LImited Source Justification_Redacted.pdf

LIMITED SOURCE S JUSTIFICATION

1. Contracting Activity United States Department of Agriculture (USDA), Agricultural Research Service (ARS) - Midwest Area 1815 N University Street Peoria, IL 61604 Debora Wells – Contract Specialist debora.wells@usda.gov

2. Nature/Description of Action The purpose of this procurement is to purchase and have the vendor install a new Liquid Chromatography High Resolution Mass Spectrometry MSn system. Vendor will also provide training on the use and maintenance of the instrument and associated software.

3. Description of Supplies/Services Liquid Chromatography High Resolution Mass Spectrometry MSn system. Mass accurate mass spectrometer with ion trap mass spectrometer capable of performing multiple MS collision events in both CID, HCD collision cells and an ESI source coupled to a UPLC chromatography system with associated analytical software. This equipment is intended to 1) identify products of microbial cultivations (e.g.

fermentation, secondary metabolite production for antibiotics, etc), i.e. metabolomics

2) determine structures of other sugar-containing molecules (e.g. oligosaccharides, glycations, glycosylations, etc), and 3) detect and identify the chemical structures of unknown compounds in extracts of plants and plant products.

Liquid Chromatography (LC) integrated with a high-resolution mass accurate mass spectrometer capable of MS-MS-MS-MS with both collision-induced (CID) and high energy collision (HCD) dissociation to generate MS fragments for chemical structure elucidation.

Ionization sources ESI and optional APCI Mass range 50-2000 AMUs Resolution greater than 300,000 FWHM Mass selection for precursor isolation to 0.4 AMUs Isotopic fidelity greater than 200,000 FWHM Ion trap capable of generating MS fragmentation to the 3rd iteration or greater

(MS/MS/MS/MS)

Mass accuracy approaching 1 ppm.

Mass ion dissociation via both collision-induced (CID) and high energy induced

(HCD)

Polarity switching capability Ultra high-pressure liquid chromatography system (UHPLC) with dual pumps, column heater, and autosampler System controller analytical computer system with software package from conditioned media and/or mammalian tissues using combinations of MSn, collision-induced fragmentation, and higher-energy collision fragmentation, with high-mass accuracy detection of parent and fragment ion; MSn analysis of permethylated isomeric oligosaccharides to determine linkage positions of the sugars with in-line chromatographic separation prior to introduction into the mass spectrometer; and to optimize the detection and identification of the chemical structures of unknowns in extracts of plants and plant products. For some examples: 1) the combination of MS, MSn (n=1-4), and accurate mass detection of the ions was needed to identify the localized difference between the novel antibiotic quinovosamine and tunicamycin (both native and permethylated) using in-line liquid chromatography separations 2) the combination of MS, MSn (n=1-3), accurate mass detection, and the high-sensitivity of the orbitrap detector were needed to detect and confirm the presence of modified TunR2 antibiotics in bovine tissue 3) The separate fragmentation methods were applied to lipopeptides where: different iturin classes were identified by higher-energy collisional dissociation; surfactin classes were identified with collisionally-induced dissociation and complimentary higher-energy collisional dissociation; and fengycins by multiple stages of collisionally-induced dissociation; followed by accurate mass detection of the fragments to differentiate amino acid sequences 4) The legacy instrument was also used for MSn analysis of permethylated isomeric oligosaccharides to determine linkage positions of the sugars with in-line chromatographic separation prior to introduction into the mass spectrometer.

6. Best Value Determination

It has been determined that placing an order against a GSA schedule represents the best value to the Government consistent with FAR 8.404(d). The Government will seek further discounts beyond the prices already found fair and reasonable. This will result in the lowest overall cost alternative (considering price, special features, administrative costs, etc.) to meet the Government’s needs.

7. Market Research is the only manufacturer of an instrument capable of MSn and high mass accuracy. The additional companies listed only produce instruments capable of a single level of fragmentation or do not have high mass accuracy capability. MS/MS is not sufficient for the identification of small molecule unknowns, which is required for this project.

July 14, 2023 a Sources Sought was posted on GSA Ebuy website with a closing date of July 21, 2023 with eight (8) vendors responding. Seven (7) of the vendors placed a “No-Bid” and one (1) Vendor submitted documentation which was

8. Additional Support.

The available high-resolution LC-MS system limited to higher energy fragmentation

(i.e. no MSn ) that can be applied to peptides and some other natural products do not support the carbohydrate work specifically outlined in our CRIS project plan. See attached spreadsheet for comparative information from venders.

9. Actions Taken to Remove Barriers to Future Competition

Market research will be ongoing and the Government is looking for alternatives to meet the need and will compete if at all possible in the future.

Requirements/Program Office:

I certify that facts and representations under my cognizance included in this justification form are complete and accurate basis for the justification.

Contracting Officer:

I certify that this justification is accurate and complete to the best of my knowledge and belief.

Chief of the Contracting Office:

and belief.

Acquisition Ombudsman

Mission Area Senior Contracting Official