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Issues for bringing digital libraries into public use

In much the same way that the field of artificial intelligence produced a cult which fervently believed that computers would soon think like human beings, the existence of electronic books has resurrected the paperless society as a utopian vision to some, an apocalyptic horror to others. In this essay we have attempted to provide realistic notions of what digital libraries are likely to become if they are a popular success. E-books are capable of subsuming most of the media we use today and have the potential for added functionality by being interactive. The environmental impact of having millions more computers will be offset to some degree, perhaps even exceeded, by the fact that televisions, stereos, VCR's, CD players, newspapers, magazines, and books will become part of the computer system or be made redundant. On the whole, large-scale use of digital libraries is likely to be a winning proposition. Whether or not this comes to pass depends on the directions taken by today's researchers and software developers. By involving the public, the effort being put into digital libraries can be leveraged into something which is big enough to make a real change for the better. If digital libraries remain the exclusive property of government, universities, and large research firms, then large parts of the world will remain without digital libraries for years to come, just as they have remained without digital phone service for far too long. If software companies try to scuttle the project by patenting crucial algorithms and using proprietary data formats, all of us will suffer. Let us reverse the errors of the past and create a truly open digital library system.

Flater, David W.↗

The virtual library: Coming of age

With the high speed networking capabilities, multiple media options, and massive amounts of information that exist in electronic format today, the concept of a 'virtual' library or 'library without walls' is becoming viable. In virtual library environment, the information processed goes beyond the traditional definition of documents to include the results of scientific and technical research and development (reports, software, data) recorded in any format or media: electronic, audio, video, or scanned images. Network access to information must include tools to help locate information sources and navigate the networks to connect to the sources, as well as methods to extract the relevant information. Graphical User Interfaces (GUI's) that are intuitive and navigational tools such as Intelligent Gateway Processors (IGP) will provide users with seamless and transparent use of high speed networks to access, organize, and manage information. Traditional libraries will become points of electronic access to information on multiple medias. The emphasis will be towards unique collections of information at each library rather than entire collections at every library. It is no longer a question of whether there is enough information available; it is more a question of how to manage the vast volumes of information. The future equation will involve being able to organize knowledge, manage information, and provide access at the point of origin.

Hunter, Judy F.↗

A Robust and Scalable Software Library for Parallel Adaptive Refinement on Unstructured Meshes

The design and implementation of Pyramid, a software library for performing parallel adaptive mesh refinement (PAMR) on unstructured meshes, is described. This software library can be easily used in a variety of unstructured parallel computational applications, including parallel finite element, parallel finite volume, and parallel visualization applications using triangular or tetrahedral meshes. The library contains a suite of well-designed and efficiently implemented modules that perform operations in a typical PAMR process. Among these are mesh quality control during successive parallel adaptive refinement (typically guided by a local-error estimator), parallel load-balancing, and parallel mesh partitioning using the ParMeTiS partitioner. The Pyramid library is implemented in Fortran 90 with an interface to the Message-Passing Interface (MPI) library, supporting code efficiency, modularity, and portability. An EM waveguide filter application, adaptively refined using the Pyramid library, is illustrated.

Lou, John Z.↗

Three-Dimensional Audio Client Library

The Three-Dimensional Audio Client Library (3DAudio library) is a group of software routines written to facilitate development of both stand-alone (audio only) and immersive virtual-reality application programs that utilize three-dimensional audio displays. The library is intended to enable the development of three-dimensional audio client application programs by use of a code base common to multiple audio server computers. The 3DAudio library calls vendor-specific audio client libraries and currently supports the AuSIM Gold-Server and Lake Huron audio servers. 3DAudio library routines contain common functions for (1) initiation and termination of a client/audio server session, (2) configuration-file input, (3) positioning functions, (4) coordinate transformations, (5) audio transport functions, (6) rendering functions, (7) debugging functions, and (8) event-list-sequencing functions. The 3DAudio software is written in the C++ programming language and currently operates under the Linux, IRIX, and Windows operating systems.

