Plasma proteomics
Proteomics analysis of human blood offers an attractive and challenging pipeline for discovery of biomarkers.
Explore how the Evosep One, with high reproducibility and robustness, is ideally suited for analysis of large sample cohorts of blood plasma.
Plasma proteomics
Proteomics analysis of human blood offers an attractive and challenging pipeline for discovery of biomarkers.
Explore how the Evosep One, with high reproducibility and robustness, is ideally suited for analysis of large sample cohorts of blood plasma.
FAST AND ROBUST PLASMA PROTEOMICs WITH THE EVOSEP ONE
Innovations in proteomics methodologies have emerged in recent years and have culminated in the identification of many potential disease-related biomarkers and potential drug targets. These innovations offer the potential for proteomics profiling to become standard practice in the clinical laboratory. Blood, plasma and serum are the predominant samples used for diagnostic analyses in clinical practices and are available in biobanks from thousands of clinical studies, but is challenging because of the high dynamic range of protein abundances.
Moreover, a plasma protein profiling workflow must be fast, robust and scalable for sampling large population cohorts in the clinic. Requiring only a finger prick of blood, plasma proteome profiling could easily be performed throughout the patient’s lifetime, from birth to the later years of life. Certainly, for a widespread adoption of proteomics in the clinic, the entire workflow from sample preparation through LC-MS and data analysis needs to become significantly faster to enable the required throughput.Â
The Evosep One is specifically designed for high throughput applications, with a focus on clinical analysis of large sample cohorts.
SIMPLIFIED WORKFLOWS WITH HIGH REPRODUCIBILITY
Simplification of workflows is preferred for standardized solutions. The Evotip serves as an integrated purification step, which saves time compared to conventional methods as some time-consuming steps can be omitted, when using the Evosep One.
The procedure is compatible with all upstream sample preparation protocols and for large cohort studies, where samples are often prepared with automated sample processing robots, which the 96-well format of the Evotips fits perfectly.
To demonstrate the reproducible performance, we performed 96 independent, parallel sample preparations and injections of the same original plasma. The total measurement time was less than two days, corresponding to a throughput of 60 samples per day. Reproducibility was excellent over all runs.
STANDARDIZED WORKFLOWS FOR PRECISE
HIGH-THROUGHPUT PROTEOMICS OF BLOOD BIOFLUIDS
The Van Eyk group from Cedars-Sinai Medical Center in Los Angeles describes the development of streamlined preanalytical proteomics workflows that achieves sensitive and robust analysis of blood-based proteomes utilizing the 60 samples per day method.
In addition to the automated digestion workflow, they also established optimal conditions for DIA analysis in plasma and adapted this to depleted plasma and whole blood. They tested eight different MS methods as the instrument cycle time is influenced by resolution settings and a number of mass windows which in turn impact the number of identifications and reproducibility.
Collectively, this paper describes the development of a streamlined process of blood biofluids covering a broad dynamic range associated with minimal hands-on time, fast turnaround, and excellent intra- and inter-day stability. Interestingly, the inter-day precision of depleted plasma was the most stable with more than 90% of peptides reproducibly detected across days. The implementation of standardized workflows like this on a large scale will facilitate the translation of candidate markers into clinical use.
PROTEOMICS OUTPERFORMS ESTABLISHED TESTS FOR DETECTING THREE STAGES OF LIVER DISEASE
In collaboration with Odense University Hospital in Denmark, the Mann group at University of Copenhagen have developed a machine learning model based on their biomarker panel, which for the first time outperforms existing tests, laying the foundation for a generic proteomics liver health assessment.
By integrating liver and plasma proteomics based on DIA with the 30 samples per day method, together with clinical data on patients and healthy controls in a clinically well-characterized cohort of alcohol-related liver disease and matched healthy controls, they were able to define plasma biomarker panels for different hepatic lesions of alcohol-related liver disease. When combined with machine learning, the plasma biomarker panels yielded predictive models that either performed as well as existing diagnostic strategies, or outperformed them, including in the context of predicting risk of future adverse liver events.
PLASMA PROTEOMICS GOES HIGH-THROUGHPUT WITH 100 SAMPLES PER DAY
In collaboration with Roman Fischer, University of Oxford and Bruker Daltonik, we combined the robustness and speed of the timsTOF Pro with PASEF together with the high throughput LC-separation provided by the Evosep One to analyze 100 ng samples of blood plasma from 192 severe infection patients at a sampling rate of 100 samples per day.
It provides robust quantification of more than 500 proteins in a single run and 772 collectively quantified if all runs are merged together.
STANDARDIZED WORKFLOWS FOR LARGE COHORT PLASMA PROFILING
Together, Thermo Fisher Scientific and Evosep are on a joint mission to develop standardized and scalable plasma protein quantitative profiling workflows. Our recent developments have been featured in an application note by the Precision Medicine Science Centre led by Dr. Emily Chen.
The aim of the study was to develop a standardized, high throughput, and reproducible workflow for bloodbased biomarker discovery using automated sample preparation. The 60 samples per day method was chosen for the study. The results demonstrated 3% CV for retention time shift over hundreds of repeated measurements and <15% CV for peak area quantification while maintaining the sensitivity.
