An Assessment of the Material Measurement Laboratory at the National Institute of Standards and Technology: Fiscal Year 2023 (2023)
Chapter: 5 Biomolecular Measurement Division
5
Biomolecular Measurement Division
The Biomolecular Measurement Division provides measurement science, technologies, and standards for the evaluation of biomolecules, including proteins, oligonucleotides, carbohydrates, lipids, metabolites, and complexes including such molecules. Key stakeholders include the pharmaceutical community, makers of analytical instruments, and clinical and forensics laboratories. The core competencies are built around methods for biomolecular measurements including mass spectrometry, mass spectrometry data analysis and library development, separations, biophysical methods, capillary electrophoresis, polymerase chain reaction techniques, genome sequencing, and production and validation of standard research materials and research-grade material standards.
The key focus areas of programmatic activity in the Biomolecular Measurement Division include mass spectrometry to support other projects and Reference Library expansion, forensics (genetics and drugs of abuse), clinical analyses (protein and nucleic acid markers), and biotherapeutics (biomanufacturing and engineering biology). The 77 federal employees and 25 associates in the Biomolecular Measurement Division are divided into five groups: the Mass Spectrometry Data Center, the Biomolecular Structure and Function Group, the Bioanalytical Science Group, the Applied Genetics Group, and the Bioprocess Monitoring Group. These groups seem to interact seamlessly within and externally to division to achieve the goals of each program area. For this reason, the following discussion is organized by program area and not research group.
Between April 2020 and March 2023, the Biomolecular Measurement Division published 135 papers, 4 workshop reports, 22 data sets, and 3 databases of standardized analytical measurements. Four patent applications have been issued, and most of these are licensed. They produced 20 standard reference materials and reference materials, 3 standard reference data sets, and 2 research-grade test materials. The division staff serve on 25 standard committees and 19 working groups—12 of these in leadership positions. The balance of activities includes basic science related to technology development (e.g., dyes for protein sequencing, sub-zero chromatography for hydrogen/deuterium exchange-mass spectrometry, and artificial intelligence for tandem mass spectrometry peptide identification), customer-driven projects, and mission-oriented product development.
The breadth and depth of the projects is impressive. The following analyses are not exhaustive, but endeavor to distill the observations from 2 days of tours, the read-ahead materials provided to the panel, and the members’ expertise and experience to recognize excellence, offer suggestions for possibilities to increase staff productivity, and provide pertinent examples.
ASSESSMENT OF TECHNICAL PROGRAMS
The technical programs are focused on developing processes and information relevant to the National Institute of Standards and Technology (NIST) mission. There are only a few examples of research that could be considered as basic, and that work seemed to be very targeted toward solving specific problems in the program areas through technology improvements. While this type of work is useful, seed projects involving research potentially relevant for meeting more long-term mission needs would be important for the Material Measurement Laboratory (MML) to pursue, if not already in progress. None were presented to us.
The work under way in response to stakeholder needs and in support of the NIST mission focus areas was quite impressive. The research addressed both the fundamental challenges in measurements relevant for major areas important to our society—with impact both nationally and globally, building consortia with customers, and providing high quality measurement processes and standards. Below are short comments about each of these areas.
Mass Spectrometry
The technical approach that the Biomolecular Measurement Division is taking to develop mass spectrometry libraries is world class. They are selecting molecules to be added to the libraries through a process based on the potential of the data to help address important societal problems. The selection of compounds to be analyzed is based on an algorithm the group developed, taking into account commercial availability, cost of the compound, and the national need for the information (e.g., chemicals in plastics, designer drugs, or food allergens). The compounds they purchase must be more than 90 percent pure prior to initiating the careful mass spectrometry required for addition of a new molecule to the library. The compounds and fragmentation profiles are then vetted, and peaks are assigned by scientists. The objectives of the group are clear, and productivity is exemplary in this program area, as illustrated by the addition of more than 40,000 compounds to the existing mass spectrometry spectral libraries, even through the COVID-19 pandemic. The staff engaged in this program area are efficient and highly productive.
The new Biomolecular Measurement Division hair peptide analysis technique was developed as part of MML’s forensics initiative and is designed to identify specific individuals; it is also scientifically impressive. The group exploited the mutations of specific hair proteins, one being keratin, and demonstrated the discrimination between individuals in terms of subtle variations in proteins. This capability is unique in that a hair strand is one sample and cannot be contaminated by DNA from other individuals (unlike many samples used for DNA analysis). This technique is quite robust and may even differentiate between hairs from identical twins. The results are outstanding, and the staff is encouraged to further validate and bolster their findings for this potential paradigm shift in forensic analysis using mass spectrometry.
