Sources Sought Notice (Mass Spectrometer) Revised.pdf

Sources Sought Notice

Title: VPP Mass Spectrometer Replacement

ID: NIAID – SS-24-2220777

Post Date: August 2, 2024

Response Date: August 9, 2024

Classification Code:

NAICS: 334516

Introduction

This is a Sources Sought notice This is NOT a solicitation for proposals, proposal abstracts, or quotations. The purpose of this notice is to obtain information regarding the availability and capability of all qualified sources.who could source a “Brand Name or Equal” Bruker Daltonics

Mass Spectrometer Model timsTOF flex.

Background

The Vaccine Production Program (VPP) is the development arm of the Vaccine Research Center.

Due the nature of our expertise, the Mass Spectrometry group provides support for the VPP, as well as collaborators outside the VPP and collaborators outside NIH. The acquisition of a new mass spectrometer ensures continued support for all programs such as Ebola, Zika, and HIV, Flu, Covid vaccine development in VPP/ VRC, and external collaborators. The acquisition of a replacement mass spectrometer will also provide redundancy for high-demand mass spectrometry workflows so that failure of one mass spectrometer does not result in significant analytical downtime.

Purpose & Objective

The National Institute of Allergy and Infectious Diseases (NIAID) conducts and supports basic and applied research to better understand, treat, and ultimately prevent infectious, immunologic, and allergic diseases. For more than 50 years, NIAID research has led to new therapies, vaccines, diagnostic tests, and other technologies that have improved the health of millions of people in the

United States and around the world. In the last decade, with increased emphasis in the last three years due to a world-wide pandemic, it has become a priority of NIAID to utilize new vaccine modalities, such as mRNA-LNP based vaccines, to combat emerging infectious diseases. The

Vaccine Production Program (VPP) is the development arm of the Vaccine Research Center

(VRC). The mission of the VRC is to create and develop potentially lifesaving vaccines for HIV, Ebola, Zika, and other known pathogens and get these potentially lifesaving products into the clinic. The Mass Spectrometry group within Analytical Development provides critical support for the Cell Culture, Cell Line, Downstream, and Formulations groups within the VPP. Due the nature of our expertise, the Mass Spectrometry group also provides support for collaborators outside the VPP and outside NIH. In Q12024, one of the VPP mass spectrometers reached its end of life and was decommissioned. In order to maintain and improve current mass spectrometry capabilities and provide redundancy for high demand mass spectrometry workflows, a replacement mass spectrometer is needed. Specifically, NIAID, VRC, VPP is seeking one (1) Brand Name or Equal Bruker Daltonics Mass Spectrometer Model timsTOF flex.

Project Requirements

Salient Characteristics are described as follows:

1) Acceptable size dimensions of no more than 275 cm in length x 100 cm in width x 260 cm in height for the equipment, potential key add-ons, and other key components combined. These dimensions are hard limits due to the physical size constraints of the space.

2) Power requirements. No more than 2x 220V plugs due to the power constraints of the lab.

3) Imaging mass spectrometer. We require the ability perform imaging mass spectrometry to look at molecules in 2D space.

4) Trapped ion mobility separation (TIMS).

a. We require the ability to assess the substance’s 3D shape in space (known as collisional cross section; CCS). Program needs to use this ability to measure CCS to distinguish between specific lipid isoforms, separate isobaric peptides, and identify unknown small molecules.

b. The equipment must be able to use the ion mobility with MALDI imaging.

c. The equipment must be able to use ion mobility with MALDI.

d. The equipment must be able to use the ion mobility with ESI and nanoESI.

e. The MS instrument must contain a dual trapped ion mobility spectrometry

(TIMS) analyzer that delivers high ion mobility resolution with parallel accumulation– these features allow for samples to be sorted by CCS prior to time of flight (TOF) analysis while the next batch of ions is loaded. This will assure ion mobility can be performed with 100% duty cycle without losing sensitivity.

f. We require that the CCS and m/z be calibrated with the same calibrant reagent

(e.g. one calibration compound(s) for both CCS and m/z), and that both of these calibrations can be applied across all compounds regardless of class.

5) High resolution QTOF.

a. TOF analysis must be high resolution with a resolving power greater than or equal to 60000 with full sensitivity resolution at m/z 1222.

b. We require that the instrument provide mass accuracy of <0.8ppm internally and

2 ppm externally calibrated. Coupled with CCS information from ion mobility, this will assure molecules are identified correctly.

c. The TOF analyzer must be able to acquire at equal to or greater than 300 Hz.

First-pass identification. We require mass spectrometer capable of first-pass identification that doesn’t require follow up evaluations in order to increase sample throughput. This first pass ID ability via ion mobility techniques allows high throughput screening of at least 20 true square pixels per seconds. First pass identification via ion mobility is required for high throughput that is needed for this project. We require the ability to run a lot of samples while being sure of the findings on the first run without requiring numerous second, more targeted runs relying on tandem mass spectrometry.

