Molecular_Foundry_Specifications.docx

Specifications and Minimum Feature Requirements

Overview:

The Molecular Foundry seeks two mass spectrometer systems to include:

1. A hybrid quadrupole/ion mobility/orthogonal acceleration time-of-flight (oa-TOF) mass spectrometer with switchable ESI/DESI source, UPLC analytical chromatography inlet, and associated software systems to support the Biological Nanostructures user facility.

2. A high-performance benchtop mass spectrometer q-Tof mass spectrometer system equipped with atmospheric pressure chemical ionization (APCI) source, UPLC analytical chromatography system inlet, and associated software systems to support the Organic facility.

The emphasis in the instrument selection will be on the ease of use, system flexibility, and performance. Key performance benchmarks include instrument ionization source capabilities, sensitivity, resolution, and accuracy.

System Specifications:

System 1: Hybrid quadrupole/ion mobility/orthogonal acceleration time-of-flight (oa-TOF) mass spectrometer system.

The instrument should be a high-resolution exact mass spectrometer capable of acquiring MS and MSn spectra from a variety of ionization methods including:

High-resolution MS Performance:

Mass resolution of >75,000 FWHM at speeds up to 30 spectra per second.

<1 ppm mass accuracy for both precursor and product ions.

Support Mass ranges of:

Mode 1: 20–64,000 m/z Mode 2: 20–32,000 m/z Quadrupole analyzer:

The instrument should be capable of unit mass resolution for precursor ion selection.

The 8K Da quadrupole should resolve 20 to 8000 m/z in resolving mode, 20 to 30,000 m/z in non-resolving mode.

Positive ion MS sensitivity: The peak at m/z 556 from a solution of 50 pg/μL leucine enkephalin in 50/50 acetonitrile/water +0.1% formic acid, infused at a flow rate of 5 μL/min, will have an intensity of greater than 62,400 counts per second, with the instrument tuned for 12,500 resolution (as demonstrated on bovine insulin)

System Sensitivity Performance:

Target enhancement mode: The peak at m/z 556 from a solution of 10 pg/μL leucine enkephalin, infused at a flow rate of 5 μL/min, will have intensity greater than 19,500 ions per second, with the instrument tuned for 25,000 resolution (as demonstrated on bovine insulin)

Positive ion MS/MS sensitivity: Using a [Glu1]-Fibrinopeptide B solution of 100 fmol/μL, at a flow rate of 5 μL/min and with the instrument tuned 12,500 resolution, the intensity of the most intense y" sequence ion from the MS/MS spectrum of the doubly charged precursor ion (m/z 785.8) will be greater than 4,800 counts per second. The instrument m/z range will be set to 2,000

Negative ion MS sensitivity: The peak at m/z 554 from a solution of 50 pg/μL leucine enkephalin in 50/50 acetonitrile/water +0.1% formic acid, infused at a flow rate of 5 μL/min, will have an intensity of greater than 20,580 counts per second, with the instrument tuned for 12,500 resolution (as demonstrated on bovine insulin)

Negative ion MS/MS sensitivity Using a solution of 500 pg/μL raffinose in 70/30 acetonitrile/water, at a flow rate of 5 μL/min and with the instrument tuned to 12,500 resolution, the intensity of the fragment ion at m/z 179.1 in the MS/MS spectrum of the precursor ion at m/z 503.2 will be greater than 2,400 counts per second. The instrument m/z range will be set to 1,200

Dynamic range High Resolution Mode is at least 4 orders of magnitude when measuring the m/z 556.2 peak from leucine enkephalin Acquisition rate Up to 30 scans per second

Ionization sources:

a. Should include electrospray ionization (ESI) via a single multimode source which includes ESI, electrospray chemical ionization (ESCi), APCI capability

b. ESI source should be an atmospheric pressure ionization source and should include a secondary probe to introduce a reference. The ESI probe should be tool free.

c. Should include a Desorption Electrospray Ionization (DESI) source.

i. DESI source should be capable of high-resolution mass spectral imaging with pixel size of 5 mm with and low flow rates of 100 to 500 nl/min.

ii. The DESI source should allow for normal resolution imaging data acquisition at <50mm with a pixel acquisition rate of greater than 30 pixels per second.

iii. DESI source and associated software should enable high throughput

iv. The DESI source should provide a X-Y inlet system providing full random-access automated movement across a sample well.

v. The DESI source should allow for the analysis of tissue slices mounted on glass microscope slides.

vi. The nitrogen gas used for the DESI sprayer should be equal or less than 7Bar and teed from the nitrogen gas of the mass spectrometer

d. System should be compatible with existing Nanolock spray nanoflow ESI source.

e. Should be compatible with ASAP, APGC, and APCI source options.