The mass spectrometry project to support the circular economy mission through plastic recycling made impressive use of liquid chromatography mass spectrometry. The staff in the mass spectrometry program area are building a library of spectra of plastic components by extracting polymeric subunits and additives out of the plastic for careful analysis. This program area may benefit from the integration of other analytical techniques (e.g., Raman spectroscopy), simultaneously building a library with spectra from both methods. This would allow for simple spectroscopy methods, such as Raman spectroscopy, to be employed in the field while coupling the field methods to the more precise liquid chromatography-mass spectrometry data acquired in a center of excellence.
The development of the NIST Urine Albumin Standard Reference Material 2925 now provides for global standardization of this critical marker in the urine. Presently, clinical laboratories—with Food and Drug Administration–approved diagnostic methods—can differ from one another by more than 40 percent in concentration measurements. This variability is significant as there are clinical guidelines that supply urine albumin cutoff values for the diagnosis of chronic kidney disease. MML will partner with external laboratories to develop reference measurement procedures using the albumin standard reference material for calibration. This global standardization of urine albumin measurements will enable consistent chronic kidney disease diagnosis across the world. Once the standardization system is in place, the staff in this program area are prepared to disseminate the information through publications and promotions to the health care community. This program area is partnered with the International Federation of Clinical Chemistry, the National Institute of Diabetes and Digestive and Kidney Diseases, and the Joint Committee for Traceability in Laboratory Medicine to achieve this mission. The Biomolecular
Measurement Division is addressing an important problem with this albumin standard and its continued collaborations with external partners.
Forensics
The Applied Genetics Group is a recognized leader in the forensic community. Their research on the statistical interpretation of DNA mixtures, use and validation of DNA sequence-based genetic loci, and introduction of novel peptide variant markers (discussed in the previous section) is high-quality and will be used to support forensic stakeholders such as law enforcement laboratories and the U.S. legal system. The applied genetics technical programs focus on meeting national goals by supporting current legacy technologies as well as providing standard reference materials and validating processes to be used with newly emerging technologies such as the next generation sequencing of forensically relevant genetic loci. They currently use next generation sequencing to analyze specific areas of the genome associated with ancestry, kinship, visible phenotypes, and personal identification. Additionally, forensic scientists have used whole-genome technologies to lay the foundation for forensic investigative genetic genealogy, which generates leads for unsolved violent crimes or the identification of missing persons. The laboratories are well equipped with the requisite instrumentation typically used in conventional forensic laboratories; Access to whole-genome sequencing equipment, which is finding significant utility in state-of-the-art laboratories, is only available through an external source. This is adequate for now, but plans for obtaining newer generation, lower cost equipment need to be considered as such equipment becomes more commercially available and used more broadly.
The standard reference materials produced by the Applied Genetics Group are used routinely by forensic laboratories for the quantitative and qualitative measurement of genetic markers. This group is revising their standard reference materials based on stakeholder needs as more genetic markers are being developed for forensics. This is demonstrated by the 2023 revision and implementation of Standard Reference Material 2391d, a polymerase chain reaction-based DNA Profiling Standard, by adding more than 11,000 additional genetic markers to it. Furthermore, they are in the process of developing a research reference material that will be used for interlaboratory studies relevant to the analysis of samples including mixtures of DNA from multiple individuals.
Clinical Analyses Using Protein and Nucleic Acid Markers
The research and development efforts in this area have focused on exhaustive development of methods for analyzing IgG and RNA. The RNA efforts produced usable standard materials for SARS-CoV-2 and Mpox in amazingly short time frames, demonstrating the skill and responsiveness of the staff to meet critical national and international needs. The methods used to analyze these molecules are widely applicable to other important proteins and nucleic acids. There is also some excellent underlying research that is important for analyzing particulates used in plastics recycling and therapeutics that will be relevant for both the circular economy project and biotherapeutic product manufacturing.
