SB1341-15-RQ-0433_SOW.pdf

STATEMENT OF WORK

LAB REQUESTING SERVICE: Material Measurement Laboratory, Biomolecular Measurement Division, Mass Spectrometry Data Center Group

I. BACKGROUND INFORMATION

The National Institute of Standards and Technology (NIST), Material Measurement Laboratory (MML), Biomolecular Measurement Division (BMD) in Gaithersburg, MD is responsible for the development of the NIST Mass Spectral Libraries (the Libraries, http://peptide.nist.gov/, http://www.nist.gov/srd/nist1a.cfm ) to accomplish NIST’s mission to provide for the collection, compilation, critical evaluation, publication and sale of standard reference data in accordance with Public Law 90-396. 90th Congress, H.R. 6279, July 11, 1968 passed by Senate and House of Representatives in 1968. The purpose of the libraries is to provide peptide reference data for laboratories, both within NIST and to the worldwide scientific community, using mass spectrometry to discover disease-related "biomarkers."

The Mass Spectrometry Data Center Group in the Biomolecular Measurement Division of the National Institute of Standards and Technology requires a mass spectrometer system capable of generating high quality tandem mass spectra of ions generated by electrospray ionization for a very wide range of ion classes and fragmentation modes. Acquiring high quality spectra covering as wide a range of applications, mixtures and fragmentation modes is consistent with the NIST mission. The goal is acquisition of dependable and reproducible data for structure determination of products of protein digests and components of natural mixtures of metabolites.

This instrument shall acquire spectra for many applications including: building mass spectrum reference libraries of all precursor ions of selected pure compounds under the most widely applied fragmentation modes; analysis of all ions arising from protein digests in order to identify of as many number and variety peptides with high quality spectra as possible; and to acquire good quality spectra for all ionized components in mixtures of metabolites and other mixtures of small molecules including environmental samples and food extracts.

Given the spectra that must be acquired, the relative concentrations over a wide range for selected ions, and the range of samples that must be examined, the required system must have the ability to perform in the following manner:

1. Generate reliable spectra for the scientific community with the employment of two fragmentation methods: a beam-type collision cell at selectable collision energies and an ion-trap capable of producing multistage fragmentation.

2. Acquire high quality spectra (as defined in the NIST publication http://pubs.acs.org/doi/pdfplus/10.1021/ac500711m) for glycopeptide and performing other analysis of post translational modifications (PTM) by electron transfer dissociation (ETD).

3. Select ions for study at sub 1 Dalton level required for the analysis of ions in very complex mixtures containing isobaric contaminants.

4. Fragment ions from one fragmentation device by another that is required for identification of classes of ions such as glycopeptides, glycans and small molecules.

5. Perform accurate quantitative analysis of isobaric coded tags, such as iTRAQ (Isobaric tags for relative and absolute quantitation) and TMT (tandem mass tags) technologies, requires isolation and fragmentation of an ion of the highest intensity to avoid contamination artefacts.

6. Operate in both the nanospray and conventional UHPLC (Ultra high performance liquid chromatography) LC (liquid chromatography) mode since the instrument is to be used for proteomic and metabolomics experiments. This may require instrument reconfiguration.

7. Be equipped with software that is compatible with the instrument for identifying ions generated by both ETD and collisional fragmentation.

8. Run conventional commercial columns with 1.7 micron particle size on a complete LC UHPLC system that is to be provided along with the instrument.

This is a brand name or equal requirement. Brand name or equal description is intended to be descriptive, but not restrictive and is to indicate the quality and characteristic of products that will be considered satisfactory to meet the agency’s requirement.

REQUIRED PRODUCTS AND SERVICES

All interested quoters shall provide a quote for all of the following line items:

LINE ITEM 0001: Quantity one (1) each Orbitrap Fusion System, Thermo Fisher Part Number FSN01-10001, or equivalent. The system must consist of all of the following components, or equivalent. The system must meet all of the salient characteristics identified herein Thermo Scientific Part No. Description Equipment FSN01-10001 System Orbitrap Fusion; A Mass Spectrometer with

Tribrid architecture combining quadrupole, linear ion trap, and Orbitrap mass analyzers, provides Multiple fragmentation techniques- CID, HCD, and optional ETD- available at any stage of MSn, with subsequent mass analysis in either the ion trap or Orbitrap mass analyzer. Provides Parallelization of MS and MSn acquisition to maximize the amount of high-quality data acquired. Uses Next-generation ion sources and ion optics increase system ease of operation and robustness as well as Innovative instrument control software to make setup easier, methods more powerful, and operation more intuitively

FETD1-10001 IC for Orbitrap Fusion (factory Install on FSN01-10001);

Optional Internal Calibration unit for the Orbitrap Fusion

OPTON-20045 KIT, preinstallation, Orbitrap Fusion;

Preinstallation Kit for the Orbitrap Fusion which contains various tubing, fittings, syringes and check standards

ES072 Nanospray Flex ion source Kit (NG);

enables the use of nanoscale flow rates and maintains excellent spray stability to ensure efficient evaporation and ionization of liquid samples Simple ion generation via Fast and flexible route for ion generation, Designed for simplicity and ease of use, Yields excellent high resolution results, Single set-up for all online nanoflow applications

5200.0345 Ultimate 3000 binary RS system;

An analytical scale Ultra High Pressure Liquid Chromatography (UHPLC) system using Binary pumps to provide fast, high resolution separation with pressures up to 1000 bar at 5 mL/min

ES269 UHPLC Liquid junction kit;

Accessory Kit for Nanospray Flex ion source

30322 SW, Sleeve 2.2 for all Omics:

Additional Tubing for “-omics” applications

PETD1-10002 ETD kit, Orbitrap Fusion;

Optional ETD Fragmentation unit for the Orbitrap Fusion

Software 30285 Tracefinder™ Software from Thermo Scientific 30313 SW, compndisc 1.0&7.0SR3;

Software- a research platform for small molecule structure ID in “known parent” workflows. Classic Metabolite ID Transformation and degradation products for chemicals in pharma, environmental, or forensics.

