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NAICS Code 334516, Analytical Laboratory Instrument Manufacturing, applies to this procurement and the size standard is 1000 employees.
This procurement consists of procuring, delivering, and installing of the Thermo Fisher Scientific Ultra High-Resolution Mass Spectrometer, Orbitrap Q Exactive HF-X Standard M and related items/accessories because this is the only instrument currently produced that meets all of the required minimum specifications.
The EPA requires an instrument that will provide highly sensitive identification and quantitation of proteins and peptides, posttranslational protein modifications (specifically: phosphorylated proteins, carbonylated proteins, acetylated, methylated and oxidized proteins) at very low picomole - femtomole concentration levels. This analysis will be done for thousands of proteins and peptides present in biological samples, in which the protein lysates come from animal tissues and cell cultures. The minimum specifications are as follows:
(1) All components of the system must be manufactured by the same vendor. Most importantly, the mass spectrometer, nanoflow/microflow High Performance Liquid Chromatograph (HPLC) and the proteomics data processing software must originate from the same manufacturer to assure availability of service and software/firmware upgrades. This is to ensure that after upgrades, service, and repair, the system's performance is not impaired.
(2) Maximum available mass spectrometer's resolving power (mass resolution) must be at least 200,000 FWHM, defined at mass-to-charge (m/z) 200. This must be the case for all scanning modes and both the positive-ion and the negative-ion scanning polarities.
(3) The mass spectrometer/HPLC system must have a demonstrated ability to perform protein quantitation after trypsin digestion. The analysis is required for whole complex proteomes obtained from cell cultures and animal tissues. Such analyses must be feasible using one-dimensional chromatography (1D-LC) and possible at both nanoliter and microliter/minute range HPLC flowrate regimes. The estimated average number of peptides in such digests that are targeted for quantification are in the 30,000 range and the corresponding number of proteins in the 4,000 range. The expectation is that such relative quantification (of treated vs controls samples) will result in the Coefficient of Variation (CV) less than 10%. The quantitation is required to be feasible based on the high-mass-resolution full scan Mass Spectrometry (MS), while utilizing tandem mass spectrometry (MS/MS) for the identification of peptides/proteins based on the database search performed by specialized proteomic software.
(4) Quantitative proteome analysis is required to be:
(a) label-free based on the high-performance nanoflow-range HPLC chromatography in combination with ultra-high mass resolving power while the mass spectrometer operates in the single MS scanning mode, described in point (3),
(b) utilizing 10-plex isobaric MS/MS mass tags while the system operates in an MS/MS (tandem MS) scanning mode,
(c) targeted quantitation for which the instrument must be capable of acquiring Selected Ion Monitoring (SIM) scan data needed for monitoring selected ions (10 simultaneously detected and displayed). The software must acquire and display multiplexed MS/MS mass spectra (up to 10 different precursor ions). The SIM and multiplexed MS/MS scans must be timed by software based on the HPLC elution characteristics of target analytes.
(5) The mass spectrometer must be capable of High-Collision energy Dissociation (HCD), in addition to the standard Collision-Induced Dissociation (CID). The HCD scan is needed to facilitate MS/MS characterization of larger-size peptides and of other molecules that are hard to fragment in the MS/MS scanning mode.
(6) The mass spectrometer must be capable of the following advanced scan functions: Selected Reaction Monitoring/Multiple Reaction Monitoring (SRM/MRM), Parallel Reaction Monitoring (PRM), Data Dependent MS/MS triggered by a Neutral-loss scan, All-Ion-Fragmentation scan for a range of precursor ion mass with high-resolution scan of the product ions.
(7) The mass spectrometer is required to have, in an MS/MS scan mode, a Normalized Collision Energy functionality to compensate for different mass and charge states of ion propensity to fragment. Also, it must possess instantaneous charge state deconvolution.
(8) The mass spectrometer must automatically control ion injection time to provide optimized ion current across the HPLC peak.
(9) The mass spectrometer must be able to temporarily exclude an ion to allow MS/MS spectra acquisition of minor precursor ions, while the MS is operating in a data-dependent scan mode.
(10) The mass spectrometer must be able to acquire high-resolution MS data (quantitative scanning), and during this scanning procedure in must detect an apex of a chromatographic (HPLC) peak and then acquire a diagnostic MS/MS compound-identification-scan.
(11) Mass spectrometer ion source/probes requirements:
(a) Heated electrospray ionization probe is required. It must be able to operate at flow rates from 1µl/min (microliter per minute) to 1 ml/min (milliliter per minute). It must possess an ion current control parameter that is automatically adjustable and optimized.
