Metabolomics Service Procurement - Statement of work - A George - Brandl Lab.pdf

Statement of Work (SOW) Metabolomic services to identify compounds

GENERAL INFORMATION

1.0 Scope of Work:

Commercial metabolomics service to conduct analysis of 105 lettuce samples obtained under various conditions using Liquid Chromatography-Mass Spectrometry (LC-MS) analysis for 3 time points with 7 cultivars on a C18 column in both positive and negative ion modes to identify plant metabolites. Metabolite extraction and preparation for LC-MS from samples sent by USDA, followed by LC- MS analysis and data bioinformatic analysis, must be conducted at the vendor’s site within 2 weeks to allow for the same plant crop to be used for further assays based on metabolomic results received by the vendor. The service must also perform untargeted rather than targeted analysis, but with inclusion of plant secondary metabolites. The service must be capable of identifying specific lettuce compounds, including lettuce flavonoids, of importance in the lettuce wound response, which is the focus of our project.

2.0 Background:

We have recently completed and published a study regarding the critical role of the lettuce wound response in the survival of foodborne pathogens in fresh-cut lettuce.

Analysis of plant secondary metabolites are important for the continuation of this research project because they are the core compounds in the plant wound response physiology. The Western Regional Research Center has neither the equipment nor the personnel to perform the lettuce sample preparation and LC-MS metabolome analysis followed by bioinformatic data analysis. Therefore, we are seeking to contract an operation that will extract plant material, perform LC-MS analysis on the plant extract, and analyze the results to identify lettuce compounds of interest to our project. This service will require the operation to have access to a large database of secondary metabolites specific to lettuce.

CONTRACTOR REQUIREMENTS

3.0 Technical Requirements/Tasks:

The specific task to be performed is a commercial untargeted metabolomics service using an LC-MS system on C18 columns in positive and negative mode.

Analysis must be conducted on samples to allow for comparison between lettuce cultivars and sampling time points Personnel must be familiar with and have performed LC-MS metabolomics on lettuce Lettuce sample extraction for LC-MS analysis must be performed in-house by the operation Must have QC samples for lettuce compounds of interest ready and available in house Must have LC-MS set up for detection of both polar and non-polar compounds

Must be able to detect and identify a wide range of compounds involved specifically in lettuce secondary metabolism

Autosampler capable of keeping samples at 4°C to prevent degradation Q-Exactive Hybrid Quadrupole-Orbitrap mass spectrometer for MS/MS analysis in positive and negative mode with resolving power of at least 15,000; and Xcalibur 4.5 operation software for data acquisition

Access to and familiarity with external metabolomic databases Available database for identification of at least 1000 plant compounds, including both phytohormones and carotenoids, and lettuce-specific metabolites

Available database and familiarity with a mass list of about 7000 plant flavonoids, including those in lettuce

Filtering of molecules from plant samples through background subtraction and exclusion of false positives.

Bioinformatic data analysis and plotting via score plots, volcano plots, heatmap construction, and pathway analysis

Bioinformatic analysis to demonstrate significant differences between metabolite profile of each lettuce genotype at various time points, and identification of these compounds

4.0 Government Furnished:

There is no Government Furnished Equipment.

5.0 Deliverables / Schedule:

CLIN 001

Deliverable

Identification of lettuce metabolites and metabolic pathways, and comparative bioinformatic analyses of metabolites from different cultivars at different time points One-way ANOVA, PCA, PLS-DA, heatmap, and Random Forest

Objective Receiving the metabolomic analysis results of the 105 lettuce samples with the associated files and forms.

Due Results will be reported no later than 2 weeks after receipt of the lettuce samples by the vendor.

6.0 Travel:

N/A

7.0 Contractor’s Key Personnel:

Sheng Zhang Andy Lui

8.0 Security Requirements:

9.0 Data Rights:

The USDA owns all rights to use, production and disclosure of the data produced from this service including all intellectual property rights.

10.0 Section 508 – Electronic and Information Technology Standards:

Attachments:

• Market Research document included to provide evaluation factors regarding supply to be produced from this service.