Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Level set method”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 973 records · Page 54
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Breeding progress and preparedness for mass‐scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar

Abstract Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output–input energy ratios: namely Panicum virgatum (switchgrass), species of the genera Miscanthus (miscanthus), Salix (willow) and Populus (poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed‐based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5 years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass‐scale deployment of PBCs.

09 BIOMASS FUELS↗
DOE OSTI2016

SU-G-JeP2-12: Quantification of 3D Geometric Distortion for 1.5T and 3T MRI Scanners Used for Radiation Therapy

Purpose: To quantify the magnitude of geometric distortion for MRI scanners and provide recommendations for MRI imaging for radiation therapy Methods: A novel phantom, QUASAR MRID3D [Modus Medical Devices Inc.], was scanned to evaluate the level of 3D geometric distortion present in five MRI scanners used for radiation therapy in our department. The phantom was scanned using the body coil with 1mm image slice thickness to acquire 3D images of the phantom body. The phantom was aligned to its geometric center for each scan, and the field of view was set to visualize the entire phantom. The dependence of distortion magnitude with distance from imaging isocenter and with magnetic field strength (1.5T and 3T) was investigated. Additionally, the characteristics of distortion for Siemens and GE machines were compared. The image distortion for each scanner was quantified in terms of mean, standard deviation (STD), maximum distortion, and skewness. Results: The 3T and 1.5T scans show a similar absolute distortion with a mean of 1.38mm (0.33mm STD) for 3T and 1.39mm (0.34mm STD) for 1.5T for a 100mm radius distance from isocenter. Some machines can have a distortion larger than 10mm at a distance of 200mm from the isocenter. The distortions are presented with plots of the x, y, and z directional components. Conclusion: The results indicate that quantification of MRI image distortion is crucial in radiation oncology for target and organ delineation and treatment planning. The magnitude of geometric distortion determines the margin needed for target contouring which is usually neglected in treatment planning process, especially for SRS/SBRT treatments. Understanding the 3D distribution of the MRI image distortion will improve the accuracy of target delineation and, hence, treatment efficacy. MRI imaging with proper patient alignment to the isocenter is vital to reducing the effects of MRI distortion in treatment planning.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

White Box Access to Quantum Testbeds for Co-Design

At Lawrence Livermore National Laboratory (LLNL), we operate and maintain the Quantum Device and Integration Testbed (QuDIT) facility, a small quantum testbed that supports about 10 active research teams (including our own) and over 50 internal and external collaborators. This testbed is designed to give remote white box access to users for research, training, and outreach. A guiding principle behind the development of our testbed infrastructure, software and user interfaces is to empower users to perform experiments at the cutting edge of quantum information science at any level of abstraction, from materials studies, device physics and control and characterization techniques to algorithm development and quantum operating system design. Our testbed targets a multilevel quantum system (qudit) to expand the accessible Hilbert space of a simple-to-manufacture quantum device and focuses on quantum simulation, typically implemented through custom gates designed with quantum optimal control methods, rather than on a universal computing framework with a fixed gate set. We leverage the Lab’s high-performance computing (HPC) program and related expertise to simulate quantum systems, develop hybrid algorithms, and generate gates optimized for given simulations. Additionally, we have adopted a co-design philosophy from the HPC community in designing new hardware, so that the systems we develop are optimized for the specific physics simulations we plan to use them for.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

A Two-Fold Structural Classification Method for Determining the Accurate Ensemble of Protein Structures