Rizzi, Stephen A.↗

Comparing Thick Target Neutron Yield Calculations for Alphas on F-19 using MCNP6 1.1 Beta with TENDL 2012 Libraries

Because of the heritage of MCNPX, the first production release of MCNP6{sup TM} used physics models, instead of ACE (A Compact Evaluated Nuclear Data File) formatted libraries, for simulating the transport of alpha particles at all energies, as MCNPX could not yet read ACE formatted light ion libraries. For non-Coulombic interactions, the physics models have suggested minimums of ∼ 20-200 MeV. The first production release of MCNP6, MCNP6{sup TM} 1.0, was still capable of transporting alphas to low energies; however, the physics models resulted in poor prediction of inelastic reactions at energies below the suggested minimums. This poorer prediction at low energies resulted in orders of magnitude lower neutron yields for events resulting from light ion interactions at low energies. For example, F-19(α,n)Na-22 from U-234 decay in UF{sub 6} produced poor neutron production results. Modeling these types of interactions correctly is vital for signal analysis for nonproliferation safeguards and nuclear security as well as for correctly characterizing source terms for radiation protection and shielding calculations. The TALYS computer code was developed to simulate nuclear reactions involving neutrons, photons, protons, deuterons, tritons, alphas and He-3 particles, in the 1 keV - 200 MeV energy range. TENDL is a nuclear data library, which provides the output of the TALYS nuclear model code system for direct use in applications (i.e. ACE formatted cross sections). Since 2008, TENDL had publicly provided ACE formatted libraries for alpha transport; however, not until the release of MCNP6{sup TM} 1.1 beta, had MCNP6 publicly possessed the capability to read such libraries. At the Radiation Protection and Shielding Division topical meeting in 2014, initial testing of MCNP6 1.1 beta showed that MCNP6 using TENDL 2012 resulted in poor prediction when compared to the compilation of experiment data provided in R. Heaton et al. Further comparisons for PuBe sources, using the MCNP6 1.1 beta spontaneous decay alpha feature coupled with alpha transport, were also given in the winter American Nuclear Society meeting in 2014, where the results showed large discrepancies with measured data. For F-19(α,n)Na-22 interactions, the R. Heaton et al. paper is a conglomeration of several important references; and the data provided by R. Heaton et al. used a numerical fit of the excitation function provided by Norman et al.. Norman et al. has recently published their (α,n) thick target yield data for PbF{sub 2} in tabular form, backing out the thick target yields of F-19(α,n)Na-22 and computing F{sub 2} and UF{sub 6} thick target neutron yields (as supplements to the PbF{sub 2} data). Here we compared measured thick target yields of E. B. Norman et al. to MCNP6 1.1 beta using TENDL 2012 libraries. Deterministically backing out the thick target yield from measured values involves using the stopping power. MCNP uses either the SPAR code or an interpolation of the Spar code and Bethe-Boch formula for computing stopping powers. As a result one may believe that these separate methods will arrive at separate thick target yields independent of the production cross section. In our MCNP calculations, we simulated the alpha until the alpha completely stopped in the medium. The energy loss in the condensed history algorithm is not continuous but discrete and related to the stopping powers. Because the neutron production yield is energy dependent, the energy loss dictates the emission of secondary neutrons; and therefore the difference in stopping powers used may have some slight effect on the yield difference. For this study, we chose to use the default condensed history algorithm setup, while future studies should address tightening steps in the condensed history algorithm to prove whether or not choice of stopping power actually matters. The fact that all 5 evaluated isotopic compositions resulted in different thick target yield percent differences does warrant this type of investigation. A typical user may not be only interested in integral emission, taking 10 s to 100 s of processor hours to simulate, but rather a timely generation of the spectra. Such an application would require biasing the production of secondaries from alpha sources such that millions of secondaries could be produced, emulating a converged energy dependent spectra. Neutron production biasing from alpha sources does not currently exist; however, developing a biasing algorithm for neutron production from alpha sources should be investigated in the future.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Comparing Measured (a,n) Thick Target Yields to MCNP6 using TENDL 2012 Libraries - Paper 31