EVOSEP WEBINAR
MEET OUR USERS IN PLASMA RESEARCH
EVOSEP WEBINAR: Plasma proteomics WITH EVOSEP ONE
Available on demand
In this webinar you will learn how the Evosep One, with high reproducibility and robustness, is ideally suited for analysis of large sample cohorts of blood plasma.
“Standardized and robust workflows are essential for quantitative protein profiling in large sample cohorts. With pre-set gradients, the Evosep One is easy to operate, while maintaining reproducibility and sensitivity in a high-throughput manner.“
Emily Chen, Sr. Director,
Thermo Fisher Precision Medicine Science Center
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find all publications, product brochures and presentations with Evosep One
More research on plasma
Here you can see publications available on plasma research featuring Evosep One. For a full overview of publications published using the Evosep One Technology visit our Literature room here
| Title | Subject | Material | Year | Summary | Institute | Evosep method | MS instrumentation | Learn More |
|---|---|---|---|---|---|---|---|---|
| The potential of plasma HLA peptides beyond neoepitopes | DDA, DIA, Plasma | Publication | 2023 | Whisper 40 SPD | Bruker timsTOF Ultra | |||
| Trans-Omics analysis of post injury thrombo-inflammation identifies endotypes and trajectories in trauma patients | Clinical proteomics, DIA, Plasma | Publication | 2023 | timsTOF Pro | ||||
| Plasma extracellular vesicles in people living with HIV and type 2 diabetes are related to microbial translocation and cardiovascular risk | DDA, Extracellular vesicles, HIV, Plasma | Publication | 2021 | This publication, led by the Trøseid group at Oslo University Hospital investigates the potential role of plasma extracellular vesicles (EVs) in relation to gut microbiota alterations and low-grade endotoxemia in HIV and type 2 diabetes. | 30 SPD | Thermo Q Exactive HF | ||
| Plasma Proteomics with the Evosep One | DIA, Liver, Plasma | Webinar | 2021 | In this webinar you will learn how the Evosep One, with high reproducibility and robustness, is ideally suited for analysis of large sample cohorts of blood plasma. | 30 SPD | Bruker timsTOF Pro, Thermo Orbitrap Exploris 480 | ||
| Immunophenotyping assessment in a COVID-19 cohort (IMPACC): A prospective longitudinal study | Covid-19, Plasma | Publication | 2021 | This resource by the IMmunoPhenotyping Assessment in a Covid-19 cohort (IMPACC) describes a longitudinal study designed to enroll 1000 hospitalized patients with Covid-19. The Evosep One will be used to analyze depleted plasma samples. | Bruker timsTOF Pro | |||
| A blood atlas of COVID-19 defines hallmarks of disease severity and specificity | Covid-19, DDA, Plasma | Publication | 2021 | This publication is a major collaboration led by the Knight group at University of Oxford describing the hallmarks of Covid-19 severity and specificity. It is an integrative multi-omics analysis, where the Evosep One was used for measuring 340 plasma proteomes providing excellent patient stratification. | 100 SPD | Bruker timsTOF Pro | ||
| Standardized workflow for precise mid- and high-throughput proteomics of blood biofluids | Automation, Clinical research, DIA, Plasma | Webinar | 2021 | In this seminar from the Canadian National Proteomics Network (CNPN) meeting 2021, Angela McArdle presents a standardized workflow for precise high-throughput proteomics of blood biofluids. They established optimal conditions for sample preparation and DIA analysis in plasma, then automated and adapted this for depleted plasma and whole blood. | 60 SPD | Thermo Orbitrap Exploris 480 | ||
| The COVIDome Explorer Researcher Portal | Clinical research, Covid-19, DDA, Plasma | Publication | 2021 | Researchers from University of Colorado led by Joaquin M. Espinosa, have created a user-friendly researcher portal enabling easy access and real-time analysis of matched multi-omics datasets for COVID-19, termed the COVIDome Explorer. They illustrate the use through a multi-omics analysis of biosignatures associated with C-reactive protein (CRP), an established marker of poor prognosis in COVID-19. | 30 SPD | Bruker timsTOF Pro | ||
| A robust mass spectrometer for precision medicine – the Orbitrap Exploris 240 mass spectrometer for large-scale plasma protein profiling | DDA, Plasma | Application note | 2021 | This application note from Thermo Fisher Scientific Precision Medicine Science Center demonstrates the reliability and robustness of the Evosep One coupled with the Orbitrap Exploris 240 MS for large-scale, untargeted plasma protein profiling. They observed excellent reproducibility of protein and peptide identifications over 100 injections of human serum performed five weeks apart. | 60 SPD | Thermo Orbitrap Exploris 240 | ||
| Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers | Clinical research, DIA, Fibrosis, Plasma | Publication | 2021 | In this study, the Theis and Schiller groups at the Helmholtz Zentrum München, investigated the correspondence of cell state changes in diseased organs to peripheral protein signatures in pulmonary fibrosis patient cohorts. From plasma proteome profiling of more than 122 patients, they propose CRTAC1 protein levels in plasma as a novel biomarker. | 100 SPD, 60 SPD | Thermo Q Exactive HF | ||