Biotherapeutics, Biomanufacturing, and Engineering Biology
The focus in this program area leveraged the availability of the NIST monoclonal antibody (NIST mAb) and the NIST Chinese Hamster Ovaries cell line that produces the monoclonal antibody to validate protein manufacturing processes and products. These are great tools, and both are and will continue to be important standards. Furthermore, the group developing these standards appreciates their value for education. For example, the NIST Chinese Hamster Ovaries cells can be put through bench-scale fermentation procedures to produce antibodies in teaching laboratories with minimal facilities development—a very powerful tool for workforce development, especially when coupled with metrics for the processes and their products. The research staff is interested in developing new tools for
biomanufacturing and bioprocess monitoring but does not possess much expertise outside of their current analytical methods, most of which are too expensive or impractical for implementation in a large-scale biomanufacturing operation. Thus, the staff’s focus on providing information from high-resolution systems that can validate lower resolution data in processing operations makes sense.
The staff in this program area has developed simulations for overall biotherapeutic product stability and manufacturing quality control. This cutting-edge approach was achieved by combining nuclear magnetic resonance, electron paramagnetic resonance spectroscopy, small-angle X-ray scattering, small-angle neutron scattering, and hydrogen/deuterium exchange mass spectrometry techniques to validate the simulations. These approaches are on the forefront of biomanufacturing technologies and definitely position the team to lead these efforts in the field.
ASSESSMENT OF SCIENTIFIC EXPERTISE
The Biomolecular Measurement Division has a deep pool of knowledgeable scientific staff. This pool includes chemists, physicists, data and computer scientists, life and biological scientists, and forensic scientists. This matrixed expertise has produced world-class results and assisted the United States in staying at the forefront of biomolecular measurements. The expertise at NIST supports the technical programs well, meeting deadlines and achieving the overall goals for the organization and its stakeholders.
Mass Spectrometry
In terms of mass spectrometry, based on the presentations the panel received, tours, and interactions with the staff, MML definitely has a group that is world-class. The mixture of mass spectrometrists and data and computer scientists is particularly strong. The mass spectroscopy reference library is supplied, along with periodic updates that include expanded analyses, with spectrometers sold by most major suppliers and are critical to analytical laboratories worldwide. Thus, this product makes a major contribution to NIST’s international reputation. In addition, the mass spectrometry group develops new methods for analytics that pushes the capabilities for molecular analysis at the cutting edge.
Forensics
The Biomolecular Measurement Division has a portfolio of scientists that are considered leaders in the global forensic genetics community and are well recognized in the field through their publications, presentations, and workshops. The applied genetics scientists support the organization’s mission by providing best methods to interpret data through focused research on rapid DNA analysis, mixture interpretation, development of novel genetic markers, validation studies of new instrumentation and forensic genetic test kits, and coordination of interlaboratory studies associated with measurement of genetic data. The scientists support the division’s mission by improving the legacy standard reference materials to include new genetic loci and systems. An area that could potentially use more expertise is the application of genomic techniques, particularly in the area of forensic investigative genetic genealogy, as this technology becomes increasingly accessible and moves into forensics laboratories. This expertise could be gained through collaboration with other NIST divisions supporting human genome science, especially the Biosystems and Biomaterials Division.
Clinical Analyses Using Protein and Nucleic Acid Markers
The research staff have the expertise to use a wide variety of analytical methods to evaluate protein and nucleic acid biomarkers. The choice of problems on which the staff focus is largely driven by
their responsiveness to big companies or industry-government consortia, demonstrating that the staff are very responsive to national needs in biomanufacturing. The two standard methods for assessing albumin in urine (mentioned above) were developed in response to stakeholder requests. The same is true for the standards under development for diagnosing food allergens (a growing area). The development of standards for RNA identification from viruses of immediate concern (e.g., SARS-CoV-2 and Mpox) showed how fast and how well the staff can produce vital results, giving high credibility to their expertise. The exploration of methods for analyzing extracellular vesicles and nanoparticles is a developing area that will be extremely important in the future as these types of therapeutics are expanding rapidly. MML will be at the forefront of defining acceptable product metrics for use in vaccines, drug delivery, and regenerative medicine. The staff have the expertise and drive to conduct important applied research and early-stage development in this area, especially in separations as well as analytics.
Biotherapeutics, Biomanufacturing, and Engineering Biology
This team seems to be relatively new. They are just building their expertise base and could use more staff (as well as redeveloping the facilities in space available to the Biomolecular Measurement Division in the Institute for Bioscience and Biotechnology Research [IBBR]). Biotherapeutics is an important area for the U.S. economy, and the need for standard analytical methods during processing as well as for product validation is critical, especially analytics for use in-line during biomanufacturing processes. NIST is relying on its customers and the National Institute for Innovation in Manufacturing Biopharmaceuticals collaborators for technical expertise, which is good, but NIST needs to strengthen its in-house expertise to make a long-term impact in biomanufacturing.