Atomic-level structural characterization of flexible proteins, such as intrinsically disordered proteins and multi-domain proteins connected by flexible linkers, is challenging as they possess distinct conformations in physiological conditions. Significant efforts have been made to develop integrated approaches by combining small angle neutron/X-ray scattering experiments with molecular simulations to reveal the distinct atomic structures and the corresponding populations for these flexible proteins. One widely used method, the basis-set supported ensemble method, classifies the simulation-generated protein conformations into a set of structural basis and then derives the corresponding populations by fitting to the experimental data. This method makes an implicit assumption that protein conformations of similar structures have similar small angle scattering profiles.The present work demonstrates that, for various protein systems ranging from compact globular proteins and flexible multidomain proteins through to intrinsically disordered proteins, this method provides inaccurate assessment of the structural ensemble of the protein molecules due to the breakdown of the assumption made. To alleviate this problem, a two-fold-clustering method is developed to cluster the simulation-generated protein structures using information on both 3D structure and scattering profiles. As benchmarked by both simulation and experimental results, this new method yields much more accurate populations of structural basis of protein molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Prediction of Mass Spectral Response Factors from Predicted Chemometric Data for Druglike Molecules

A method is developed for the prediction of mass spectral ion counts of drug-like molecules using in silico calculated chemometric data. Various chemometric data, including polar and molecular surface areas, aqueous solvation free energies, and gas-phase and aqueous proton affinities were computed, and a statistically significant relationship between measured mass spectral ion counts and the combination of aqueous proton affinity and total molecular surface area was identified. In particular, through multilinear regression of ion counts on predicted chemometric data, we find that log{sub 10}(MS ion counts) = –4.824 + c{sub 1}•PA + c{sub 2}•SA, where PA is the aqueous proton affinity of the molecule computed at the SMD(aq)/M06-L/MIDI!//M06-L/MIDI! level of electronic structure theory, SA is the total surface area of the molecule in its conjugate base form, and c{sub 1} and c{sub 2} have values of –3.912 × 10{sup –2} mol kcal{sup –1} and 3.682 × 10{sup –3} Å{sup –2}. On a 66-molecule training set, this regression exhibits a multiple R value of 0.791 with p values for the intercept, c{sub 1}, and c{sub 2} of 1.4 × 10{sup –3}, 4.3 × 10{sup –10}, and 2.5 × 10{sup –6}, respectively. Application of this regression to an 11-molecule test set provides a good correlation of prediction with experiment (R = 0.905) albeit with a systematic underestimation of about 0.2 log units. This method may prove useful for semiquantitative analysis of drug metabolites for which MS response factors or authentic standards are not readily available. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2013

Passive Neutron Non-Destructive Assay for Remediation of Radiological Waste at Hanford Burial Grounds- 13189

The Hanford burial grounds contains a broad spectrum of low activity radioactive wastes, transuranic (TRU) wastes, and hazardous wastes including fission products, byproduct material (thorium and uranium), plutonium and laboratory chemicals. A passive neutron non-destructive assay technique has been developed for characterization of shielded concreted drums exhumed from the burial grounds. This method facilitates the separation of low activity radiological waste containers from TRU waste containers exhumed from the burial grounds. Two identical total neutron counting systems have been deployed, each consisting of He-3 detectors surrounded by a polyethylene moderator. The counts are processed through a statistical filter that removes outliers in order to suppress cosmic spallation events and electronic noise. Upon completion of processing, a 'GO / NO GO' signal is provided to the operator based on a threshold level equivalent to 0.5 grams of weapons grade plutonium in the container being evaluated. This approach allows instantaneous decisions to be made on how to proceed with the waste. The counting systems have been set up using initial on-site measurements (neutron emitting standards loaded into surrogate waste containers) combined with Monte Carlo modeling techniques. The benefit of this approach is to allow the systems to extend their measurement ranges, in terms of applicable matrix types and container sizes, with minimal interruption to the operations at the burial grounds. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Direct pulse-level compilation of arbitrary quantum logic gates on superconducting qutrits

