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Clinical Proteomics

Plasma analysis has proven to be a powerful and attractive tool for biomarker discovery over large cohorts.

Identification of several disease targets, diagnosis, prognosis, therapeutic areas, clinical research organizations, translational studies, target molecules for drug interactions, and studies related to biomarker structural morphology can be done.

 

Comprehensive proteome analysis is difficult due to the dynamic protein range. Advancements in recent technologies have overcome such challenges. Profiling allows a paradigm shift towards a ‘rectangular’ strategy of biomarker research, in which the proteome patterns of large cohorts are correlated with their phenotypes in physiological states.

Blood proteins can be classified into two broad categories – First contains abundant proteins having a functional role in blood. The second contains tissue leakage proteins that do not have a dedicated role in the circulation.

Concentration range of proteins in serum and plasma

Clinical Proteomics

Reference:

  • Revisiting biomarker discovery by plasma proteomics. (2017). Molecular System Biology.

  • PASEF enables high-throughput quantitative large-scale plasma proteomics and application to COVID-19, Bruker.

  • PASEF™ on a timsTOF Pro defines new performance standards for shotgun proteomics with dramatic improvements in MS/MS data acquisition rates and sensitivity, Bruker.

  • https://www.biochem.mpg.de/6440523/clinical-proteomics

A) A large cohort is investigated in the discovery phase with as much proteome coverage as possible. In the validation phase, another cohort is analyzed to confirm the biomarker candidates, but it uses the same technology and similar cohort size. Both cohorts can be analyzed in parallel, but only the proteins that are statistically significantly different in both studies (red) are validated as biomarkers.

B) Plasma proteome profiling of diverse lifestyle, disease, treatment, or other relevant alterations will over time build up a knowledge base that connects plasma protein changes to perturbations in a general manner . The plasma proteome profile of a given individual can then be deconvoluted using the information and algorithms associated with the knowledge base.

A)Physicians making treatment decisions based on a few known biomarkers and patient history.

B)Adding new biomarkers according to the patient’s clinical condition could improve the effectiveness of the treatment.

C)Multi-protein panels combined with the patient’s past clinical history can aid in the precise decision of treatment.

Applications:

  • prm PASEF method – sensitive, selective and specific method showing high reproducibility and accurate quantification of proteins. This method is particularly used for clinical targeted proteomics experiments to quantify a list of peptide markers with accuracy and robustness.

  • Integrated ion mobility with timsTOF pro using PASEF facilitates deep proteome analysis of specific cells of the body like the beta islet cells of the pancreas supporting research in diabetes and numerous other applications.

  • Adding 4th dimension to separation – 4D omics.

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  • The timsTOF Pro with PASEF® (Parallel Accumulation Serial Fragmentation) technology delivers revolutionary solutions related to scanning speed, with enhanced specificity and high sensitivity optimized for shotgun proteomics needs.

Know More

timsTOF Pro

Plasma/ Serum
Sample Preparation
DDA – PASEF
Data Processing

Case Study

PASEF application In COVID - 19

 

About 3,04,58,251 cases of covid 19 have been registered in India as of June 2021. 2,95,48,302 patients have recovered and 4,00,312 deaths have been reported.

 

One of the most accessible biofluids and a primary sample of interest in clinical proteomics for biomarker discovery is the blood, plasma, and serum. Due to the large dynamic range of protein concentrations, comprehensive proteome analysis of plasma is challenging. Depletion of these abundant proteins can be carried out using antibodies. This enhances the detection of lower abundant proteins. A disadvantage of this depletion strategy is quantitative variability between the samples, extra work, time, and cost for analysis in the case of cohorts. In addition, many high abundance plasma proteins may serve as carriers for other proteins that are then also lost in the process. All of these issues favor the direct analysis of undepleted samples. Parallel accumulation, serial elution, and fragmentation (PASEF) on the tims TOF Pro have proven to be highly sensitive and fast for in-depth or near-complete proteome quantitation.

 

Nearly 320 proteins could be quantified without depletion from a single sample in 21 minutes.

With such further improvements in sample preparation and acquisition strategies in the existing platform, not only hundreds but thousands of plasma proteomes could be quantified in a routine manner leading to population-wide cohorts tackled with PASEF.

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