Electron Transfer Dissociation (ETD) or Electron Capture Dissociation (ECD):

The system should provide the ability to perform electron transfer dissociation or electron capture dissociation. ETD/ECD provides a complementary method to collision induced dissociation (CID) and provides a method to increase structural information from intact proteins and peptides with post translational modifications (phosphopeptides, glycopeptides).

Ion Mobility Separation:

a. The instrument should incorporate a traveling-wave ion mobility separation cell that has the following functionality:

i. Enables separation based on mass, charge state, and size

ii. Accepts and accumulates ions that are produced in the source

iii. Releases packets of ions for separation based on their ion mobility

iv. Can also act as a collision cell to fragment ions

v. Can separate mixtures of ions according to their ion mobility with a resolution of over 36 Ω/ΔΩ (cross-section/delta cross section)

vi. Should be able to measure drift time between 33 microseconds and 90 milliseconds

b. Should be able to produce time aligned parallel fragmentation spectra.

c. Should be able to use different gasses for mobility separation.

d. Should enable control of traveling-wave height and velocity with linear ramps or user defined programs as well as allowing comprehensive manual control.

Vacuum system:

a. The instrument must incorporate a clean differentially pumped, automated vacuum system including a single, oil free, dry backing pump, and air-cooled turbomolecular pumps for the source, quadrupole, ion mobility chamber, transfer optics and oa-Tof regions of the instrument.

b. The system should be equipped with analyzer penning vacuum gauges. Vacuum and system vent/pump cycles should be digitally monitored to provide software control and ensure fail-safe operations in the event of power failure.

UPLC and Ancillary Devices:

a. A UPLC system should be provided for LC/MS operation. The system shall include a solvent degasser, UPLC pump capable of quaternary solvent pump with gradient production that supplies direct (non-split) flow at up to 15,000 PSI operating pressure at flow rates from 0.001 to 2.000 mL/min for high-resolution chromatographic separations, diode array UV detector, auto-sampler with Peltier temperature regulating capability to maintain samples over a range of 4 to 40°C and the ability to reliably inject 1 out of 4uL with carryover performance <0.002%, and a column heating module able to maintain column temperature from ambient +5°C to 65°C with software switching flow to 4 columns of 4.6x100mm. Automated sample manager should house a minimum of 10 microtiter plates or array plates for at least eight 48x2ml vails with temperature control from 4 to 40°C.

b. Additionally, the system should include auxiliary pumps to handle calibrant addition with programmable flow rates ranging from 200 nL/min to 5uL/min under acquisition software control.

c. Analog inputs must be available for interfacing to ancillary LC detectors (UV, ELSD etc.)

d. External contact start/stop/events must be provided via a user I/O board.

e. System should include an emergency battery power source capable of powering the entire instrument and data acquisition system for at least 10 minutes and integrate with control software for safe shutdown of the system in case of power outage.

Instrument control and data processing hardware and software:

a. A pc workstation with monitor for data acquisition with all software installed should be included. The acquisition pc must control both the MS and UPLC systems.

The acquisition pc should have the following minimum configuration:

• Operating System: English version of Microsoft® Windows® 10 Enterprise LTSB version 1607.

• CPU: 2 x Intel Xeon Gold processor 5122 3.6G 4C 105W.

• Memory: 8 x 8 GB (64 GB RAM) DDR4 2666 ECC RDIMM.

• Graphics card: 1 x Nvidia Quadro P-1000 4-GB 4mDP HP.

• SSD M.2 PCle OPAL: 1x 512 GB.

• Spinning storage drives: 1 x 10-TB HD 7200RPM 3.5" SATA3.