Advanced simulations and calculations on quantum computers require high-fidelity implementations of quantum operations. The universal gateset approach builds complex unitaries from a small set of primitive gates, often resulting in a long gate sequence, which is typically a leading factor in the total accumulated error. Compiling a complex unitary for processors with higher-dimensional logical elements, such as qutrits, exacerbates the accumulated error per unitary, since an even longer gate sequence is required. Optimal control methods promise time- and resource-efficient compact gate sequences and, therefore, higher fidelity. These methods generate pulses that can directly implement any complex unitary on a quantum device. In this work, we demonstrate that any arbitrary qubit and qutrit gate can be realized with high fidelity, which can significantly reduce the length of a gate sequence. We generate and test pulses for a large set of randomly selected arbitrary unitaries on several quantum processing units (QPUs): the Lawrence Livermore National Laboratory Quantum Device and Integration Testbed’s (QuDIT’s) standard QPU and three of Rigetti’s QPUs: Ankaa-2, Ankaa-9Q-1, and Aspen-M-3. On the QuDIT platform’s standard QPU, the average fidelity of random qutrit gates is 97.9 ± 0.5% measured with conventional QPT and 98.8 ± 0.6% from QPT with gate folding. Rigetti’s Ankaa-2 achieves random qubit gates with an average fidelity of 98.4 ± 0.5% (conventional QPT) and 99.7 ± 0.1% (QPT with gate folding). On Ankaa-9Q-1 and Aspen-M-3, the average fidelities with conventional qubit QPT measurements were higher than 99% (see Appendix). Here we show that optimal control gates are robust to drift for at least 3 h and that the same calibration parameters can be used for all implemented gates. Our work promises that the calibration overheads for optimal control gates can be made small enough to enable efficient quantum circuits based on this technique.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

High-Accuracy Heats of Formation for Alkane Oxidation: From Small to Large via the Automated CBH-ANL Method

It is generally challenging to obtain high-accuracy predictions for the heat of formation for species with more than a handful of heavy atoms, such as those of importance in standard combustion mechanisms. To this end, we construct the CBH-ANL approach and illustrate that, for a set of 194 alkane oxidation species, it can be used to produce ΔH f (o K) values with 2σ uncertainties of 0.2-0.5 kcal mol -1 . This set includes the alkanes, hydroperoxides, and alkyl, peroxy, and hydroperoxyalkyl radicals for 17 representative hydrocarbon fuels containing up to 10 heavy atoms with various degrees of branching in the alkane backbone. The CBH-ANL approach, automated in the QTC and AutoMech software suites, builds balanced chemical equations for the calculation of ΔH f (o K), in which the reference species may be up to five heavy atoms. The high-level ANLo and ANL1 reference ΔH f (o K) values are further refined for even the largest of these reference species with a novel laddering approach. We perform a comprehensive quantification of the uncertainties for both the individual reference species (the largest of which is 0.15 kcal mol -1 ) and the propagation of those uncertainties when used in the calculation of ΔH f (o K) for the 194 target species. Here we examine the sensitivity of the predicted ΔH f (o K) values to (i) electronic energies from various methods, including ωB97X-D/cc-pVTZ, B2PLYP-D3/cc-pVTZ, CCSD(T)-F12b/cc-pVDZ-F12//B2PLYP-D3/cc-pVTZ, and CCSD(T)-F12b/cc-pVTZ-F12//B2PLYP-D3/cc-pVTZ; (ii) the zero-point vibrational energies (ZPVEs), where we consider harmonic ZPVEs as well as two scaling-based estimates of the anharmonic ZPVEs, all implemented for both ωB97X-D/cc-pVTZ and B2PLYP-D3/cc-pVTZ calculations; (iii) the particular CBH-ANL scheme employed; and (iv) the procedure for choosing the reference conformer for the analyses. The discussion concludes with a summary of the estimated overall uncertainty in the predictions and a validation of the predictions for the alkane subset.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Comparison between simulated and observed LHC beam backgrounds in the ATLAS experiment at E beam =4 TeV

Results of dedicated Monte Carlo simulations of beam-induced background (BIB) in the ATLAS experiment at the Large Hadron Collider (LHC) are presented and compared with data recorded in 2012. During normal physics operation this background arises mainly from scattering of the 4 TeV protons on residual gas in the beam pipe. Methods of reconstructing the BIB signals in the ATLAS detector, developed and implemented in the simulation chain based on the \textsc{Fluka} Monte Carlo simulation package, are described. The interaction rates are determined from the residual gas pressure distribution in the LHC ring in order to set an absolute scale on the predicted rates of BIB so that they can be compared quantitatively with data. Through these comparisons the origins of the BIB leading to different observables in the ATLAS detectors are analysed. The level of agreement between simulation results and BIB measurements by ATLAS in 2012 demonstrates that a good understanding of the origin of BIB has been reached.