20137 Proteome Discoverer™ Software from Thermo Scientific;

30266 Simglycan® 5.0 desktop edition, by Premier Biosoft;

30163 Byonic™ software from Protein Metrics;

Salient Characteristics

1. The mass spectrometer must contain multiple ion fragmentation and detection devices, and be equipped with a complete LC UHPLC system with all components required for nanospray other than the LC system

2. A nanospray LC system is not required in this procurement, but all components required for nanospray other than the LC system shall be included;

3. Sensitivity of 100 fg reserpine leading to 100:1 S/N for fragmentation to major ions

4. MS2 maximum scan rate of at least 12 Hz

5. Minimum mass of 50 Da or lower

6. Maximum resolution equal to 400,000 at 200 m/z or higher

7. Mass accuracy of 1 ppm or lower with automatically supplied internal standard

8. Dynamic intrascan range of at least 5,000 orders of magnitude

9. Low mass ions (50-500 Da) for fragmentation must be isolatable within 0.2 m/z.

Installation:

The system shall be installed by the contractor and meet all salient characteristics. Installation, at a minimum, shall include uncrating/unpackaging of all equipment, rigging (as appropriate), setup and hook-up of the system, demonstration of all specifications, and removal of trash.

Onsite installation and training shall be done at NIST, Gaithersburg, Maryland and shall be completed not later than 30 days after delivery

Training:

The contractor shall conduct one (1) training session for up to six (6) technical personnel at NIST. The training shall provide a thorough demonstration of all system/solution functions, maintenance, data administration, and basic troubleshooting. The training may be completed at NIST immediately after installation/set-up and on-site measurements demonstrating that no damage or misalignment issues arose during transportation and installation. Training shall be completed not later than 30 days after installation.

One (1) year Warranty.

The contractor shall provide a one year warranty for the system. The warranty shall:

Provide all labor, equipment, consumable supplies, and repair parts for this equipment.

Provide on-site service for all required repairs not later than 48 hours from the date the repair call is placed with the Contractor

Provide unlimited, on-site repair visits to repair instrumentation to an operating condition and minimize downtime

Provide parts necessary for repairs; Provide consumables/supplies for repair, including normal wear-and-tear items such as liners, seals, lamps and tubing when needed

Include travel and labor.

Preventative Maintenance Service (OPTION LINE ITEMS).

The contractor shall perform preventative service and repairs for the instrument at the expiration of the warranty period for up to three (3) option years. Preventative Maintenance Services shall:

Provide all labor, equipment, consumable supplies, and repair parts for this equipment.

Provide on-site service for all required repairs not later than 48 hours from the date the repair call is placed with the Contractor

Provide unlimited, on-site repair visits to repair instrumentation to an operating condition and minimize downtime

Provide parts necessary for repairs; Provide consumables/supplies for repair, including normal wear-and-tear items such as liners, seals, lamps and tubing when needed

Include travel and labor.

II. PLACE OF PERFORMANCE

The installation of the equipment, training, warranty services, and preventative maintenance services shall be performed at NIST, Gaithersburg, Maryland campus site. Normal duty hours at NIST are Monday through Friday 8:00 am to 5:00 pm Eastern Time with the exception of Federal holidays or other official closures (http://www.opm.gov/operating_status_schedules/fedhol/2012.asp).

III. DELIVERABLES

Delivery, installation and training shall be completed not later than seven (7) months from the date of award.

The warranty shall commence upon final acceptance by the Government.

IV. GENERAL INFORMATION

Safety: The Contractor employee shall be responsible for knowing and complying with NIST installation safety prevention regulations (http://www-i.nist.gov/mml/safety/policies/index.htm.)

Such regulations include, but are not limited to, general safety, fire prevention, and waste disposal.

Security: NIST is a restricted campus. An identification badge is required for access for entry into buildings and also is shown to the armed Security Police when entering the campus.

Identification Badges: Contractor employees shall comply with NIST identification and access requirements. The Contractor employee is responsible for absences due to expired identification and access documents. Each Contractor employee shall wear a visible identification badge provided by the NIST Security Office. The badge must show the full name, title, and if required by NIST, the words “Contractor” in front. The Contractor employee shall turn in the NIST identification badge and vehicle pass to the TPOC, COR, or Contracting Officer (CO) upon termination of their services under this contract.

Vehicle Registration: All Contractor employees must register their vehicles with the NIST Security Office to gain access to the campus. A valid driver’s license, Government-furnished civilian ID, proof of insurance and current registration must be presented to the NIST Security Office, at which time a NIST vehicle pass will be issued. The pass shall be displayed on the vehicle’s rear view mirror in accordance with instructions. The Contractor employee shall follow NIST procedures for removal and turn-in of the vehicle pass upon termination of services under this contract.