• NIC: Integrated 2-port Gigabit10 Ethernet (i219LM and i210).

· 27 inch monitor display

• Serial port: 1.

• DVD: CD-RW Rambo W10. 1

b. A separate offline data processing workstation with monitor, keyboard, and mouse with all software installed should be included.

The data processing workstation should have the following minimum specifications:

· Processor: The Lenovo P5 workstation for Waters Connect is equipped with 12 cores.

· Operating System: The workstation runs on Windows 10 Enterprise LTSC 2021 edition (version 21H2).

· Memory: 64 GB of memory

· Hard Drives: 512 GB solid-state drive for the operating system and applications.

· Video Card: The workstation requires a discrete video card with a minimum of 4 GB memory (Direct 11 or higher compatible).

· Network Interface Cards: The workstation requires two 1-Gbps or higher network interface cards.

· Monitor: A minimum of 27 inch monitor with a minimum resolution of 1920x1080 is required.

c. Mass spectral acquisition and analysis software should be compatible with existing software including Masslynx 4.2.

d. The system must include data analysis software that will allow state of the art quantification using the most common data analysis algorithms.

e. The spectrometer should be capable of automated tuning, calibration, QC, and system diagnostics.

f. The acquisition software should allow for automated MS, MS/MS, SONAR and data dependant acquisitions (DDA). The instrument and software should be capable of MSE data acquisitions whereby low and elevated collision energy data are acquired simultaneously to provide fragmentation data for all detectable molecular ions. The instrument should alternate between low and elevated energy in the collision cell at user-defined intervals. In the low-energy acquisition it records the mass spectrum exhibiting mainly precursor ions, and in the elevated-energy acquisition their respective fragment ions.

g. The software must be capable of aligning MSE data according to UPLC retention time and then automatically associating the precursor ion for each sample component to its fragment ion spectrum. It must be possible to automatically interrogate the processed MSE dataset.

h. Control and data acquisition must be provided within the MS acquisition software for UPLC systems, single channel, multi-channel and diode array UV detectors, and a variety of HPLC for the acquisition of LC/MS, LC/MS/MS spectra.

i. Control software must be able to control source voltages and incorporate active feedbacks.

j. Data processing software must incorporate an elemental composition calculator that allows for interpretation of actual isotope patterns including a goodness of fit from actual to theoretical isotopes. The ability to filter out incorrect elemental composition calculations through the use of intelligent spectral interpretation algorithms must be incorporated.

k. The software should offer data directed analysis whereby the instrument automatically switches into MS/MS mode during acquisition based upon data acquired in MS mode in the previous scan based on user defined criteria (threshold, target mass, excluded mass). Must be able to take advantage of ion mobility separations such that only ions of a given range of characteristic drift time and m/z values can be selected for MS/MS.

l. The software should be capable of data acquisitions whereby high and low collision energy data is acquired simultaneously to provide fragmentation data for all detectable molecular ions.

m. The software should provide for quantification of LCMS data providing automated peak detection, calibration and quantification. Peak detection should include methods for detection based on second derivative of acquired data.

n. Software should be designed to facilitate the visualization and manipulation of multidimensional data such as peak detection for 3D (m/z, intensity, and drift time) or 4D (m/z, intensity, drift time and retention time) datasets.

o. The software should provide the ability to generate ion mobility calibration profiles for a range of samples of known collision cross-section for use as standards when analyzing unknown samples. The software should enable the generation of theoretical collision cross section values from one or more protein databank files for comparison with experimental data.

p. Should include a processing software for the accurate mass biopharma analysis and the large molecule license required to access processing workflows and tools such as Analytical Workbench, MaxEnt, BayesSpray, Peptide Mapping, Intact Protein, Top Down or functionally similar processing.

q. Should include a processing software for accurate mass small molecule analysis and for workflows and processing tools such as Accurate Mass Screening, Pathway Profiling and Structural Elucidation Toolkit or functionally similar processing.

r. Should include a processing software for the monitoring of biopharmaceutical Product Quality Attributes (PQA) at the peptide level or functionally similar processing.

s. Should include a processing software suitable for biologics mass confirmation and purity determination of oligonucleotides, peptides, protein and conjugates or functionally similar processing.