47 OTHER INSTRUMENTATION↗
DOE OSTI2018

Evidence for associated production of a Higgs boson with a top quark pair in final states with electrons, muons, and hadronically decaying τ leptons at $ \sqrt{s}=13 $ TeV

Results of a search for the standard model Higgs boson produced in association with a top quark pair ($\mathrm{t\overline{t}}$H) in final states with electrons, muons, and hadronically decaying $\tau$ leptons are presented. The analyzed data set corresponds to an integrated luminosity of 35.9 fb$^{-1}$ recorded in proton-proton collisions at $\sqrt{s} =$ 13 TeV by the CMS experiment in 2016. The sensitivity of the search is improved by using matrix element and machine learning methods to separate the signal from backgrounds. The measured signal rate amounts to 1.23$^{+0.45}_{-0.43}$ times the production rate expected in the standard model, with an observed (expected) significance of 3.2$\sigma$ (2.8$\sigma$), which represents evidence for $\mathrm{t\overline{t}}$H production in those final states. In conclusion, an upper limit on the signal rate of 2.1 times the standard model production rate is set at 95% confidence level.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2014

An evaluation of experimental decadal predictions using CCSM4

This study assesses retrospective decadal prediction skill of sea surface temperature (SST) variability in initialized climate prediction experiments with the Community Climate System Model version 4 (CCSM4). Ensemble forecasts initialized with two different historical ocean and sea-ice states are evaluated and compared to an ensemble of uninitialized coupled simulations. Both experiments are subject to identical twentieth century historical radiative forcings. Each forecast consists of a 10-member ensemble integrated over a 10-year period. One set of historical ocean and sea-ice conditions used for initialization comes from a forced ocean-ice simulation driven by the Coordinated Ocean-ice Reference Experiments interannually varying atmospheric dataset. Following the Coordinated Model Intercomparison Project version 5 (CMIP5) protocol, these forecasts are initialized every 5 years from 1961 to 1996, and every year from 2000 to 2006. A second set of initial conditions comes from historical ocean state estimates obtained through the assimilation of in-situ temperature and salinity data into the CCSM4 ocean model. These forecasts are only available over a limited subset of the CMIP5 recommended start dates. Both methods result in retrospective SST prediction skill over broad regions of the Indian Ocean, western Pacific Ocean and North Atlantic Ocean that are significantly better than reference skill levels from a spatio-temporal auto-regressive statistical model of SST. However the subpolar gyre region of the North Atlantic stands out as the only region where the CCSM4 initialized predictions outperform uninitialized simulations. Some features of the ocean state estimates used for initialization and their impact on the forecasts are discussed.

Meteorology & Atmospheric Sciences↗
DOE OSTI2022

Insights into Methodologies and Operational Details of Resource Adequacy Assessment: A Case Study with Application to a Broader Flexibility Framework

Assessing and maintaining resource adequacy (RA) is a core pillar of power systems. However, recent changes in the physical makeup of these systems and the conditions under which these systems must operate have yielded a renewed interest in the methods, metrics, and assumptions that underpin RA assessments. In this paper, we systematically explore a wide range of RA modeling dimensions, including: the objective function and level of operational detail in the underlying model formulation; the quantity (look-ahead) and quality (accuracy) of data that is available for making operational decisions within those models; and the physical configuration of solar photovoltaics (PV) with battery storage hybrid resources. We apply a set of probabilistic RA tools and production cost modeling tools to a realistic test system based loosely on a future Electric Reliability Council of Texas power system dominated by solar PV resources. Under the assumptions of our system and models, we find that multi-stage probabilistic assessments may provide a more robust evaluation of RA by capturing a wider range of operational and system interactions, but this comes at a computational cost of 1-2 orders of magnitude longer run time depending on the specific configuration. In addition, the information on thermal generator availability impacts RA performance by an order of magnitude more than solar resource forecasts, which is driven by the comparatively larger magnitude of thermal outages than solar forecast errors within our test system. Lastly, the flexibility provided by hybrid and other resources can help reduce system load-shedding event frequencies and enable the system to be more robust to inaccurate forecast information, and alternative hybrid inverter sizes can impact RA levels by 1-2 orders of magnitude. Our results point to the importance of a broader flexibility framework to describe the interaction between (1) flexibility "supply" from both physical resource capabilities and operational constraints considered in the modeling, and (2) flexibility "demand" from forecast errors, thermal generator outages, and other sources of uncertainty, as well as their RA impacts. Results are likely sensitive to the system buildout explored; future work could consider additional system configurations and conditions.

