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Proteomic discovery of non-invasive biomarkers of localized prostate cancer using mass spectrometry


Prostate cancer is the second most frequently diagnosed non-skin cancer in men worldwide. Patient outcomes are remarkably heterogeneous and the best existing clinical prognostic tools such as International Society of Urological Pathology Grade Group, pretreatment serum PSA concentration and T-category, do not accurately predict disease outcome for individual patients. Thus, patients newly diagnosed with prostate cancer are often overtreated or undertreated, reducing quality of life and increasing disease-specific mortality. Biomarkers that can improve the risk stratification of these patients are, therefore, urgently needed. The ideal biomarker in this setting will be non-invasive and affordable, enabling longitudinal evaluation of disease status. Prostatic secretions, urine and blood can be sources of biomarker discovery, validation and clinical implementation, and mass spectrometry can be used to detect and quantify proteins in these fluids. Protein biomarkers currently in use for diagnosis, prognosis and relapse-monitoring of localized prostate cancer in fluids remain centred around PSA and its variants, and opportunities exist for clinically validating novel and complimentary candidate protein biomarkers and deploying them into the clinic.

Key points

  • Standard-of-care clinical tools for the management of localized prostate cancer result in substantial overdiagnosis and overtreatment.

  • Fluid-based protein biomarkers have the potential to complement clinical decision-making.

  • Advances in mass spectrometry, such as increased scan speeds and mass resolution, have enabled the systematic discovery and validation of protein biomarkers in prostate-associated fluids.

  • Appropriate sample selection for biomarker discovery and validation can improve detection of prostate-derived proteins in fluids.

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Fig. 1: The role of biomarkers in prostate cancer management.
Fig. 2: Biomarker discovery to translation into the clinic.
Fig. 3: Clinically relevant fluids in prostate cancer.


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This work was partially funded by the National Cancer Institute Early Detection Research Network (1U01CA214194-01), a Prostate Cancer Canada Discovery Grant (400398) and a Canadian Cancer Society Impact Grant (705649). A.K. was supported by an Ontario Graduate Scholarship and a Paul STARITA Graduate Student Fellowship. L.Y.L. was supported by a CIHR Vanier Award. This work was supported by the NIH/NCI under award number P30CA016042.

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Related links

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The Human Protein Atlas:


Protein abundance

A measure of the number of proteins in a sample, estimated from direct measurements of peptide abundance.

Mass spectrometry

(MS). An analytical technique that separates ions by mass:charge ratio in a mass analyser.


The large-scale study of proteomes, which are sets of proteins produced in a biological context such as by a cell, tissue or organism.

Shotgun proteomics

An untargeted workflow for identifying and quantifying proteins by mass spectrometry via proteolytic digestion of proteins into peptides.

Dynamic range

In mass spectrometry, this term is the range of protein abundances in a sample.

Precursor ion

Intact ions that later dissociate into smaller fragment ions.

Fragment ion

An ion that is the product of fragmentation. For peptides, fragment ions are produced from fragmentation at the peptide backbone.

Data-dependent acquisition

(DDA). A mass-spectrometry acquisition method in which the top N most intense peptides are selected for fragmentation.

Data-independent acquisition

(DIA). A mass-spectrometry acquisition method in which all peptides within a given mass window (such as 15–50 m/z) are selected for fragmentation. Peptides in a selected mass range are fragmented using sequential windows.

Selected reaction monitoring/multiple reaction monitoring

(SRM/MRM). A targeted mass spectrometry method that sequentially isolates and records pre-selected fragment ion masses from a peptide.

Triple-quadrupole mass spectrometer

A tandem mass spectrometer consisting of two quadrupole mass analysers arranged sequentially for mass isolation with an additional quadrupole in the middle that is used for collision-induced dissociation.

Parallel reaction monitoring

(PRM). A targeted mass spectrometry method that isolates and records all fragment ion masses from a peptide.

Orbitrap mass analyser

An ion-trap mass analyser that detects m/z signals by oscillating ions around a cylindrical electrode with tapered ends.


The large-scale study of the glycoproteome, the set of glycosylated proteins, by selective enrichment of N-glycosylated or O-glycosylated peptides.

Patient-derived xenografts

(PDX). Tumours grown from the implantation of a patient’s tumour cells into immunodeficient or immunocompromised mice.

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Khoo, A., Liu, L.Y., Nyalwidhe, J.O. et al. Proteomic discovery of non-invasive biomarkers of localized prostate cancer using mass spectrometry. Nat Rev Urol 18, 707–724 (2021).

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