Attachment A - Performance Work Statement.docx

RFQ# 12805B23Q0161

Performance Work Statement Proteomic Analysis of Human Plasma Samples

Study Summary USDA-ARS (specifically the Grand Forks Human Nutrition Research Center) is focused on improving our understanding of the health roles of foods and physical activity. USDA-ARS is interested in finding plasma markers at the protein level that may be downstream from specific genetic variants suspected to play a role in the reinforcing value of exercise (based on the hypothesis that some people have stronger desire to exercise). The key objective of this study is to generate a comprehensive proteomics profile of plasma samples from participants who are deemed to have either high or low exercise reinforcement. The study is part of a pilot project aimed at validating specific markers of interest while also assessing novel markers that may be relevant.

Platform Requirements Hyper Reaction Monitoring (HRM) mass spectrometry that includes Data Independent Acquisition-based protein quantification technology. HRM is necessary for the deepest unbiased profiling of biofluids (e.g., plasma) proteomes on a large scale. Platform must search the complete proteome to quantify thousands of the most relevant proteins, including an unlimited number of proteoforms.

The work described is an untargeted proteomic analysis of 40 samples from an existing study to identify protein factors in human plasma that are different between subjects that find exercise reinforcing and those who do not.

· Contractor will provide GFHNRC or designated representatives with instruction on how to ship human plasma samples to them to ensure safe and intact arrival.

· Contractor will verify receipt of samples promptly.

· Contractor will store samples at -75°C to -80°C.

· Contractor will use immunodepletion to remove the top 14 most abundant proteins from the samples as they are not of interest to this investigation.

· Samples will be further processed for analysis which may include deglycosylation, reduction, and trypsin digestion.

· Samples will be analyzed using an ultra-deep acquisition workflow LCMS platform with high-mass resolution capabilities.

· Contractor will apply a sample analysis platform of Hyper Reaction Monitoring (HRM) mass spectrometry that includes Data Independent Acquisition-based protein quantification technology. HRM is necessary for the deepest unbiased profiling of biofluids (e.g., plasma) proteomes on a large scale. Platform must search the complete proteome to quantify thousands of the most relevant proteins, including an unlimited number of proteoforms.

· Peptide sequences will be identified and compared against a study-specific spectral library of the human proteome to identify species. Sequences and identification will be provided to the GFHNRC along with lists of unknown peaks.

· Quantitative information with respect to species will be provided to GFHNRC scientists and/or designated representatives for analysis. Quantitative services will include:

· Experimental design

· Overview of the identified proteins in each sample

· Exploratory data analysis, e.g. Principal Component Analysis (PCA), Partial Least Square Discriminant Analysis (PLS-DA), hierarchical clustering

· Differential abundance analysis, e.g. t-test between sample groups

· Functional analysis, e.g. GO enrichment analysis, PPI network analysis

· Quality control reporting

· Data delivery will include:

· Microsoft Excel table

· Table of content

· Sample table

· List of proteins identified

· Normalized protein intensities

· Results of statistical analysis

· Samples will be returned to GFHNRC or disposed of after consultation with GFHNRC scientists.

· The GFHNRC reserves the right to add follow-on contracts for additional samples, method development upon successful performance of early stages of this work.

Anticipated Period of Performance: 4-6 Weeks ARO