Sample Treatment for Tissue Proteomics in Cancer, Toxicology, and Forensics

Cole, Laura; Clench, Malcolm R.; Francese, Simona

doi:10.1007/978-3-030-12298-0_4

Cited by 6 publications

(7 citation statements)

References 120 publications

(97 reference statements)

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“…Spatially resolved microproteomics is achieved by the collaboration of LC-MS and microextraction approaches. Laser microdissection (LMD) and liquid microjunction (LMJ) are two general microextraction approaches that help extract proteins from a relatively limited area of the sample surface ( 296 – 298 ).…”

Section: Spatially Resolved Microproteomics In Endocrine Tumorsmentioning

confidence: 99%

Applications of spatially resolved omics in the field of endocrine tumors

et al. 2023

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Endocrine tumors derive from endocrine cells with high heterogeneity in function, structure and embryology, and are characteristic of a marked diversity and tissue heterogeneity. There are still challenges in analyzing the molecular alternations within the heterogeneous microenvironment for endocrine tumors. Recently, several proteomic, lipidomic and metabolomic platforms have been applied to the analysis of endocrine tumors to explore the cellular and molecular mechanisms of tumor genesis, progression and metastasis. In this review, we provide a comprehensive overview of spatially resolved proteomics, lipidomics and metabolomics guided by mass spectrometry imaging and spatially resolved microproteomics directed by microextraction and tandem mass spectrometry. In this regard, we will discuss different mass spectrometry imaging techniques, including secondary ion mass spectrometry, matrix-assisted laser desorption/ionization and desorption electrospray ionization. Additionally, we will highlight microextraction approaches such as laser capture microdissection and liquid microjunction extraction. With these methods, proteins can be extracted precisely from specific regions of the endocrine tumor. Finally, we compare applications of proteomic, lipidomic and metabolomic platforms in the field of endocrine tumors and outline their potentials in elucidating cellular and molecular processes involved in endocrine tumors.

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Section: Spatially Resolved Microproteomics In Endocrine Tumorsmentioning

confidence: 99%

Applications of spatially resolved omics in the field of endocrine tumors

et al. 2023

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“…In the early stage of proteomics, 2D gel electrophoresis was a widely used method in protein purification. With the progress in technology, more new sample preparation strategies are exploited (Alexovič, Urban, Tabani, & Sabo, 2020; Chutipongtanate, Chatchen, & Svasti, 2017; Cole, Clench, & Francese, 2019; Padula et al, 2017; Sánchez‐Juanes & González‐Buitrago, 2019; Tubaon, Haddad, & Quirino, 2017). The sample preparation method used in a particular study depends on the types of samples and purposes of the experiment.…”

Section: Applicationsmentioning

confidence: 99%

Nano‐LC: An updated review

Lian¹,

Jones²

2022

Biomedical Chromatography

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Low-flow chromatography has a rich history of innovation but has yet to reach widespread implementation in bioanalytical applications. Improvements in pump technology, microfluidic connections, and nano-electrospray sources for MS have laid the groundwork for broader application, and innovation in this space has accelerated in recent years. This article reviews the instrumentation used for nano-flow LC, the types of columns employed, and strategies for multidimensionality of separations, which are key to the future state of the technique to the high-throughput needs of modern bioanalysis. An update of the current applications where nano-LC is widely used, such as proteomics and metabolomics, is discussed. But the trend toward biopharmaceutical development of increasingly complex, targeted, and potent therapeutics for the safe treatment of disease drives the need for ultimate selectivity and sensitivity of our analytical platforms for targeted quantitation in a regulated space.The selectivity needs are best addressed by mass spectrometric detection, especially at high resolutions, and exquisite sensitivity is provided by nano-electrospray ionization as the technology continues to evolve into an accessible, robust, and easy-touse platform.

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“…This is particularly true in fresh frozen tissue samples, in which tissue will be subject to predictable ischemic changes in the ex vivo state, such as apoptosis and in situ coagulation until freezing occurs. The timeliness of such processing would affect the accuracy and quality of biomarker analysis across a range of analytes, including more sensitive proteins [36].…”

Section: Tissuementioning

confidence: 99%

“…Formalin-fixed, paraffin-embedded (FFPE) samples increase the longevity of the specimen regardless of storage temperature. However, residual paraffin (even after appropriate treatment) can contaminate the analysis of such a preserved sample [36]. There are tradeoffs of additional processing considerations for FFPE samples obtained for clinical evaluation.…”

Section: Tissuementioning

confidence: 99%

Classification of Molecular Biomarkers

Shah

Grimberg²,

Inman³

2020

Société Internationale D’Urologie Journal

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A “biomarker” is any measurable characteristic that indicates the presence or absence of disease or the biological response to a stimulus, typically an exposure or intervention. The FDA-NIH Biomarker Working Group has produced a document called Biomarkers, EndpointS and other Tools (BEST), which defines 7 categories of biomarkers according to their clinical usage: susceptibility and risk, diagnostic, monitoring, prognostic, predictive, pharmacodynamic and treatment response, and safety. We approach the classification of biomarkers in 2 additional ways: their bodily source and their measurement type. In the context of their use in genitourinary malignancy, we also consider factors that influence their use and reliability in clinical and research applications.

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Sample Treatment for Tissue Proteomics in Cancer, Toxicology, and Forensics

Cited by 6 publications

References 120 publications

Applications of spatially resolved omics in the field of endocrine tumors

Applications of spatially resolved omics in the field of endocrine tumors

Nano‐LC: An updated review

Classification of Molecular Biomarkers

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