Recent advances in mass spectrometry based clinical proteomics: applications to cancer research

Abstract

Cancer biomarkers have transformed current practices in the oncology clinic. Continued discovery and validation are crucial for improving early diagnosis, risk stratification, and monitoring patient response to treatment. Profiling of the tumour genome and transcriptome are now established tools for the discovery of novel biomarkers, but alterations in proteome expression are more likely to reflect changes in tumour pathophysiology. In the past, clinical diagnostics have strongly relied on antibody-based detection strategies, but these methods carry certain limitations. Mass spectrometry (MS) is a powerful method that enables increasingly comprehensive insights into changes of the proteome to advance personalized medicine. In this review, recent improvements in MS-based clinical proteomics are highlighted with a focus on oncology. We will provide a detailed overview of clinically relevant samples types, as well as, consideration for sample preparation methods, protein quantitation strategies, MS configurations, and data analysis pipelines currently available to researchers. Critical consideration of each step is necessary to address the pressing clinical questions that advance cancer patient diagnosis and prognosis. While the majority of studies focus on the discovery of clinically-relevant biomarkers, there is a growing demand for rigorous biomarker validation. These studies focus on high-throughput targeted MS assays and multi-centre studies with standardized protocols. Additionally, improvements in MS sensitivity are opening the door to new classes of tumour-specific proteoforms including posttranslational modifications and variants originating from genomic aberrations. Overlaying proteomic data to complement genomic and transcriptomic datasets forges the growing field of proteogenomics, which shows great potential to improve our understanding of cancer biology. Overall, these advancements not only solidify MS-based clinical proteomics' integral position in cancer research, but also accelerate the shift towards becoming a regular component of routine analysis and clinical practice.

Evaluation of the potential of Pap test fluid and cervical swabs to serve as clinical diagnostic biospecimens for the detection of ovarian cancer by mass spectrometry-based proteomics

“…Future clinical applications may include ELISA tests using Pap test fluid or cervical swabs as the diagnostic biospecimen, or multiplexed proximity extension assays could be developed for use on Pap tests to sensitively quantify multiple proteins of interest [ 49 , 50 ]. Alternatively, SRM-based targeted proteomic assays are increasingly being used in the measurement of clinically significant proteins, allowing for cost effective, high throughput, sensitive, robust, multiplexed analysis and quantification [ 46 , 51 ]. Furthermore, since self-sampling improves participation in screening for human papilloma virus and is as sensitive as physician-obtained samples [ 52 , 53 ], in the future it may be possible that this method could be translated into a self-administered home test, where swabs collected by women at home are sent to a central laboratory for analysis of proteins that would diagnose ovarian cancer.…”

Mass Spectrometry-Based Omics for the Characterization of Triple-Negative Breast Cancer Bio-Signature

“…Mass spectrometry has a well-established role in clinical proteomics, as described in a recent review by Macklin et al [ 54 ]. In cancer research, proteome profiling is the most promising approach, but for now high-resolution mass spectrometry still lacks in many aspects, such as high costs, the required expertise (to run the instruments and analyze the data) and standardization [ 54 , 55 ].…”

“…Mass spectrometry has a well-established role in clinical proteomics, as described in a recent review by Macklin et al [ 54 ]. In cancer research, proteome profiling is the most promising approach, but for now high-resolution mass spectrometry still lacks in many aspects, such as high costs, the required expertise (to run the instruments and analyze the data) and standardization [ 54 , 55 ]. To overcome some of these aspects, some revolutionary MS-based instruments are under development, such as the iKnife [ 56 ] and the MasSpec Pen [ 57 ], both used for intra-operatory diagnosis.…”

The Implementation of Mass Spectrometry-Based Proteomics Workflows in Clinical Routines of Acute Myeloid Leukemia: Applicability and Perspectives

“…Denaturants, e.g., urea, guanidinium hydrochloride and trifluoroethanol (TFE), which induce cell lysis, and detergents, e.g., sodium dodecyl sulfate (SDS), sodium deoxycholate (SDC) and 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS), which disrupt cell membranes, are commonly used to extract proteins from cell samples. SDS is a superior agent also for solubilization and denaturation of proteins, but it will interfere with downstream enzymatic digestion, reversed-phase separations and MS, and must therefore be removed from the sample preparations [ 91 ]. Removal of contaminants and SDS can be accomplished with the filter-aided sample preparation (FASP) method, which enables proficient wash out of SDS (≥99.9%) with urea [ 92 , 93 , 94 ].…”

“…Removal of contaminants and SDS can be accomplished with the filter-aided sample preparation (FASP) method, which enables proficient wash out of SDS (≥99.9%) with urea [ 92 , 93 , 94 ]. To further remove MS-incompatible and interfering chemicals, a clean-up method (also called desalting) of the peptide sample is usually performed before the LC-MS/MS data acquisition [ 91 ]. Moreover, the sample complexity of the peptide mixture can be reduced by fractionation and/or enrichment prior to the LC-MS/MS analysis.…”