Below are examples of projects that have been completed by the core team. Key findings have been published in subject-specific highly ranked peer-reviewed journals.
2D-HPLC scheme with accurate peptide retention prediction in both dimensions for high-throughput bottom-up proteomics.
We describe the practical implementation of a new RP (pH 10- pH 2) 2D HPLC-ESI/MS scheme for large-scale bottom-up analysis in proteomics. When compared to the common SCX-RP (mudPIT) approach, it provides a higher separation efﬁciency in the ﬁrst dimension and increases the number of identiﬁed peptides/proteins.
Compared to the SCX-RP scheme, the RP-RP method increases the number of identiﬁed proteins, simpliﬁes fraction manipulation and instrument maintenance, and offers the possibility of accurate retention prediction in both dimensions.
Development of an SRM / MRM method for absolute quantitation of MYDGF/C19orf10 protein.
PROTEOMICS - CLINICAL APPLICATIONS
The protein MYDGF/C19orf10 was identified in fibroblast-like synoviocytes from Rheumatoid Arthritis patients. Later this protein was found to be associated with Hepatocellular carcinoma, and recently has been reported for mediating cardiac repair after Myocardial infarction (Nature Medicine 2015).
Unavailability of reliable antibodies for ELISA, WB limits detection and absolute quantitation of MYDGF. Therefore, establishment of quantitative SRM / MRM based assay could prove to be instrumental for absolute quantiation of this molecule in biological samples.
The effects of infliximab therapy on the serum proteome of rheumatoid arthritis patients.
ARTHRITIS REAEARCH & THERAPY
Although the clinical effects of infliximab therapy in rheumatoid arthritis have been documented extensively, the biological effects of this intervention continue to be defined. We sought to examine the impact of infliximab therapy on the serum proteome of rheumatoid arthritis patients by means of a mass spectrometry-based approach.
The present study demonstrates that a robust clinical response to infliximab is associated with the downregulation of a spectrum of serum proteins regulated by TNF-α, and provides a possible basis for defining the broader biological effects of the treatment in vivo.
Proteomic Approaches to Identify Differentially Expressed Proteins in Cardiac Surgery Associated Acute Kidney Injury.
Acute kidney injury (AKI) after cardiopulmonary bypass (CPB) is an important cause of morbidity and mortality. Mass-spectrometry (MS) based proteomics may allow us to improve our understanding of ischemia-reperfusion injury (IRI) and identify ‘at-risk’ individuals.
This study provides high quality protein quantitation in AKI vs non-AKI patients throughout IRI. The differential proteomic changes identified may provide insight into the pathophysiology of IRI and potential novel biomarker identification. This works establish basic methodologies for MS grade urine sample preparation.