Development of parallel reaction monitoring (PRM)-based quantitative proteomics applied to HER2-Positive breast cancer

Guérin, Mathilde; Gonçalvès, Anthony; Toiron, Yves; Baudelet, Emilie; Pophillat, Matthieu; Granjeaud, Samuel; Fourquet, Patrick; Jacot, William; Tarpin, Carole; Sabatier, Renaud; Agavnian, Emilie; Finetti, Pascal; Adélaı̈de, José; Birnbaum, Daniel; Ginestier, Christophe; Charafe‐Jauffret, Emmanuelle; Viens, Patrice; Bertucci, François; Borg, Jean-Paul; Camoin, Luc

doi:10.18632/oncotarget.26031

Cited by 17 publications

(12 citation statements)

References 45 publications

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“…FAIMS-PRM increased the quantitation sensitivity of the clinically relevant biomarker HER2, reducing the LLOQ from 137 to 46 amol/μg. This compares favorably with reported LLOQs from SRM assays of 125 amol/μg 37 , 5 fmol/μg 38 , 155 amol/μg 39 , and 83 amol/μg 40 , although these assays employed different matrices and LLOQ calculation methods.…”

Section: Discussionsupporting

confidence: 81%

The addition of FAIMS Increases Targeted Proteomics Sensitivity from FFPE Tumor Biopsies

Sweet

Chain

Yao

et al. 2022

Preprint

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Mass spectrometry-based targeted proteomics allows objective protein quantitation of clinical biomarkers from a single section of formalin-fixed, paraffin-embedded (FFPE) tumor tissue biopsies. We combined high-field asymmetric waveform ion mobility spectrometry (FAIMS) and parallel reaction monitoring (PRM) to increase assay sensitivity. The modular nature of the FAIMS source allowed direct comparison of the performance of FAIMS-PRM to PRM. Limits of quantitation were determined by spiking synthetic peptides into a human spleen matrix. In addition, 20 clinical samples were analyzed using FAIMS-PRM and the quantitation of HER2 was compared with that obtained with the Ventana immunohistochemistry assay. FAIMS-PRM improved the overall signal-to-noise ratio over that from PRM and increased assay sensitivity in FFPE tissue analysis for four (HER2, EGFR, cMET, and KRAS) of five proteins of clinical interest. FAIMS-PRM enabled sensitive quantitation of basal HER2 expression in breast cancer samples classified as HER2 negative by immunohistochemistry. Furthermore, we determined the degree of FAIMS-dependent background reduction and showed that this correlated with an improved lower limit of quantitation with FAIMS. FAIMS-PRM is anticipated to benefit clinical trials in which multiple biomarker questions must be addressed and the availability of tumor biopsy samples is limited.

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Section: Discussionsupporting

confidence: 81%

The addition of FAIMS Increases Targeted Proteomics Sensitivity from FFPE Tumor Biopsies

Sweet

Chain

Yao

et al. 2022

Preprint

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“…Such developments will facilitate research by providing detailed functional information, like for example the activity of specific pathways (65,67). On the other hand, less complex but more robust targeted acquisition approaches will likely become more relevant in clinical settings and could complement antibody-based detection for diagnosis and stratification (88)(89)(90). Biochimica Et Biophysica Acta Bba -Proteins Proteom 1844, 917-926 33.…”

Section: Discussionmentioning

confidence: 99%

An Introduction to Advanced Targeted Acquisition Methods

Bentum

Selbach

2021

Molecular & Cellular Proteomics

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This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

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“…This was applied to monitor treatment effects in cell lines, PDX models, and extended to 46 frozen tissue lysates. Interestingly, a subset of the clinically annotated HER-2 positive tissues showed only minimal levels of HER2 by PRM [113]. Targeted LC-MS provides improved levels of detection and quantitation by only focussing on a subset of the proteome, but on occasion, particularly from complex tissue samples, target concentrations are still below reproducible levels of quantitation.…”

Section: Targeted and Multi-site Validationmentioning

confidence: 99%

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

2020

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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.

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Development of parallel reaction monitoring (PRM)-based quantitative proteomics applied to HER2-Positive breast cancer

Cited by 17 publications

References 45 publications

The addition of FAIMS Increases Targeted Proteomics Sensitivity from FFPE Tumor Biopsies

The addition of FAIMS Increases Targeted Proteomics Sensitivity from FFPE Tumor Biopsies

An Introduction to Advanced Targeted Acquisition Methods

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

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