scholarly journals A streamlined mass spectrometry-based proteomics workflow for large scale FFPE tissue analysis

2019 ◽  
Author(s):  
Fabian Coscia ◽  
Sophia Doll ◽  
Jacob Mathias Bech ◽  
Andreas Mund ◽  
Ernst Lengyel ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Large Scale ◽  
Clinical Pathology ◽  
Ffpe Tissue ◽  
Great Promise ◽  
Glass Slides ◽  
Lower Protein ◽  
Ffpe Tissues ◽  
Ffpe Material ◽  
Efficient Extraction

ABSTRACTFormalin fixation and paraffin-embedding (FFPE) is the most common method to preserve human tissue for clinical diagnosis and FFPE archives represent an invaluable resource for biomedical research. Proteins in FFPE material are stable over decades but their efficient extraction and streamlined analysis by mass spectrometry (MS)-based proteomics has so far proven challenging. Here, we describe an MS-based proteomic workflow for quantitative profiling of large FFPE tissue cohorts directly from pathology glass slides. We demonstrate broad applicability of the workflow to clinical pathology specimens and variable sample amounts, including less than 10,000 cancer cells isolated by laser-capture microdissection. Using state-of-the-art data dependent acquisition (DDA) and data independent (DIA) MS workflows, we consistently quantify a large part of the proteome in 100 min single-run analyses. In an adenoma cohort comprising more than 100 samples, total work up took less than a day. We observed a moderate trend towards lower protein identifications in long-term stored samples (>15 years) but clustering into distinct proteomic subtypes was independent of archival time. Our results underline the great promise of FFPE tissues for patient phenotyping using unbiased proteomics and prove the feasibility of analyzing large tissue cohorts in a robust, timely and streamlined manner.

scholarly journals A streamlined mass spectrometry–based proteomics workflow for large‐scale FFPE tissue analysis

2020 ◽  
Vol 251 (1) ◽  
pp. 100-112 ◽  
Author(s):  
Fabian Coscia ◽  
Sophia Doll ◽  
Jacob Mathias Bech ◽  
Lisa Schweizer ◽  
Andreas Mund ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Large Scale ◽  
Ffpe Tissue ◽  
Tissue Analysis

Algorithm of combining chromatography mass spectrometry-untargeted profiling and multivariate analysis for identification of marker-substances in samples of complex composition

2020 ◽  
Vol 86 (7) ◽  
pp. 12-19
Author(s):  
I. V. Plyushchenko ◽  
D. G. Shakhmatov ◽  
I. A. Rodin
Keyword(s):  
Mass Spectrometry ◽  
Multivariate Analysis ◽  
Large Scale ◽  
Complex Composition ◽  
Unified Protocol ◽  
Chromatography Mass Spectrometry ◽  
Marker Substances ◽  
Selection Testing ◽  
Untargeted Profiling

A viral development of statistical data processing, computing capabilities, chromatography-mass spectrometry, and omics technologies (technologies based on the achievements of genomics, transcriptomics, proteomics, metabolomics) in recent decades has not led to formation of a unified protocol for untargeted profiling. Systematic errors reduce the reproducibility and reliability of the obtained results, and at the same time hinder consolidation and analysis of data gained in large-scale multi-day experiments. We propose an algorithm for conducting omics profiling to identify potential markers in the samples of complex composition and present the case study of urine samples obtained from different clinical groups of patients. Profiling was carried out by the method of liquid chromatography mass spectrometry. The markers were selected using methods of multivariate analysis including machine learning and feature selection. Testing of the approach was performed using an independent dataset by clustering and projection on principal components.

scholarly journals Automated 16-Plex Plasma Proteomics with Real-Time Search and Ion Mobility Mass Spectrometry Enables Large-Scale Profiling in Naked Mole-Rats and Mice

2021 ◽  
Vol 20 (2) ◽  
pp. 1280-1295
Author(s):  
Aleksandr Gaun ◽  
Kaitlyn N. Lewis Hardell ◽  
Niclas Olsson ◽  
Jonathon J. O’Brien ◽  
Sudha Gollapudi ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Real Time ◽  
Ion Mobility ◽  
Large Scale ◽  
Ion Mobility Mass Spectrometry ◽  
Plasma Proteomics ◽  
Rats And Mice

scholarly journals Infrared spectral histopathology using haematoxylin and eosin (H&E) stained glass slides: a major step forward towards clinical translation

The Analyst ◽  
2017 ◽  
Vol 142 (8) ◽  
pp. 1258-1268 ◽  
Author(s):  
Michael J. Pilling ◽  
Alex Henderson ◽  
Jonathan H. Shanks ◽  
Michael D. Brown ◽  
Noel W. Clarke ◽  
...  
Keyword(s):  
Diagnostic Tool ◽  
Clinical Translation ◽  
Great Promise ◽  
Stained Glass ◽  
Major Step ◽  
Glass Slides ◽  
Important Diagnostic Tool ◽  
Infrared Spectral ◽  
Spectral Histopathology

Infrared spectral histopathology has shown great promise as an important diagnostic tool, with the potential to complement current pathological methods.