| Seroconversion stages COVID19 into distinct pathophysiological states | Clinical research, Covid-19, Plasma | Publication | 2020 | In this study, researchers from University of Colorado led by Joaquin M. Espinosa, found highly variable seroconversion status among hospitalized Covid-19 patients. Their results support the existence of distinct pathophysiological states, with seroconversion status being potentially useful as a surrogate marker of underlying processes. | 30 SPD | Bruker timsTOF Pro | ||
| Gradient off-set focusing HPLC insturment for robust and high throughput clinical proteomics | Clinical research, Plasma, Technology | Application note | 2017 | Evosep One for clinical analysis | ||||
| A Novel LC System Embeds Analytes in Pre-formed Gradients for Rapid, Ultra-Robust Proteomics | DDA, DIA, Plasma, Technology | Publication | 2018 | Description of Evosep | 60 SPD | Thermo Q Exactive HF-X | ||
| Robust and Reprodusible Protein Quantification in Plasma Using the Evosep One and the Agilent 6495 Triple Quadrupole LC/MS | Plasma, Targeted workflow, Technology | Application note | 2020 | Agilent feasibility study | 60 SPD | Agilent 6495 Triple Quadrupole | ||
| High dynamic range proteome analysis with BoxCar DIA and super-resolution Orbitrap mass spectrometry | DIA, Plasma, Technology | Poster | 2020 | BoxCar DIA | 100 SPD, 30 SPD | Thermo Orbitrap Exploris 480 | ||
| Clinical proteomics | Clinical research, Plasma | Poster | 2018 | Clinical proteomics poster | Thermo | |||
| Development of a Novel LC Concept for Clinical Proteomics | DDA, Plasma, Technology | Poster | 2018 | Description of Evosep One | 60 SPD | Thermo | ||
| MaxQuant software for ion moiblity enhanced shotgun proteomics | DDA, Plasma, Technology | Publication | 2020 | MaxQuant for timsTOF analysis | 100 SPD | Bruker timsTOF Pro | ||
| Plasma proteomics goes high-throughput – timsTOF Pro with PASEF and 4D feature alignment to quantify 500 plasma proteins in 11.5 min | Clinical research, DDA, Plasma | Application note | 2019 | The timsTOF Pro with PASEF and the Evosep One for biomarker discovery in large sample cohorts of human blood plasma (blood plasma from 192 severe infection patients). | 100 SPD | Bruker timsTOF Pro | ||
| Consistency, consistency – Automated Sample Prep for Translational Proteomics | Clinical research, Plasma | Video | 2020 | In this webinar, Emily Chen, Sr. Director at the Thermo Fisher Precision Medicine Science Center presents an automated, robust and scalable sample preparation pipeline for large-scale clinical research samples. | 60 SPD | Thermo | ||
| An Ultra High-Throughput Plasma Protein Profiling (uHTPPP) Workflow Using a Modified Quadrupole-Orbitrap Mass Spectrometer | Clinical research, DDA, Lung, Plasma, Serum, Tissue | Application note | 2020 | In this application note, the group of Emily Chen at the Thermo Fisher Precision Medicine Science Center describes a high-throughput plasma and serum proteomics analysis workflow for large population cohort studies that utilizes a standardized sample preparation method, high-throughput data acquisition, and easy to implement QC standard. | 30 SPD, 60 SPD | Thermo Orbitrap Exploris 240 | ||
| Scalable and Automated Plasma Workflow Based on the Thermo Scientific Q Exactive HF-X MS Platform | Clinical research, DDA, Lung, Plasma, Serum | Application note | 2019 | In this application note, the group of Emily Chen at PMSC describes a high-throughput plasma and serum proteomics analysis workflow for large population cohort studies that utilizes a standardized sample preparation method, high-throughput data acquisition, and easy to implement QC standard. | 100 SPD, 30 SPD, 60 SPD | Thermo Q Exactive HF-X | ||
| A paired liver biopsy and plasma proteomics study reveals circulating biomarkers for alcohol-related liver disease | Clinical research, DIA, Liver, Plasma | Publication | 2020 | This publication from Matthias Mann groups in Copenhagen and Münich describes a paired liver biopsy and plasma proteomics study, which make use of Boxcar DIA scanning for a large clinical cohort of nearly 600 patients. They have developed a machine learning model based on their biomarker panel, which for the first time outperforms existing tests, … | 30 SPD | Thermo Q Exactive HF-X | ||
| Fast Confirmatory Analysis of Rhuepos in Plasma for Horseracing Doping Control | Plasma, rHuEPO, Targeted workflow | Application note | 2019 | This application note describes a rapid targeted analysis monitoring two tryptic rHuEPO peptides in plasma for horseracing doping control. The results illustrate the promising capabilities of the Evosep One innovative technology for the analysis of protein/peptide-based drugs in the context of drug testing. | 100 SPD | Thermo Q Exactive HF |
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Evosep One solves the proteomics dilemma – covering high throughput analysis and proteome depth
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