BUDGET, FACILITIES, EQUIPMENT, AND HUMAN RESOURCES
In fiscal year 2023 the budget of the Biomolecular Measurement Division was $36 million—61 percent of this comes from appropriations; 32 percent from providing standard reference materials and data and a working capital fund; and 7 percent from reimbursable work for other federal agencies.
All of the groups in the Biomolecular Measurement Division are generating tremendous amounts of data. They need more expert staff support in laboratory information management systems development and data management. While the mass spectrometry group includes these experts, as well as bioinformatics experts, the level of computational support was highly variable across the mission areas. The groups that rely on centralized support from information technology and data management experts received inconsistent support. More personnel to support the other groups would leverage their existing expertise and increase productivity.
The staff is very dedicated to their missions and invested in disseminating the products of their labors. The young federal staff members are especially enthusiastic about the opportunities they have for expanding their research endeavors and developing leadership skills. The postdocs enjoy what they are doing, and in many cases really appreciate the independence they have to focus on projects of their choosing, but some of them feel very isolated and uncertain about what future directions they could pursue after time at NIST. Mentoring of postdocs seems to be uneven, and postdocs in particular could benefit from a mentoring program that includes information about what constitutes short-term success in MML and long-term career development opportunities.
The support from the human resources office, especially in terms of replacing lost staff, could be significantly improved. Hiring new administrative staff is inordinately slow, taking up to 6 months just to release standard advertisements. Even when the jobs are posted and interviews conducted, instances were reported when the group has agreed to hire someone and the notification letter never went out from human resources to the prospective employee. Bringing postdocs on board can take months after they accept the offer and complete their PhD, during which time some of the new postdocs have no income. The procedure for hiring federal scientists and engineers was not clear. The availability of positions
related to MML programs and mission-focused areas seems to have been put on the back burner as human resources work priorities focus on hiring to support new work deriving from the CHIPS and Science Act of 2022. These problems will impact group productivity and need to be fixed.
Conclusion 5-1: The current staff is scientifically outstanding, but maintaining a critical mass of scientists and engineers with critical expertise is challenging. More timely support from the human resources department would make the projects more competitive and ease the frustrations of existing staff whose research progress is hampered by vacancies in administrative support, hiring of postdoctoral fellows, or staffing of existing mission areas. Postdocs could benefit from increased mentorship in terms of networking and career development.
Recommendation 5-1: The Biomolecular Measurement Division should work with the Material Measurement Laboratory (MML) leadership and the National Institute of Standards and Technology’s headquarters human resources personnel to develop effective procedures for the hiring and career development of staff. Internally, MML should improve their mentorship of postdoctoral fellows to address career development planning.
In terms of facilities, Building 227 is old and outdated, but still functional. The air handling and plumbing systems are a particular problem. Building 221 appears to be an ongoing disaster and a calamity waiting to happen. Too much high-tech equipment is crowded into a space that is under-resourced in terms of air handling, electrical supply, and safety infrastructure. Facility upkeep by NIST maintenance workers appears to be an issue, especially with inadequate heating, ventilation, and air conditioning systems. The mass spectrometry equipment is considered state of the art and adequate for the projects being undertaken and to complete all of the tasks for stakeholders. However, temperature fluctuations already threaten the quality of the mass spectrometry data, which is critical for a key NIST product, the Mass Spectrometry Data Library. These mass spectrometry instruments are very sensitive to temperature changes; if the room temperature varies too much—e.g., between 68 to 85 degrees Fahrenheit—the mass spectrometers may produce erroneous results as the spectral peaks will be shifted. This can limit productivity for the group and will be an ever-present issue until remedied. The infrastructure problems in Building 221 have reached a critical stage; building 227 also needs upgraded heating, ventilation, and air conditioning systems. Funding for these types of major renovations needs to come from appropriated funds as the level of funding from overhead income is far from sufficient.
In contrast, space at IBBR is high quality. Moving the entire division to IBBR would solve its space problem, provide space in Building 227 for other NIST researchers (as well as present an opportunity for renovation), and encourage increased interactions with researchers from universities across Maryland who also work in IBBR. The space is currently available at IBBR and some funding to begin appropriate renovation in preparation for them to move in has already been identified.
Conclusion 5-2: Existing facilities do not support continued work at the world-class level. Facilities staff are fighting a losing battle trying to keep existing systems—especially the heating, ventilation, air conditioning, plumbing, and building integrity—operational. The research staff lose valuable time making ad hoc workarounds to facility shortcomings and are, at times, unable to operate and maintain high-tech equipment owing to maintenance issues. Facilities renovation is too expensive to be covered by internal Material Measurement Laboratory funding.
