Battelle PNNL RFP 746072 Am2_Questions.pdf

Batelle PNNL RFP 746072 Amendment 2 Ques�ons/Answers/Clarifica�ons

June 26, 2023

1. Please clarify the overall throughput requirements for ASAP:

• Should the system be designed to meet throughput (phase 1 = 32 samples in 8hrs, phase II = 80 samples in 8hrs) at steady state?

o PNNL Response: Not sure what is meant by this ques�on.

• Or should it be designed to complete the en�re workflow on all samples (from beginning of sieving on first sample to comple�on of solid phase extrac�on on the last sample) in 8 hours?

o PNNL Response: Not sure what is meant by this ques�on, but the 8 hours does not include sieving. Sieving is done by hand prior to being loaded on the system. Samples can be interleaved to maximize efficiency in the smallest footprint. The idea is that samples begin being loaded at the start of the 8 hours and they can be loaded over �me either a�er prior samples have completed or they can load a�er prior samples go on to subsequent stages. Mul�ple samples could be loaded at the same �me and processed in parallel, etc. All samples should be completed by the end of the day so they can be loaded on the Mass Spec.

o If so, this will increase the amount of equipment required, resul�ng in increased cost and floor space needed.

o If so, please provide the �ming assump�ons that we should use to calculate throughput and equipment selec�on/quan��es.

Sample prepara�on �me ahead of aliquot and weigh step per soil sample

• PNNL Response: Sample Prep Time ahead of aliquo�ng: Core cu�ng, core sec�oning, sieving, tube labelling, etc. should take about an hour.

Note that these steps are manual and can be accomplished before the “8 hour workday” with regards to the throughput.

Solid phase extrac�on �me per filtered extractant sample using current manual process

• PNNL Response: SPE �me per filtered sample using current manual process: done at scale ~20 samples/ 1.5 hours (samples are run in parallel) o Please confirm that the �me associated with mass spectrometry read and data analysis are not to be considered when calcula�ng throughput.

PNNL Response: Throughput is only to produce the soil aliquots for other tes�ng and the final extracted samples in MicroSolv tubes ready to be loaded onto mass spec.

2. Please clarify soil sample introduc�on requirements:

• Are all soil samples (phase 1 = 32 samples, phase II = 80 samples) to be introduced to the process (i.e begin sieving) at the beginning of the day?

o PNNL Response: No (see below).

o If so, this will increase the amount of equipment required, resul�ng in increased costs and floor space needed.

• Or will soil samples be introduced gradually throughout the day?

o If so, please provide the soil sample introduc�on schedule/rate that we should use to calculate throughput and equipment selec�on/quan��es

PNNL Response: Sample cores will be received into the lab all at once and to be processed same day for bio�c measurements. Cores are generally processed one at a �me (approximately 1 hour processing �me) with all cores being stored at 4C un�l their turn to be processed.

3. Please clarify the sample agita�on requirements for solvent extrac�on:

• From SOW: Gently rock or rotate the tubes to mix the soil and solvent for 1 hour.

• Can you describe the ideal mo�on profiles required for this step? For example:

o At what rate does it need to be rocked? e.g 180 degrees of mo�on in 1 second.

o When rota�ng, does the sample need to be completely inverted?

o PNNL Response: Currently: sample lie on their sides on an orbital shaker. Speed is 150 rpm, throw (orbital radius) is typically 5 cm, but it varies by shaker and isn’t cri�cal.

o PNNL Response: The idea is that PNNL doesn’t want the sample to stay in a sta�c, upright posi�on and have soil pellet down to the botom. We want soil to fully contact with solvent.

o PNNL Response: The model of the typical shaker is: New Brunswick Innova 2180 Orbital Shaker o PNNL Response: Til�ng is an acceptable op�on instead of orbital shaking, and they do not need to be fully inverted. Use the guidance above to determine angle and speed.

Not vigorous, but enough to ensure good soil-solvent contact.

4. Is it acceptable or desirable to provide so�ware toolsets that empower PNNL to develop their own solu�ons, such as LIMS integra�ons, samples level tracking, and custom user interfaces, rather than deployment of a turn-key solu�on by the vendor? Some clients find benefits in being able to easily re-configure and maintain solu�ons themselves, rather than constantly requiring the involvement of a third-party vendor.

a. PNNL Response: We would like the solu�on to be ready to run, but with the access and training so that we can handle the process valida�on changes and future improvements on our own as much as possible. In other words, we don’t want a blank slate that we have to program before we can use, but we also don’t want a black box that prevents us from making changes.

5. Please confirm which data connec�ons must be encrypted? Does that apply to connec�ons within the private network?

a. PNNL Response: Our assump�on is that the system and all so�ware live in our private network, so nothing needs to be encrypted. If so�ware needs to be hosted outside of PNNL, we would need to look into what security steps are required.

6. The endpoint for this automated assay appears to be FTICR mass spectrometry. Should the mass spectrometry device and associated results be managed by the ASAP system? Or is that considered out of scope for this project? Although physical integra�on of mass spectrometry devices is typically difficult, we have so�ware solu�ons that might enable to so�ware integra�on.

a. PNNL Response: Scope is limited to producing microsolv vials ready to be loaded by hand onto the mass spec. No need to integrate hardware-wise or so�ware-wise at this �me.

7. When performing solid-phase extrac�on, there are a few different ways to move the mobile phase through the solid phase. Some examples are nega�ve pressure (vacuum), posi�ve pressure, and centrifuga�on. Do you have a preferred technique? Or are you open to recommenda�ons on techniques that facilitate automa�on? Please note that these would be recommenda�ons, not guarantees.

a. PNNL Response: PNNL doesn’t have a preference and are open recommenda�ons as to whichever is most automa�on friendly.

8. Can you please confirm that there is no requirement for automated storage below +4degC?

a. PNNL Response: Confirmed.

9. Does an unguarded, collabora�ve robot meet ASAP safety requirements? Collabora�ve robots meet industry standards for safety without guarding and largely improve user experience when interac�ng with work cells. Or do all work cells need to be fully enclosed to prevent operators from hazards regardless of this?

a. PNNL Response: “Collabora�ve robo�cs are acceptable for use provided they have warning s�ckers to iden�fy pinch points and are listed by an OSHA approved NRTL.

Electrical equipment that is not listed by an OSHA approved NRTL (Na�onally Recognized Tes�ng Laboratory - e.g. UL, CSA, TUV) must be inspected by an approved third party evaluator either prior to arrival or upon receipt, prior to use.

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