MCNP6, due to the heritage of MCNPX, has always possessed the capability to transport the light ions, such as alpha particles. Two types of competing physics take place during the particle transport: atomic and nuclear physics. Charged particles lose energy to media due to Coulombic interactions. MCNP6 models Coulombic interactions through the use of the continuous slowing down approximation. Stopping powers are calculated at a variety of energies using the Bethe-Bloch formula with Sternheimer and Peierls density effect correction. For energies less than 1.31 MeV/AMU, a low-energy SPAR model is used. When the energy of the particle is high enough, there is a transition from nuclear interactions to nucleon interactions. MCNP6 possess various physics models to account for these types of intra-nuclear cascades. These models are less accurate at low energies. Even though MCNP6 will transport these light ions to low energies (i.e. less than 20 MeV), most of the available model physics in MCNP6, for nuclear interactions, has a suggested minimum energy of ∼20-200 MeV. The result of the poorer prediction at low energies causes important light ion events, such as F-19(a,n)Na-22 from U-234 decay in UF{sub 6}, to produce orders of magnitude fewer neutrons in MCNP6 than should be emitted. As with neutrons, ACE (A Compact ENDF) formatted light ion libraries have been developed from several different evaluations. These libraries possess better physics at low energies where the physics models break down. The TENDL 2012 evaluations possess alpha transport libraries, in ACE format, such that they can easily be used with codes like MCNP6 that read ACE formatted cross sections. As a result, a capability was developed for MCNP6 to read and implement these library cross sections when the light ion reached energies below the library upper energy cutoff. Perfectly modelling an experiment for benchmark comparisons to a code calculation can be tricky. For complex setups, systematic error is always possible; and usually a hefty uncertainty analysis is required to quantify just the geometry setup and material combination choices. For an (a,n) interaction, a thick target yield is defined as the amount of neutrons emitted given that the alpha ranges out in the material. For alpha transport at low energy <10 MeV, in reasonably dense materials (>1-2 g/cc), with a material dimension length larger than a few hundred microns, alpha particles will tend to completely stop and range out in the material. For Li, Be, B, C, N, O, F, Na, Mg and Al thick target yields exist in 200 keV intervals from 1 to 9.8 MeV (most of the elements do have (a,n) thresholds above 1 MeV). Because modelling a thick target yield in MCNP6 is much easier than attempting to account for the complexity of systematic error from a full out experiment, we present here comparisons of (a,n) thick target yields to those calculated in MCNP6 using the TENDL 2012 alpha library evaluations.

61 RADIATION PROTECTION AND DOSIMETRY↗

Testing nuclear data libraries with burnup for reactor applications

Recently US and European nuclear data libraries have been released, namely ENDF/B-VIII.0 and JEFF-3.3 libraries, which are the result of years of evaluation and validation work in both communities. Consequently, efforts have been made to validate the evaluations in calculations of integral experiments (critical benchmarks, ..etc). Nevertheless, less stringent testing and validation efforts were performed on burnup applications before releasing the libraries. The presented work focusses on the testing of these recent nuclear data libraries for burnup calculations on two benchmarks at the pin and at the assembly level. Monte-Carlo depletion calculations were performed using the VESTA 2.2 code. The K{sub ∞} results between nuclear data libraries are compared. A strong k{sub ∞} bias is observed with burnup using both JEFF-3.3 and JEFF-4T0 compared to all other libraries, and especially ENDF/B-VIII.0, consisting in a strong k{sub ∞} over-estimation at low burnup and a high under-estimation at high burnup. JEFF-3.3 {sup 235}U and {sup 239}Pu evaluations mainly explain this result, as well as fission yields. New {sup 235}U and {sup 239}Pu evaluations were proposed for JEFF-4T0, but they do not address totally the bias issue, even if JEFF-4T0 {sup 239}Pu allows slightly reducing the k{sub ∞} underestimation at high burnup.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Development of the multigroup cross section library for the CASL neutronics simulator MPACT: Verification

The MPACT neutronics module of the Consortium for Advanced Simulation of Light Water Reactors (CASL) core simulator is a 3D whole core transport code being developed for the CASL toolset, known as the Virtual Environment for Reactor Analysis (VERA). Key characteristics of the MPACT code include a subgroup method for resonance self-shielding and a whole-core transport solver with a 2D/1D synthesis method. Depletion capability is supported by coupling SCALE-ORIGEN with MPACT. A new ENDF/B-VII.1 MPACT 51-group library has been developed by using the AMPX/SCALE and CASL-XSTools code packages based on the procedure introduced in the companion paper, “Development of the Multigroup Cross Section Library for the CASL Neutronics Simulator MPACT: Method and Procedure.” The cross section library generation procedure, cross section library, and MPACT transport capability have been verified by performing various benchmark calculations and comparing the benchmark results to the continuous-energy (CE) Monte Carlo results. Furthermore, the code-to-code comparison for the benchmarks shows that the CASL neutronics simulator MPACT and its 51-group library are working reasonably.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

