019;18(10):2018–2028. 10.1074/mcp.ra119.001554

[36]

Parker BL, Burchfield JG, Clayton D, Geddes TA, Payne RJ, Kiens B, Wojtaszewski JFP, Richter EA, James DE. Multiplexed temporal quantification of the exercise-regulated plasma peptidome. Mol Cell Proteomics. 2017;16(12):2055–2068. 10.1074/mcp.ra117.000020

[37]

Piovesana S, Cerrato A, Antonelli M, Benedetti B, Capriotti AL, Cavaliere C, Montone CM, Laganà A. A clean-up strategy for identification of circulating endogenous short peptides in human plasma by zwitterionic hydrophilic liquid chromatography and untargeted peptidomics identification. J Chromatogr A. 2020;1613:460699. 10.1016/j.chroma.2019.460699

[38]

Zheng X, Baker H, Hancock WS. Analysis of the low molecular weight serum peptidome using ultrafiltration and a hybrid ion trap-fourier transform mass spectrometer. J Chromatogr A. 2006;1120(1–2):173–184. 10.1016/j.chroma.2006.01.098

[39]

10.1016/j.trac.2019.115658

[40]

Arndt JR, Wormwood MoserKL, Van AkenG, Doyle RM, Talamantes T, DeBord D, Maxon L, Stafford G, Fjeldsted J, Miller B, et al.High-resolution ion-mobility-enabled peptide mapping for high-throughput critical quality attribute monitoring. J Am Soc Mass Spectrom. 2021;32(8):2019–2032. 10.1021/jasms.0c00434

[41]

Peeters MKR, Baggerman G, Gabriels R, Pepermans E, Menschaert G, Boonen K. Ion mobility coupled to a time-of-flight mass analyzer combined with fragment intensity predictions improves identification of classical bioactive peptides and small open reading frame-encoded peptides. Front Cell Dev Biol. 2021;9:720570. 10.3389/fcell.2021.720570

[42]

10.1021/acs.analchem.0c05023

[43]

Jeanne Dit FouqueK, Hegemann JD, Santos-Fernandez M, Le TT, Gomez-Hernandez M, van derDonkWA, Fernandez-Lima F. Exploring structural signatures of the lanthipeptide prochlorosin 2.8 using tandem mass spectrometry and trapped ion mobility-mass spectrometry. Anal Bioanal Chem. 2021;413(19):4815–4824. 10.1007/s00216-021-03437-x

[44]

10.1021/pr900929m

[45]

Fricker LD. Neuropeptides and other bioactive peptides: From discovery to function . San Rafael (CA): Morgan & Claypool; 2012. 10.4199/c00058ed1v01y201205npe003

[46]

Fricker LD, Lim J, Pan H, Che FY. Peptidomics: Identification and quantification of endogenous peptides in neuroendocrine tissues. Mass Spectrom Rev. 2006;25(2):327–344. 10.1002/mas.20079

[47]

Tossi A, Sandri L. Molecular diversity in gene-encoded, cationic antimicrobial polypeptides. Curr Pharm Des. 2002;8(9):743–761. 10.2174/1381612023395475

[48]

Quiroz C, Saavedra YB, Armijo-Galdames B, Amado-Hinojosa J, Olivera-Nappa Á, Sanchez-Daza A, Medina-Ortiz D. Peptipedia: A user-friendly web application and a comprehensive database for peptide research supported by machine learning approach. Database. 2021;2021:baab055. 10.1093/database/baab055

[49]

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

Andy T Kong, Felipe V Leprevost, Dmitry M Avtonomov et al.

Nature Methods 2017 10.1038/nmeth.4256

[50]

Probability-based protein identification by searching sequence databases using mass spectrometry data

David N. Perkins, Darryl J. C. Pappin, David M. Creasy et al.

ELECTROPHORESIS 1999 10.1002/(sici)1522-2683(19991201)20:18<3551::aid-elps3551>3.0.co;2-2

Showing 50 of 143 references

Cited By

24

Bioinspired chiral nanozymes: Synthesis strategies, classification, biological effects and biomedical applications

Xinyu Zhang, Ziheng An · 2024

Coordination Chemistry Reviews

Metrics

24

Citations

143

References

Details

Published: Jan 01, 2023
Vol/Issue: 4

Authors

L

Lin Li

Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, Tulane University, New Orleans, LA, USA.; Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China.

J

Jing Wu

Department of Clinical Laboratory, Third Central Hospital of Tianjin, Tianjin Institute of Hepatobiliary Disease, Tianjin Key Laboratory of Artificial Cell, Artificial Cell Engineering Technology Research Center of Public Health Ministry, Tianjin, China.

C

Christopher J. Lyon

Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, Tulane University, New Orleans, LA, USA.

L

Li Jiang

Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China.

T

Tony Y. Hu

Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, Tulane University, New Orleans, LA, USA.; Department of Biomedical Engineering, School of Science and Engineering, Tulane University, New Orleans, LA, USA.

Funding

U.S. Department of Defense Award: W8IXWH1910926

National Institute of Child Health and Human Development Award: R01HD090927

Division of Intramural Research, National Institute of Allergy and Infectious Diseases Award: R01AI144168

Cite This Article

Lin Li, Jing Wu, Christopher J. Lyon, et al. (2023). Clinical Peptidomics: Advances in Instrumentation, Analyses, and Applications. BME Frontiers, 4. https://doi.org/10.34133/bmef.0019

Clinical Peptidomics: Advances in Instrumentation, Analyses, and Applications

You May Also Like