Recommendation 5-2: The Biomolecular Measurement Division (BMD) should work with Material Measurement Laboratory leadership and the National Institute of Standards and Technology to identify, as soon as possible, laboratory facilities with the level of temperature and humidity control, and space required by BMD to perform its work safely and at a world-class level. A move of BMD to the Institute for Bioscience and Biotechnology Research could be part of this solution.
While much of the equipment is aging, most of it is working well. There is some need for new instruments to integrate new capabilities into the analytical capabilities, for example, next-generation gene and protein sequencing systems. A definite need exists for more automation of contiguous separations and analytics to increase sample throughput. Dedicated funds for both equipment and expertise in laboratory robotics would benefit multiple operations and improve the efficiency of long-term data output.
Conclusion 5-3: Much of the work in the Biomolecular Measurement Division is repetitive and highly amenable to automation. With the introduction of appropriate robotic systems and expertise, the existing staff could be even more productive. Automation is used throughout the stakeholders’ labs. Increased automation within the division would also enable the Material Measurement Laboratory to provide guidance on automated processes to its stakeholders.
Recommendation 5-3: The Biomolecular Measurement Division should increase laboratory automation to support critical steps in production of standard products and processes.
EFFECTIVENESS OF DISSEMINATION EFFORTS
The Biomolecular Measurement Division disseminates its results in multiple ways: research publications, conference presentations, round-robin trials with customers, workshops, staff participation in standards groups, and the production of standard products—both the well-characterized standard reference materials for which NIST is well known and now research-grade standards. The inclusion of the mass spectrometry libraries with commercial mass spectrometers, as well as triannual updates, is very broadly valued across academia and industry. The active participation of the Applied Genetics Group staff in the forensic standards-setting organizations—Scientific Working Group on DNA Analysis Methods and the Organization of Scientific Area Committees for Forensic Science—as well as the dissemination of peer-reviewed publications is vital to forensic stakeholders as they present scientific evidence to the courts. The extent to which NIST documentation is viewed as a source of unbiased validation of current and emerging instrumentation, protocols, and data interpretation algorithms by the U.S. legal process is noteworthy.
Across all four of its focus areas, the Biomolecular Measurement Division has strong interactions with users and manufacturers. This two-way interchange disseminates the value and results of NIST’s work and has produced a good understanding of the value chain for potential standards products. Even junior staff are encouraged to take on leadership responsibilities in working with consortia of stakeholders and do so very effectively. There is a limit to how extensive such operations can be, since there are limits on staff and funding, but the choices of where to focus the division’s energies and resources are thoughtful and effective in terms of the opportunities for the Biomolecular Measurement Division to have a real impact for its customers. As the United States puts more resources into biomanufacturing, this would be a logical area for expansion.
The involvement of the Biomolecular Measurement Division with commercial partners is consistent with MML’s mission to support the national economy with measurement science and technologies. The delivery of standards is one good metric of the division’s impact on the commercial sector and clinical practice (as described above for proteins, genes, and viruses), but the division is doing much more. There are two areas of additional Biomolecular Measurement Division activity that merit increased support: the dissemination of products to the educational sector involved in workforce development (activities in this area have begun largely through participation in the National Institute for Innovation in Manufacturing Biopharmaceuticals and educational partnerships at IBBR) and providing information to researchers on the potential advantages of using NIST standards across research endeavors
(e.g., the use of the albumin standard reference materials as calibration material for proteomic researchers using mass spectrometry).
Conclusion 5-4: The current dissemination of research and development and standards to traditional stakeholders is very effective. Products recently developed for biomanufacturing and forensics can be extremely impactful in multiple communities, including some that are less aware of these standards and processes. The dissemination of standard reference materials made by the Biomolecular Measurement Division and the documentation of processes for dissemination to both the education community that is critical for workforce development and the forensics legal community could be highly impactful.
Recommendation 5-4: The Biomolecular Measurement Division (BMD) should increase engagement with communities focused on workforce development and forensics analysis, and compile data on how often their resource materials are used. For biomanufacturing workforce development activities, instructional information related to using BMD standards and standard processes could be provided to educational and professional groups providing training for biomanufacturing. Dissemination of information about how often BMD’s published validation studies, research findings, and standard reference materials are used by the stakeholders in forensic activities could increase the appreciation of the value they provide to the legal community.