ENERGY PLANNING, POLICY, AND ECONOMY,POWER TRANSMI↗
DOE OSTI2025

The latent variable proximal point algorithm for variational problems with inequality constraints

The latent variable proximal point (LVPP) algorithm is a framework for solving infinite-dimensional variational problems with pointwise inequality constraints. The algorithm is a saddle point reformulation of the Bregman proximal point algorithm. At the continuous level, the two formulations are equivalent, but the saddle point formulation is more amenable to discretization because it introduces a structure-preserving transformation between a latent function space and the feasible set. Working in this latent space is much more convenient for enforcing inequality constraints than the feasible set, as discretizations can employ general linear combinations of suitable basis functions, and nonlinear solvers can involve general additive updates. LVPP yields numerical methods with observed mesh-independence for obstacle problems, contact, fracture, plasticity, and others besides; in many cases, for the first time. The framework also extends to more complex constraints, providing means to enforce convexity in the Monge–Ampère equation and handling quasi-variational inequalities, where the underlying constraint depends implicitly on the unknown solution. Here, in this paper, we describe the LVPP algorithm in a general form and apply it to ten problems from across mathematics.

Inequality constraints↗
DOE OSTI2023

Single-Point Extrapolation to the Complete Basis Set Limit through Deep Learning

Machine learning (ML) offers an attractive method for making predictions about molecular systems while circumventing the need to run expensive electronic structure calculations. Once trained on ab initio data, the promise of ML is to deliver accurate predictions of molecular properties that were previously computationally infeasible. In this work, we develop and train a graph neural network model to correct the basis set incompleteness error (BSIE) between a small and large basis set at the RHF and B3LYP levels of theory. Our results show that, when compared to fitting to the total potential, an ML model fitted to correct the BSIE is better at generalizing to systems not seen during training. We test this ability by training on single molecules while evaluating on molecular complexes. We also show that ensemble models yield better behaved potentials in situations where the training data is insufficient. However, even when only fitting to the BSIE, acceptable performance is only achieved when the training data sufficiently resemble the systems one wants to make predictions on. As a result, the test error of the final model trained to predict the difference between the cc-pVDZ and cc-pV5Z potential is 0.184 kcal/mol for the B3LYP density functional, and the ensemble model accurately reproduces the large basis set interaction energy curves on the S66x8 dataset.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Health intelligence: how artificial intelligence transforms population and personalized health

Advances in computational and data sciences for data management, integration, mining, classification, filtering, visualization along with engineering innovations in medical devices have prompted demands for more comprehensive and coherent strategies to address the most fundamental questions in health care and medicine. Theory, methods, and models from artificial intelligence (AI) are changing the health care landscape in clinical and community settings and have already shown promising results in multiple applications in healthcare including, integrated health information systems, patient education, geocoding health data, social media analytics, epidemic and syndromic surveillance, predictive modeling and decision support, mobile health, and medical imaging (e.g. radiology and retinal image analyses). Health intelligence uses tools and methods from artificial intelligence and data science to provide better insights, reduce waste and wait time, and increase speed, service efficiencies, level of accuracy, and productivity in health care and medicine.

