Mass spectrometry-based proteomics in cancer research

Cho, William C.

doi:10.1080/14789450.2017.1365604

Cited by 21 publications

(18 citation statements)

References 20 publications

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“…Related to this, new advances in MS instrumentation, acquisition methods, and associated informatics tools for data processing benefit the scientific community through all phases of the biomarker pipeline, i.e., discovery, verification and validation phases. MS instrumentations are becoming considerably more sensitive and faster, able to achieve higher selectivity and confidence in the peptide identification process [70]. Therefore, it is a great opportunity to screen clinically relevant samples and generate comprehensive lists of candidate biomarkers using different acquisition methods such as data-dependent acquisition (DDA) or the more recently emerged data-independent acquisition (DIA) [71].…”

Section: Discussionmentioning

confidence: 99%

Prognostic Biomarkers in Endometrial Cancer: A Systematic Review and Meta-Analysis

Rubia

Martínez‐García

Dittmar

et al. 2020

JCM

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Endometrial cancer (EC) is the sixth most common cancer in women worldwide and its mortality is directly associated with the presence of poor prognostic factors driving tumor recurrence. Stratification systems are based on few molecular, and mostly clinical and pathological parameters, but these systems remain inaccurate. Therefore, identifying prognostic EC biomarkers is crucial for improving risk assessment pre- and postoperatively and to guide treatment decisions. This systematic review gathers all protein biomarkers associated with clinical prognostic factors of EC, recurrence and survival. Relevant studies were identified by searching the PubMed database from 1991 to February 2020. A total number of 398 studies matched our criteria, which compiled 255 proteins associated with the prognosis of EC. MUC16, ESR1, PGR, TP53, WFDC2, MKI67, ERBB2, L1CAM, CDH1, PTEN and MMR proteins are the most validated biomarkers. On the basis of our meta-analysis ESR1, TP53 and WFDC2 showed potential usefulness for predicting overall survival in EC. Limitations of the published studies in terms of appropriate study design, lack of high-throughput measurements, and statistical deficiencies are highlighted, and new approaches and perspectives for the identification and validation of clinically valuable EC prognostic biomarkers are discussed.

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Section: Discussionmentioning

confidence: 99%

Prognostic Biomarkers in Endometrial Cancer: A Systematic Review and Meta-Analysis

Rubia

Martínez‐García

Dittmar

et al. 2020

JCM

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“…Moreover, extendibility of targeted proteomic MS assays to analyzing new proteins is convenient in a time-and cost-efficient manner. While it takes only a few weeks for the development of a parallel reaction monitoring (PRM) assay for new proteins, conventional antibody-based methods need months and higher costs to establish a new assay (2). All these advocate targeted proteomics as a promising screening tool in applications requiring urgent diagnostic needs.…”

mentioning

confidence: 99%

“…Targeted proteomic MS has been gaining popularity as a promising clinical diagnostic tool to track protein/peptide biomarkers, such as in cancer (2) and cardiovascular disease (3). However, its potential has not been well-exploited in infectious disease diagnostics.…”

mentioning

confidence: 99%

Multiplex targeted mass spectrometry assay for one-shot flavivirus diagnosis

Wee

Alli-Shaik

Kek

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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Targeted proteomic mass spectrometry is emerging as a salient clinical diagnostic tool to track protein biomarkers. However, its strong analytical properties have not been exploited in the diagnosis and typing of flaviviruses. Here, we report the development of a sensitive and specific single-shot robust assay for flavivirus typing and diagnosis using targeted mass spectrometry technology. Our flavivirus parallel reaction monitoring assay (fvPRM) has the ability to track secreted flaviviral nonstructural protein 1 (NS1) over a broad diagnostic and typing window with high sensitivity, specificity, extendibility, and multiplexing capability. These features, pivotal and pertinent to efficient response toward flavivirus outbreaks, including newly emerging flavivirus strains, circumvent the limitations of current diagnostic assays.fvPRM thus carries high potential in positioning itself as a forerunner in delivering early and accurate diagnosis for disease management.

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“…Most of these applications use conventional data-dependent acquisition (DDA) or targeted methods such as single or multiple reaction monitoring (SRM/MRM) which have been comprehensively reviewed elsewhere. [10][11][12] In this review, we focus on the use of dataindependent acquisition (DIA) (also known as sequential window acquisition of all theoretical mass spectra (SWATH-MS)) 13 and provide an overview of specific applications in cancer proteomics to inform molecular classification, biomarker discovery and the identification of new drug targets. This review will focus on DIA-MS applications in tissue and cell line analysis, and readers who are interested in the use of this technology in liquid biopsies and plasma proteomics are referred to these excellent reviews on the topic.…”

Section: Lukas Krasnymentioning

confidence: 99%