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User Guide
Get Started as an LBMS User
All Laboratory for BioMolecular Structure (LBMS) microscope time is allocated based on a peer-reviewed proposal process. LBMS operates in two 6-month cycles: January – June (proposal deadline Sept 15) and July – December (proposal deadline March 15). All microscope time is requested each cycle through the web-based Proposal Allocation, Safety, and Scheduling System (PASS) system.
In this system, a proposal describes the scientific experiments to be performed and identifies the experimental team. Proposals have different durations depending upon the type of proposal submitted. For any proposal that has a duration of more than one cycle, an experiment time request (ETR) must be submitted for every cycle that a user needs microscope time. Every proposal also requires a Safety Approval Form (SAF), which is also submitted through the PASS system once microscope time is allocated.
To start, you need to know three things:
- What type of proposal fits your needs? See the description of proposal types below for more details.
- Do you need a screening microscope, high-end microscope, or both? Here are the instruments available at the LBMS.
- Do you want to perform single-particle cryo-electron microscopy (cryo-EM) or cryo-electron tomography (cryo-ET)?
Questions: Please contact the User Services Office.
1. Determine the proposal type and download your template
There are three types of proposals for microscope time at LBMS, which are described below. They all follow a common life cycle that involves the following steps: proposal submission, feasibility evaluation, peer-review, allocation of microscope time, scheduling, carrying out the work, and reporting the results. They all require the submission and approval of screening data prior to the allocation of microscope time.
General User
General User (GU) proposals are for individual principal investigators that have preliminary (screening) data and require routine access to the microscope(s). More »
GU proposals are valid for two year (four cycles). Each proposal requests a lifetime number of 8-hour shifts to complete the work for each microscope requested. For each cycle that a user requests microscope time, an experiment time request (ETR) must be submitted against the GU proposal. Proposals are peer-reviewed by the LBMS Proposal Review Panel (PRP). All GU proposals are considered active until either: (a) all microscope time allocated to the proposal for its lifetime has been used, (b) the proposal is withdrawn, or (c) two years have elapsed. All users submitting a GU proposal are encouraged to contact the LBMS staff prior to submission.
At this time, GU proposals cannot be combined for NSLS-II and LBMS; a separate GU proposal must be submitted for each facility. All GU proposals should be submitted through the web-based Proposal Allocation, Safety, and Scheduling (PASS) system.
Users may find the GU Proposal template(.docx) handy for writing the proposal and then copying/pasting the information into PASS.
Rapid Access
Rapid Access (RA) proposals are specifically for rapid access to microscope time for “hot topics” or straightforward experiments with a fast turnaround time where preliminary (screening) data are available. RA is only available for the High-End Krios Microscope. More »
RA proposals are valid for one cycle and typically request a very small amount of microscope time. These proposals are peer-reviewed and allocated by the LBMS PRP with a 2 – 3 week turnaround time prior to running the experiments. Any user submitting a RA proposal must contact the LBMS staff prior to submission to ensure that microscope time is available, and that the proposal complies with the RA criteria.
All RA proposals should be submitted through the web-based Proposal Allocation, Safety, and Scheduling (PASS) system.
Users may find the RA Proposal template (.docx) handy for writing their proposal and then copying/pasting the information into PASS.
Block Allocation Groups
Block Allocation Groups (BAGs) are a mode of microscope time access intended for groups of Principal Investigators (PIs) that want to combine their short microscope time requests into a single proposal in order to permit greater flexibility in time allocation and scheduling. More »
BAG proposals may be motivated by shared scientific interest, geographical location, affiliation, or other synergistic reasons. Combining the microscope time of individual groups permits greater flexibility in the choice of projects and samples during a given allocation period and offers the individuals in the BAGs the benefit of access to more regular allocation of microscope time. The term of a BAG proposal is two years (four cycles). New BAG proposals are rigorously reviewed by the LBMS Proposal Review Panel (PRP). If a BAG proposal scores well, this results in an initial microscope time allocation. For time requests in future cycles, BAGs will be required to submit a progress report reviewing their past work and a shift estimate for the next cycle. The reports are reviewed at the PRP meeting and an allocation for the next cycle will be considered. All users submitting a BAG proposal are required to contact the LBMS staff prior to submission.
At this time, BAG proposals cannot be combined for NSLS-II and LBMS; a separate BAG proposal must be submitted for each facility. All BAG proposals should be submitted through the web-based Proposal Allocation, Safety, and Scheduling (PASS) system.
Users may find the BAG Proposal template (.docx) handy for writing their proposal and then copying/pasting the information into PASS.
Proprietary
Proprietary research is work conducted under a Class Waiver for Proprietary Users of Energy Research Designated User Facilities. Private individuals, representatives from educational institutions, nonprofit organizations, or industry, may conduct such research. More »
Under the terms of the DOE Class Waiver, the user is obligated to pay the full-cost recovery rate for use of LBMS. In return, the user has the option to take title to any inventions made during the proprietary research program and to treat as proprietary all technical data generated during the proprietary research program. The terms and conditions under which proprietary research may be conducted at LBMS are set forth in the Proprietary User's Agreement, which must be in place before any experiment can commence. Proprietary work requires the submission of a Proprietary Proposal, which must contain a functional non-proprietary description of the work. Proprietary proposals are rapid-access proposals that are reviewed by LBMS management.
Users may find the Proprietary Proposal template (.docx) handy for writing their proposal and then copying/pasting the information into PASS.
2. Determine the microscope(s) you need for your experiment
The LBMS offers access to state-of-the-art cryo-electron microscopes and laboratory equipment for sample preparation. Currently, the facility has one high-end Krios G3i microscope ("Empire" microscope) with a cryo-sample autoloader designed for automated applications such as single particle analysis (SPA) and cryo-electron tomography (Cryo-ET) and a K3 Direct Electron Detector with a BioQuantum energy filter for increased signal-to-noise ratio of recorded images.
LBMS also has two screening microscopes – a Talos L120C ("Powell" microscope) and a Jeol 2100F ("Stonewall" microscope). For details, see the LBMS instruments and laboratory equipment pages.
3. Submit your proposal into the PASS system
All LBMS proposals and beam time requests (BTRs) must be submitted online using the Proposal Allocation Safety Scheduling (PASS) System. Access to the PASS system requires an ORCID iD, which is a requirement for all U.S. Department of Energy user facilities. If you do not have an ORCID, you can obtain one here.