(b) The ion source must be compatible with an APCI ionization probe.
(c) The ion source must include high-voltage dual-polarity power control, sheath and auxiliary gas flow control.
(d) The system must have a nanospray ion source with integrated column heating. The source must be fully compatible with the 50 nanoliter/min-low microliter/min flow rates from the HPLC system into the mass spectrometer.
(12) The instrument must require no cryogens (liquid helium or nitrogen). This is necessary because cryogens are expensive, cumbersome and dangerous to handle.
(13) The instrument must possess full software control for the following HPLC models: Thermo Accela UPLC, Agilent 1200, U3000 Nano RSLCnano.
(14) Mass spectrometer scanning speed requirement: the scanning speed range must be in the range of 1-40 scans/second (or higher).
(15) Mass accuracy requirement:
(a) Less than 3 Parts Per Million Root Mean Square (PPM RMS), achieved with external calibration effective over 24 h period (without mass recalibration).
(b) Less than 1 ppm RMS when analysis is performed with internal calibration.
(16) Mass range: the mass spectrometer must operate within the mass range of, at minimum, 50 - 6,000 m/z (mass-to-charge).
(17) Polarity switching: the mass spectrometer is required to perform fast ion polarity (positive/negative) switching with the frequency of at least 1 Hz without compromising mass accuracy.
(18) HPLC system requirements:
(a) The HPLC system must be manufactured by the same maker as the mass spectrometer.
(b) The system must possess a binary high-pressure gradient pump reproducibly delivering nanoliter/minute solvent flow rates, 50-1,500 nL/min; and the microliter/minute flow rates: capillary LC column-compatible flow rate of 0.5-10 microliters/min, and the higher microflow rate of 10-50 microliters/min. This wide flow rate range requirement is to make the system suitable for all required low flow applications and the associated LC column types for: bottom-up proteomics, metabolomics, and for small molecule analyses.
(c) The system is required to have a second tertiary low-pressure gradient pump capable of delivering flow rates in the range of 5-2,500 microliters/minutes. This pump is necessary for preconcentrating samples, trapping samples, and for two-dimensional chromatography work.
(d) The system must have the column temperature ranging from ambient to 75 C.
(e) The system must have an autosampler able to reproducibly and accurately deliver a wide range of sample volumes. The autosampler must have sample tray temperature control (cooling).
(f) All components of the system must be compatible with proteomic applications (analysis of complex mixtures of proteins or peptides). They must have been designed with this purpose to avoid protein and peptide losses due to physical and chemical adsorption by the system's components.
(g) The HPLC system must come equipped with all the necessary components to allow quantitation of peptides, metabolites and small molecules at the flow rates described above. Specifically, the system must include: flow selectors, flow meters, (for all three required flow ranges: nanoliter/minute, low microliter/min, high microliter/min), low dispersion valves (a 10 port and a 6 port valves suitable for 2D-LC proteomics work), tubing, fittings, sample loop(s), nano LC start-up kit, CAP LC start-up kits, microflow emitter, and CAP LC preconcentration start-up kit.
(h) The HPLC system must come with a system control software package that is integrated with the mass spectrometer software: one software package must fully control all system's components.
(19) The system must come with the software data analysis package capable of producing quantitative analysis data reports for small molecules and metabolites. The system must come with an upgrade of our existing Proteome Discoverer (PD) software to the level of the currently highest quantitative (QUAN PD) version. The PD will be used for generating differential protein quantitation reports based on the database search algorithm.
(20) The mass spectrometer must be compatible with our existing Nanomate Triversa Advion robotic liquid handling system for the task of protein/peptide identification from the 2D-DIGE gel spot digests.
Refurbished or remanufactured units are not acceptable.
THIS NOTICE OF INTENT IS NOT A REQUEST FOR COMPETATIVE QUOTATIONS. This notice satisfies the requirement at FAR 5.201(b)(1) for publicizing the proposed contract action. It is the Government's intent to award a single, firm-fixed price contract. Sources wishing to be considered MUST submit documentation to the office identified in this notice. Supporting evidence must be furnished in sufficient detail to demonstrate compliance. Information MUST be sent electronically to [email protected]. Telephone responses will not be honored. Responses must be received by 3:00pm Eastern Time on April 3, 2019. A determination by the Government not to compete this acquisition based on responses to this notice is solely within the discretion of the Government.