SCALE/AMPX multigroup libraries for sodium-cooled fast reactor systems

New multigroup cross section libraries and associated covariance files that are optimized for the analysis of sodium-cooled fast reactors were generated with the AMPX tools distributed with the SCALE code system. These new libraries account for the fast neutron flux spectrum with sufficient resolution of resonances in the higher energy range to reproduce continuous-energy reference results and to provide the basis for sensitivity and uncertainty analyses of fast spectrum systems with the SCALE code system. The performance of the new libraries was investigated in terms of the eigenvalue, the neutron flux and reaction rates in criticality calculations, and the generation of group constants. A library using 302 energy groups and a fast neutron flux spectrum as the weighting function led to very good agreement with reference continuous-energy results. As a result, the performance of the new library was demonstrated in calculations of experiments from the International Criticality Safety Benchmark Evaluation Project handbook.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

ENDF/B-VIII.1: Updated Nuclear Reaction Data Library for Science and Applications

The ENDF/B-VIII.1 library is the newest recommended evaluated nuclear data file by the Cross Section Evaluation Working Group (CSEWG) for use in nuclear science and technology applications, and incorporates advances made in the six years since the release of ENDF/B-VIII.0. Among key advances made are that the 239 Pu file was reevaluated by a joint international effort and that updated 16,18 O, 19 F, 28–30 Si, 50–54 Cr, 55 Mn, 54,56,57 Fe, 63,65 Cu, 139 La, 233,235,238 U, and 240,241 Pu neutron nuclear data from the IAEA coordinated INDEN collaboration were adopted. Over 60 neutron dosimetry cross sections were adopted from the IAEA's IRDFF-II library. In addition, the new library includes significant changes for 3 He, 6 Li, 9 Be, 51 V, 88 Sr, 103 Rh, 140,142 Ce, Dy, 181 Ta, Pt, 206–208 Pb, and 234,236 U neutron data, and new nuclear data for the photonuclear, charged-particle and atomic sublibraries. Numerous thermal neutron scattering kernels were reevaluated or provided for the very first time. On the covariance side, work was undertaken to introduce better uncertainty quantification standards and testing for nuclear data covariances. The significant effort to reevaluate important nuclides has reduced bias in the simulations of many integral experiments with particular progress noted for fluorine, copper, and stainless steel containing benchmarks. Data issues hindered the successful deployment of the previous ENDF/B-VIII.0 for commercial nuclear power applications in high burnup situations. These issues were addressed by improving the 238 U and 239,240,241 Pu evaluated data in the resonance region. The new library performance as a function of burnup is similar to the reference ENDF/B-VII.1 library.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

SU-G-201-04: Can the Dynamic Library of Flap Applicators Replace Treatment Planning in Surface Brachytherapy?

Purpose: Contemporary brachytherapy treatment planning systems-(TPS) include the applicator model libraries to improve digitization; however, the library of surface-flap-applicators-(SFA) is not incorporated into the commercial TPS. We propose the dynamic library-(DL) for SFA and investigate if such library can eliminate applicator reconstruction, source activation and dose normalization. Methods: DL was generated for the SFA using the C++class libraries of the Visualization Toolkit-(VTK) and Qt-application framework for complete abstraction of the graphical interface. DL was designed such that the user can initially choose the size of the applicator that corresponds to the one clinically placed to the patient. The virtual applicator-(VA) has an elastic property so that it can be registered to the clinical CT images with a real applicator-(RA) on it. The VA and RA matching is performed by adjusting the position and curvature of the VA. The VA does not elongate or change its size so each catheter could always be at a distance of 5mm from the skin and 10mm apart from the closest catheter maintaining the physical accuracy of the clinical setup. Upon the applicator placement, the dwell positions were automatically activated, and the dose is normalized to the prescription depth. The accuracy of source positioning was evaluated using various applicator sizes. Results: The accuracy of the applicator placement was in the sub-millimeter range. The time-study reveals that up to 50% of the planning time can be saved depending on the complexity of the clinical setup. Unlike in the classic approach, the planning time was not highly dependent on the applicator size. Conclusion: The practical benefits of the DL of the SFA were demonstrated. The time demanding planning processes can be partially automated. Consequently, the planner can dedicate effort to fine tuning, which can result in the improvement of the quality of treatment plans in surface brachytherapy.