t. The software must include a Data Interface feature allowing for automated exchange of data with a third-party system with vendor agnostic file formats.

u. A walk-up sample submission, acquisition, and data reporting software solution should be provided with a minimum of two instrument licenses. The system should allow for non-expert users to easily enter sample data, select most appropriate method for analysis, and automate the acquisition, processing, and reporting of results. This system should at a minimum provide a customized report in PDF format emailed to user that displays UV, TIC chromatograms and mass spectra for all significant peaks in chromatograms with integrations. Ideally this software would be web enabled and allow data retrieval and analysis via a web browser. The solution should allow for administrative user and data management. This solution should be compatible with the two systems outlined here and also with a Waters SQD2 single quadrupole MS system running Masslynx 4.2.

System 2: Hybrid quadrupole time-of-flight (q-TOF) mass spectrometer system.

The instrument must be benchtop in design, having a footprint no bigger than 1503 mm x 723 mm x 1067 mm (H x W x D).

The instrument should be a high-resolution mass spectrometer capable of acquiring MS and MS/MS spectra The instrument should be equipped with a high resolution, high stability quadrupole analyzer (MS1), plus pre-filters to maximize resolution and transmission while minimizing contamination. The instrument is also equipped with a high performance oaTof mass analyzer (MS2):

High-resolution MS Performance:

The TOF mass range is m/z 20 to 100,000.

Mass Resolution:

Resolution Mode: >40,000 FWHM Sensitivity Mode: >30,000 FWHM

Mass Accuracy:

1. The mass measurement accuracy of the instrument will be better than 1 ppm RMS in MS and MS/MS modes.

2. MS sensitivity (ESI+): The peak at m/z 556 from a solution of 50 pg/μL leucine enkephalin in 50/50 acetonitrile/water+ 0.1% formic acid, will have an intensity of greater than 120,000 counts per sec. The instrument will be tuned to >30,000 FWHM resolution (as demonstrated on bovine insulin) and the mass range will be set to m/z 1200.

3. MS sensitivity (ESI-): The peak at m/z 503 from a solution of 500 pg/μL raffinose in 70/30 acetonitrile/water (no additives), will have an intensity of greater than 165,000 counts per sec. The instrument will be tuned to >30,000 FWHM resolution (as demonstrated on bovine insulin), and the mass range will be set to m/z 1200.

4. MS/MS sensitivity: Using a [Glu1] -Fibrinopeptide B solution of 100 fmol/μL with the instrument tuned for >30,000 resolution (as demonstrated on bovine insulin), the intensity of the most intense y” sequence ion from the MS/MS spectrum of the doubly charged precursor ion (785.8 Da) will be greater than 7,500 counts per second.

Quadrupole analyzer:

a. The instrument should be configured with a high resolution, high stability quadrupole mass filter, for the efficient transmission of ions in the RF-only MS mode and efficient selection of precursor ions for MS/MS analysis.

b. The quadrupole should include pre-filters to maximize resolution and transmission while preventing contamination.

c. The quadrupole should be capable of unit mass resolution for precursor ion selection up to m/z 2000.

d. The quadrupole mass range is m/z 20 to 16,000 in non-resolving mode and m/z 20 to 4,000 in resolving mode.

e. System should provide for a XS Collision Cell for optimal MS/MS performance at high data acquisition rates; Software programmable collision energy control.

Ion Source:

1. Should include a combined ESI/APCI source (ESCi) must be provided as standard with the ESI source. ESI and APCI ionization should be achievable using a single probe. Voltage supplies must be alternated between the probe (ESI) and the corona pin (APCI). The facility of combined ESI/APCI must permit switching between the two ionization types during a single LCMS experiment

2. Should include APCI probe.

3. Standard APCI must operate with LockSpray ionization source to allow simplified exact mass measurement for APCI type applications.

4. System should be compatible with optional ion sources including DESI, nano flow ESI, atmospheric GC, UniSpray, and atmospheric solids analysis probe.

Vacuum system:

System supplied with a differentially pumped, automated vacuum system comprising air-cooled turbomolecular pumps and single, oil free, backing pump Vacuum read backs and system vent/pump cycles are digitally monitored and software controlled ensuring fail-safe operation in the event of power failure.

