Proteome-wide evaluation of plasma depletion methods vis-à-vis fractionation techniques

ABSTRACT: Human plasma is one of the most widely used tissues in clinical analysis, and plasma-based biomarkers are used for monitoring patient health status and/or response to medical treatment to avoid unnecessary invasive biopsy. Data driven plasma proteomics has suffered from a lack of throughput and detection sensitivity, largely due to the complexity of the plasma proteome, and in particular the enormous quantitative dynamic range, estimated to be between 9-13 orders of magnitude between the lowest and highest abundance protein. A major challenge is to identify workflows which can achieve depth of plasma proteome coverage, while minimizing the complexity of sample workup and maximizing sample throughput. In this study, we have performed intensive depletion of high abundant plasma proteins or enrichment of low abundant proteins using Hu6, Hu14 and ProteoMiner followed by SDS PAGE and C18 prefractionation techniques. We compared the performance of each of these fractionation approaches to identify the method which satisfies requirements for analysis of clinical samples, and to include good plasma proteome coverage in combination with reasonable sample output. In this study, we have reported that gel-based prefractionation approaches can replace expensive and time-consuming chromatographic separation, thereby significantly accelerating analysis time. In addition, we showed that a variety of methodologies can achieve similarly high proteome coverage, allowing flexibility depending on project specific needs. These considerations are important in the effort to accelerate plasma proteomics research so as to provide efficient, reliable and accurate diagnoses for the population as a whole.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma

SUBMITTER: Gurjeet Kaur  

LAB HEAD: Gurjeet Kaur

PROVIDER: PXD022469 | Pride | 2021-02-17

REPOSITORIES: Pride