60 APPLIED LIFE SCIENCES↗

ECP libraries and tools: An overview

The Exascale Computing Project (ECP) Software Technology and Co-Design teams addressed the growing complexities in high-performance computing (HPC) by developing scalable software libraries and tools that leverage exascale system capabilities. As we enter the exascale era, the need for reusable, optimized software solutions that can handle the unique challenges posed by these systems becomes increasingly important. The primary challenges the ECP teams faced were to create software libraries and tools that are performant on exascale architectures and portable and usable across diverse hardware platforms. Efforts addressed issues related to concurrent execution, memory management, and the integration of heterogeneous computing resources, such as GPUs from multiple vendors. The ECP’s strategy involved a structured development process encompassing the creation, optimization, and deployment of software in collaboration with industry, academia, and national laboratories. The project was organized into several technical areas: co-design of domain-specific suites with target applications, programming models and runtimes, development tools, mathematical libraries, data and visualization tools, and software ecosystem and delivery mechanisms. ECP has successfully developed a large portfolio of software libraries and tools that demonstrate significant improvements in performance and scalability on exascale systems. These products have been integrated into the Department of Energy’s computing facilities, supporting various scientific applications and ensuring robust performance across different hardware setups. ECP advancements in software development for exascale computing highlight the importance of a collaborative and adaptive approach to handling next-generation HPC systems complexities. The lessons learned emphasize the need for continuous engagement with end-users and vendors, and the importance of maintaining a balance between innovation and practical implementation. Future efforts will focus on ensuring scalability, keeping pace with rapid hardware advancements, and further enhancing the interoperability and usability of the software ecosystem. In conclusion, subsequent articles in this special issue provide in-depth discussions and case studies into specific library and tool efforts.

97 MATHEMATICS AND COMPUTING↗

Damsel: A Data Model Storage Library for Exascale Science

Computational science applications have been described as having one of seven motifs (the “seven dwarfs”), each having a particular pattern of computation and communication. From a storage and I/O perspective, these applications can also be grouped into a number of data model motifs describing the way data is organized and accessed during simulation, analysis, and visualization. Major storage data models developed in the 1990s, such as Network Common Data Format (netCDF) and Hierarchical Data Format (HDF) projects, created support for more complex data models. Development of both netCDF and HDF5 was influenced by multi-dimensional dataset storage requirements, but their access models and formats were designed with sequential storage in mind (e.g., a POSIX I/O model). Although these and other high-level I/O libraries have had a beneficial impact on large parallel applications, they do not always attain a high percentage of peak I/O performance due to fundamental design limitations, and they do not address the full range of current and future computational science data models. The goal of this project is to enable exascale computational science applications to interact conveniently and efficiently with storage through abstractions that match their data models. The project consists of three major activities: (1) identifying major data model motifs in computational science applications and developing representative benchmarks; (2) developing a data model storage library, called Damsel, that supports these motifs, provides efficient storage data layouts, incorporates optimizations to enable exascale operation, and is tolerant to failures; and (3) productizing Damsel and working with computational scientists to encourage adoption of this library by the scientific community. The product of this project, Damsel library, is openly available for download from http://cucis.ece.northwestern.edu/projects/DAMSEL. Several case studies and application programming interface reference are also available to assist new users to learn to use the library.

97 MATHEMATICS AND COMPUTING↗

A library of building occupant behaviour models represented in a standardised schema

During the past four decades, a significant body of literature has reported on the impacts of occupant behaviour (OB) on building technologies, operation, and energy consumption. A large number of data-driven behavioural models have been developed based on field data. These models lack standardisation and consistency, leading to difficulties in applications and comparison. To address this concern, an ontology was developed using the drivers-needs-actions-systems (DNAS) framework. Recent work has been carried out to implement the theoretical DNAS framework into an eXtensible Markup Language (XML) schema, titled ‘occupant behaviour XML’ (obXML) which is a practical implementation of OB models that can be integrated into building performance simulation (BPS) programs. This paper presents a newly developed library of OB models represented in the standardised obXML schema format. This library provides ready-to-use examples for BPS users to employ more accurate occupant representation in their energy models. The library, which contains an initial effort of 52 OB models, was made publicly available for the BPS community. As part of the library development process, limitations of the obXML schema were identified and addressed, and future improvements were proposed. Authors hope that by compiling this library building, energy modellers from all over the world can enhance their BPS models by integrating more accurate and robust OB patterns.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

A Library of Proton-Transfer Reactions of H{sub 3}O{sup +} Ions Used for Trace Gas Detection

We have collected data on the proton-transfer reactions with H{sub 3}O{sup +} ions for trace gas detection into an online and publicly available library. The library allows users of proton-transfer-reaction mass spectrometry (PTR-MS) and selected-ion flow-tube mass spectrometry (SIFT-MS) to look up at which m/z a trace gas of interest is detected. Vice versa, the library also allows looking up what trace gas may have been responsible for a product ion detected in PTR-MS and SIFT-MS. Finally, the library may serve as a dataset for further research on calculating instrument sensitivity and product-ion fragmentation, improving identification and quantification of newly detectable compounds as advances in instrumentation continue. To demonstrate the utility of the library, we present a brief analysis of product-ion fragmentation. We show that oxygenated organic compounds exhibit trends in neutral loss according to their functionality, and that on average neutral losses decrease the carbon number and increase the extent of unsaturation of product ions. .