Integrated mass spectrometry-based multi-omics for elucidating mechanisms of bacterial virulence

2021 ◽  
Author(s):  
Lok Man ◽  
William P. Klare ◽  
Ashleigh L. Dale ◽  
Joel A. Cain ◽  
Stuart J. Cordwell
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Large Scale ◽  
Lipid A ◽  
Phenotypic Characterization ◽  
Post Translational Modification ◽  
Form Of Life ◽  
Antimicrobial Interventions

Despite being considered the simplest form of life, bacteria remain enigmatic, particularly in light of pathogenesis and evolving antimicrobial resistance. After three decades of genomics, we remain some way from understanding these organisms, and a substantial proportion of genes remain functionally unknown. Methodological advances, principally mass spectrometry (MS), are paving the way for parallel analysis of the proteome, metabolome and lipidome. Each provides a global, complementary assay, in addition to genomics, and the ability to better comprehend how pathogens respond to changes in their internal (e.g. mutation) and external environments consistent with infection-like conditions. Such responses include accessing necessary nutrients for survival in a hostile environment where co-colonizing bacteria and normal flora are acclimated to the prevailing conditions. Multi-omics can be harnessed across temporal and spatial (sub-cellular) dimensions to understand adaptation at the molecular level. Gene deletion libraries, in conjunction with large-scale approaches and evolving bioinformatics integration, will greatly facilitate next-generation vaccines and antimicrobial interventions by highlighting novel targets and pathogen-specific pathways. MS is also central in phenotypic characterization of surface biomolecules such as lipid A, as well as aiding in the determination of protein interactions and complexes. There is increasing evidence that bacteria are capable of widespread post-translational modification, including phosphorylation, glycosylation and acetylation; with each contributing to virulence. This review focuses on the bacterial genotype to phenotype transition and surveys the recent literature showing how the genome can be validated at the proteome, metabolome and lipidome levels to provide an integrated view of organism response to host conditions.

scholarly journals Evaluation of an Interprofessional Problem-based Learning Module on Care of Persons Living with HIV/AIDS

2010 ◽  
Vol 1 (2) ◽  
Author(s):  
Marcel D'Eon ◽  
Peggy Proctor ◽  
Jane Cassidy ◽  
Nora McKee ◽  
Krista Trinder
Keyword(s):  
Student Satisfaction ◽  
Interprofessional Education ◽  
Large Scale ◽  
Interprofessional Collaboration ◽  
Learning Experience ◽  
Problem Based Learning ◽  
Great Promise ◽  
Persons Living With Hiv ◽  
Post Test ◽  
Hiv Aids

Background: Interprofessional education (IPE) holds great promise in continuing to reform the management of complex chronic conditions such as HIV/AIDS, and Problem-based Learning (PBL) is a suitable format for IPE. This study aimed to evaluate the effectiveness of a large scale, compulsory interprofessional PBL module on HIV/AIDS education. In 2004, 30 physical therapy and 30 medical students at the University of Saskatchewan engaged in the HIV/AIDS PBL module. By 2007 over 300 students from seven healthcare programs were involved.Methods and Findings: The module was evaluated over the years using student satisfaction surveys, focus groups, self-assessments, and in 2007 with written pretest/post-tests. Students rated the learning experience about both HIV/AIDS and about interprofessional collaboration, at 4 or 5 out of 6 and effect sizes fell between d = .70 and 3.19. That only one pre-test/post-test study was conducted at a single institution is one of the limitations of this study.Conclusions: Students generally thought highly of the interprofessional PBL module on HIV/AIDS and learned a considerable amount. Although more research is needed to substantiate the self-assessment data, establish what and how much is being learned, and compare PBL to alternative methodologies, PBL is a promising approach to IPE.

scholarly journals Challenges in Large-Scale Computational Mass Spectrometry and Multiomics

2016 ◽  
Vol 15 (3) ◽  
pp. 681-682
Author(s):  
Oliver Kohlbacher ◽  
Olga Vitek ◽  
Susan T. Weintraub
Keyword(s):  
Mass Spectrometry ◽  
Large Scale

scholarly journals A Pilot Study of Rare Renal Amyloidosis Based on FFPE Proteomics

Molecules ◽  
2021 ◽  
Vol 26 (23) ◽  
pp. 7234
Author(s):  
Shuang Meng ◽  
Wenwen Xia ◽  
Li Xia ◽  
Li Zhou ◽  
Jing Xu ◽  
...  
Keyword(s):  
Pilot Study ◽  
Bioinformatics Analysis ◽  
Great Promise ◽  
Individual Treatment ◽  
Renal Amyloidosis ◽  
Tissue Samples ◽  
Retrospective Diagnosis ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
End Stage

Renal amyloidosis typically manifests albuminuria, nephrotic-range proteinuria, and ultimately progresses to end-stage renal failure if diagnosed late. Different types of renal amyloidosis have completely different treatments and outcomes. Therefore, amyloidosis typing is essential for disease prognosis, genetic counseling and treatment. Thirty-six distinct proteins currently known to cause amyloidosis that have been described as amyloidogenic precursors, immunohistochemistry (IHC) or immunofluorescence (IF), can be challenging for amyloidosis typing especially in rare or hereditary amyloidosis in clinical practice. We made a pilot study that optimized the proteomics pre-processing procedures for trace renal amyloidosis formalin-fixed paraffin-embedded (FFPE) tissue samples, combined with statistical and bioinformatics analysis to screen out the amyloidosis-related proteins to accurately type or subtype renal amyloidosis in order to achieve individual treatment. A sensitive, specific and reliable FFPE-based proteomics analysis for trace sample manipulation was developed for amyloidosis typing. Our results not only underlined the great promise of traditional proteomics and bioinformatics analysis using FFPE tissues for amyloidosis typing, but also proved that retrospective diagnosis and analysis of previous cases laid a solid foundation for personalized treatment.

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