6) Tandem mass spectrometry collision cell.

a. This instrument must have the ability to fragment ions in a collision cell.

b. Fragmenting ions is used as an additional identification parameter and is necessary for many mass spectrometry-based analyses.

c. Collision cell must be after ion mobility (TIMS) separation, so that mobility-separated ions can be fragmented and identified.

d. The quadrupole in front of the collision cell must be able to isolate ions with m/z values up to 3000, and pass ions up to m/z 40,000 without isolation.

7) MALDI laser specifications. We require that the MALDI laser:

a. Have a minimum laser spot size of 20 m or smaller.

b. Have a square pixel for MALDI imaging, which prevents overlap/oversampling of the sample.

c. Have the ability to operate at greater than or equal to 10 kHz at its minimum focus

(≤20 m). This allows for high-throughput mass spectrometry analysis.

8) MALDI source specifications. We require that the MALDI source:

a. Allow for rapid switching between ESI and MALDI (<30 seconds), without physical hardware changes or venting of instrument. Venting the instrument delays instrument use and decreases sample throughput.

b. Have the ability to analyze a MALDI target with ≥1536 sample spots. We anticipate using MALDI for high-throughput analyses so a MALDI target with a large number of spots is necessary.

9) Bottom-up proteomics. We extensively use bottom-up proteomics and require that the mass spectrometer meet or exceed current bottom-up proteomics capabilities.

a. We require that the mass spectrometer should be able to identify >40,000 unique peptides in a single run from a complex mixture in order to perform bottom-up proteomics experiments.

b. This spec can be shown in a publication.

10) Native ESI. We require that the ability to perform native ESI experiments.

https://doi.org/10.1038%2Fs41597-022-01216-6

11) Include ultra-performance liquid chromatography instrument.

a. The UPLC must include an autosampler, pumps, column oven, and UV detector.

12) Nanospray Source.

a. The mass spectrometer must include a nanospray source to improve instrument sensitivity.

13) Compatible with Waters M-class HPLC.

a. The new MS instrument must provide software (not contact-closure) control of previously purchased and currently in use Waters M-class UPLC.

b. Coupled with the nanospray source, this allows for nano-scale separations.

14) The mass spectrometer software must provide.

a. Data format output that is compatible with third party software (Byos) to seamlessly integrate into current workflows.

b. Data analysis software that allows manual interpretation of mass spectrometry data.

c. Maximum Entropy deconvolution (or equivalent).

15) Real-time bottom-up proteomics data processing. We require that the instrument include software that allows real-time processing (e.g. data is processed while being acquired) of bottom-up proteomics data. This increases sample throughput by eliminating the need to manually set up and run data analysis.

Anticipated Period of Performance

It is anticipated that an award will be made on or about September 27, 2024. Delivery of the

Mass Spectrometer system is preferred as soon as possible and required within 30 days.

Capability Statement/Information Sought

If your organization has the potential capacity to provide a Bruker UPLC/MS system Brand

Name or equal with the components outlined in the attached BOM which meet the minimum technical requirements and performance capabilities listed above, please provide the following information:

1. Organization name, address, point of contact, email address, website address, telephone number, UEI number.

2. Type of business (e.g., 8(a), HUBZone, Other than Small, etc.) pursuant to the applicable NAICS code.

3. Identification of any Best-In-Class contract vehicles including Government Wide

Acquisition Contracts (GWAC) (e.g., GSA schedule) they may possess or are aware of that would support this possible requirement. If your organization does not provide the products/services under a GWAC, please identify availability as OPEN MARKET

ONLY.

4. Tailored capability statement addressing the capability of the high throughput Bruker

UPLC/MS (Ultra Performance Liquid Chromatography/Mass Spectrometry) to meet

NIAID’s minimum requirements. Capability document shall be no more than six pages.

5. Place of manufacture for the high throughput Bruker UPLC/MS system and components. If this instrument is not manufactured in the United States, please state if the instrument is TAA compliant.

6. Evidence that the organization is an authorized reseller or manufacturer of the high throughput Bruker UPLC/MS. Authorized resellers shall identify the OEM of the equipment proposed in their capability statement. Only OEM products are acceptable.

7. Provide information regarding sustainability considerations of the equipment and any associated parts. Are any parts of the system energy efficient consistent with Energy

Start certification or FEMP designated products. Furthermore, are there any sustainability practices or materials such as the use of recovered materials, biobased products, or alternative to ozone-depleting substances used in the manufacturing process of the high throughput Bruker UPLC/MS .

Confidentiality

No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s).

Submission Instructions

Interested businesses who consider themselves qualified to provide the above listed Mass

Spectrometer with the required specifications are invited to submit a response to this Sources

Sought Notice by August 9, 2024, at 3:00 PM ET. All responses under this Sources Sought

Notice must be emailed to uju.obii-obioha@nih.gov.

Disclaimer and Important Notes

This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization’s qualifications to perform the mailto:uju.obii-obioha@nih.gov work. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, a pre-solicitation synopsis and solicitation may be published in SAM.gov. However, responses to this notice will not be considered adequate responses to a solicitation.