74 ATOMIC AND MOLECULAR PHYSICS↗

Development of ORIGEN Libraries for Mixed Oxide (MOX) Fuel Assembly Designs

In this research, ORIGEN cross section libraries for reactor-grade mixed oxide (MOX) fuel assembly designs have been developed to provide fast and accurate depletion calculations to predict nuclide inventories, radiation sources and thermal decay heat information needed in safety evaluations and safeguards verification measurements of spent nuclear fuel. These ORIGEN libraries are generated using two-dimensional lattice physics assembly models that include enrichment zoning and cross section data based on ENDF/B-VII.0 evaluations. Using the SCALE depletion sequence, burnup-dependent cross sections are created for selected commercial reactor assembly designs and a representative range of reactor operating conditions, fuel enrichments, and fuel burnup. The burnup dependent cross sections are then interpolated to provide problem-dependent cross sections for ORIGEN, avoiding the need for time-consuming lattice physics calculations. The ORIGEN libraries for MOX assembly designs are validated against destructive radiochemical assay measurements of MOX fuel from the MALIBU international experimental program. This program included measurements of MOX fuel from a 15 × 15 pressurized water reactor assembly and a 9 × 9 boiling water reactor assembly. The ORIGEN MOX libraries are also compared against detailed assembly calculations from the Phase IV-B numerical MOX fuel burnup credit benchmark coordinated by the Nuclear Energy Agency within the Organization for Economic Cooperation and Development. Finally, the nuclide compositions calculated by ORIGEN using the MOX libraries are shown to be in good agreement with other physics codes and with experimental data.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Evaluation of In Silico Multifeature Libraries for Providing Evidence for the Presence of Small Molecules in Synthetic Blinded Samples

The current gold standard for unambiguous molecular identification in metabolomics analysis is comparing two or more orthogonal properties from the analysis of authentic reference materials (standards) to experimental data acquired in the same laboratory with the same analytical methods. This represents a significant limitation for comprehensive chemical identification of small molecules in complex samples. The process is time-consuming and costly, and the majority of molecules are not yet represented by standards. Thus, there is a need to assemble evidence for the presence of small molecules in complex samples through the use of libraries containing calculated chemical properties. To address this need, we developed a Multi-Attribute Matching Engine (MAME) and a library derived in-part from our in silico Chemical Library Engine (ISiCLE). Here, we describe an initial evaluation of these methods in a blinded analysis of synthetic chemical mixtures as part of the U.S. Environmental Protection Agency’s (EPA) Non-Targeted Analysis Collaborative Trial (ENTACT, Phase 1). For molecules in all mixtures, the initial blinded false negative rate (FNR), false discovery rate (FDR), and accuracy were 57%, 77%, and 91%, respectively. For high evidence scores, the FDR was 35%. After unblinding of the sample compositions, we optimized the scoring parameters to better exploit the available evidence, and increased the accuracy for molecules suspected as present. The final FNR, FDR, and accuracy were 67%, 53%, and 96%, respectively. For high evidence scores, the FDR was 10%. This study demonstrates that multi-attribute matching methods in conjunction with in silico libraries may one day enable reduced reliance on experimentally-derived libraries for building evidence for the presence of molecules in complex samples.

Nunez, Jamie↗

Rapid Generation of Tandem Mass Spectrometry Reference Libraries Using Immediate Drop-on-Demand Liquid Handling Coupled to an Open Port Sampling Interface

In metabolomics, tandem MS (MS2) fragmentation libraries are important for the identification of unknown features, but generating these libraries takes many valuable hours of instrument and operator time. Here, an immediate droplet-on-demand/open port sampling interface was used to rapidly acquire tandem MS of standards arrayed in a 96-well plate format. A workflow was developed for automated, high-throughput control of MS2 library generation. Pure standard mass spectral libraries were collected on Orbitrap and Q-TOF mass spectrometers for 192 compounds using 6 different collision energies with a throughput of 4 and 7.8 s/spectrum, respectively. Libraries were acquired using different solvent additives, precursor adducts, and ion polarities.

Cahill, John [ORNL] (ORCID:0000000298664010)↗