System Fluidics:

Automated, integral fluidics should be present that facilitates seamless instrument calibration, Lockmass introduction and sample introduction into the source.

UPLC and Ancillary Devices:

A UPLC system should be provided for LC/MS operation. The system shall include a solvent degasser, UPLC pump binary solvent pump with gradient production that supplies direct (non-split) flow at up to 15,000 PSI operating pressure at flow rates from 0.001 to 2.000 mL/min for high-resolution chromatographic separations, diode array UV detector, auto-sampler with Peltier temperature regulating capability to maintain samples over a range of 4 to 40°C and the ability to reliably inject 1 out of 4uL with carryover performance <0.002%, and a column switching and heating module able to maintain column temperature from ambient +5°C to 65°C with software switching flow to 2 columns of 4.6x150mm. Should include capability to sense the columns attached to system and log column usage and performance data.

Instrument control and data processing hardware and software:

1. A pc workstation with monitor display for data acquisition with all software installed should be included.

The data acquisition workstation should have the following minimum specifications:

· Processor: The Lenovo P5 workstation for Waters Connect is equipped with 12 cores.

· Operating System: The workstation runs on Windows 10 Enterprise LTSC 2021 edition (version 21H2).

· Memory: 64 GB of memory

· Hard Drives: 512 GB solid-state drive for the operating system and applications.

· Video Card: The workstation requires a discrete video card with a minimum of 4 GB memory (Direct 11 or higher compatible).

· Network Interface Cards: The workstation requires two 1-Gbps or higher network interface cards.

· Monitor: A minimum of 27-inch monitor with a minimum resolution of 1920x1080 is required.

2. The acquisition software and instrument should be capable of SONAR data acquisitions, whereby MS/MS results are collected from a data independent acquisition experiment. This is achieved by sliding the quadrupole window over a specified mass range during an MS scan

3. The acquisition software should allow for automated MS, MS/MS, SONAR and data dependant acquisitions (DDA). The instrument and software should be capable of MSE data acquisitions whereby low and elevated collision energy data are acquired simultaneously to provide fragmentation data for all detectable molecular ions. The instrument should alternate between low and elevated energy in the collision cell at user-defined intervals. In the low-energy acquisition it records the mass spectrum exhibiting mainly precursor ions, and in the elevated-energy acquisition their respective fragment ions.

4. The software must be capable of aligning MSE data according to UPLC retention time and then automatically associating the precursor ion for each sample component to its fragment ion spectrum. It must be possible to automatically interrogate the processed MSE dataset.

5. The instrument should be capable of high-resolution MRM data acquisitions, whereby a precursor ion is selected in the quadrupole, fragmented in the collision cell, and one of the resulting fragment ions is monitored in the Tof. In this mode of operation, the timing of the Tof scans should be intelligently synchronized with the ions exiting the collision cell in order to maximize the duty cycle. This should enable targeted quantitative experiments where the resulting signal-to-noise is improved when compared to full scan data.

6. The software should provide a quantitation package as standard which provides quantification of LCMS data. It should quickly process groups of samples, providing automated peak detection, calibration and quantification. APEX Peak Tracking, which determines the location of the peak and the baseline through the use of the second derivative of the acquired data. Most programs utilize the first derivative, Slope Intercept, to locate peaks and set baselines. APEX provides superior performance in samples that exhibit a wide range of concentrations.

7. Should include a processing software for accurate mass small molecule analysis and for workflows and processing tools such as Accurate Mass Screening, Pathway Profiling and Structural Elucidation Toolkit or functionally similar processing.

8. A walk-up sample submission, acquisition, and data reporting software solution should be provided with a minimum of two instrument licenses. The system should allow for non-expert users to easily enter sample data, select most appropriate method for analysis, and automate the acquisition, processing, and reporting of results. This system should at a minimum provide a customized report in PDF format emailed to user that displays UV, TIC chromatograms and mass spectra for all significant peaks in chromatograms with integrations. Ideally this software would be web enabled and allow data retrieval and analysis via a web browser. The solution should allow for administrative user and data management. This solution should be compatible with the two systems outlined here and also with a Waters SQD2 single quadrupole MS system running Masslynx 4.2.

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