Shaban-Nejad, Arash↗
DOE OSTI2019

Characterization of the 2-methylvinoxy radical + O 2 reaction: A focal point analysis and composite multireference study

Vinoxy radicals are involved in numerous atmospheric and combustion mechanisms. High-level theoretical methods have recently shed new light on the reaction of the unsubstituted vinoxy radical with O 2 . The reactions of 1-methylvinoxy radical and 2-methylvinoxy radical with molecular oxygen have experimental high pressure limiting rate constants, k ∞ , 5–7 times higher than that of the vinoxy plus O 2 reaction. In this work, high-level ab initio quantum chemical computations are applied to the 2-methylvinoxy radical plus O 2 system, namely, the formation and isomerization of the 1-oxo-2-propylperoxy radical, the immediate product of O 2 addition to the 2-methylvinoxy radical. Multireference methods were applied to the entrance channel. No barrier to O 2 addition could be located, and more sophisticated treatment of dynamic electron correlation shows that the principal difference between O 2 addition to the vinoxy and 2-methylvinoxy radicals is a larger steric factor for 2-methylvinoxy + O 2 . This is attributed to the favorable interaction between the incoming O 2 molecule and the methyl group of the 2-methylvinoxy radical. Via the focal point approach, energetics for this reaction were determined, in most cases, to chemical accuracy. The coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] correlation energy and Hartree–Fock energies were independently extrapolated to the complete basis set limit. A correction for the effect of higher excitations was computed at the CCSDT(Q)/6-31G level. Corrections for the frozen-core approximation, the Born–Oppenheimer approximation, the nonrelativistic approximation, and the zero-point vibrational energy were included. From the 1-oxo-2-propylperoxy radical, dissociation to reactants is competitive with the lowest energy isomerization pathway. The lowest energy isomerization pathway ultimately forms acetaldehyde, CO, and ·OH as the final products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Plackett-Burman experimental design to facilitate syntactic foam development

The use of an eight-experiment Plackett–Burman method can assess six experimental variables and eight responses in a polysiloxane-glass microsphere syntactic foam. The approach aims to decrease the time required to develop a tunable polymer composite by identifying a reduced set of variables and responses suitable for future predictive modeling. The statistical design assesses the main effects of mixing process parameters, polymer matrix composition, microsphere density and volume loading, and the blending of two grades of microspheres, using a dummy factor in statistical calculations. Responses cover rheological, physical, thermal, and mechanical properties. The cure accelerator content of the polymer matrix and the volume loading of the microspheres have the largest effects on foam properties. These factors are the most suitable for controlling the gel point of the curing foam, and the density of the cured foam. The mixing parameters introduce widespread variability and therefore should be fixed at effective levels during follow-up testing. Some responses may require greater contrast in microsphere-related factors. As a result, compared to other possible statistical approaches, the run economy of the Plackett–Burman method makes it a valuable tool for rapidly characterizing new foams.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements

As the capability of mass spectrometry-based proteomics has matured, tens of thousands of peptides can be measured simultaneously, which has the benefit of offering a systems view of protein expression. However, a major challenge is that with an increase in throughput, protein quantification estimation from the native measured peptides has become a computational task. A limitation to existing computationally-driven protein quantification methods is that most ignore protein variation, such as alternate splicing of the RNA transcript and post-translational modifications or other possible proteoforms, which will affect a significant fraction of the proteome. The consequence of this assumption is that statistical inference at the protein level, and consequently downstream analyses, such as network and pathway modeling, have only limited power for biomarker discovery. Here, we describe a Bayesian model (BP-Quant) that uses statistically derived peptides signatures to identify peptides that are outside the dominant pattern, or the existence of multiple over-expressed patterns to improve relative protein abundance estimates. It is a research-driven approach that utilizes the objectives of the experiment, defined in the context of a standard statistical hypothesis, to identify a set of peptides exhibiting similar statistical behavior relating to a protein. This approach infers that changes in relative protein abundance can be used as a surrogate for changes in function, without necessarily taking into account the effect of differential post-translational modifications, processing, or splicing in altering protein function. We verify the approach using a dilution study from mouse plasma samples and demonstrate that BP-Quant achieves similar accuracy as the current state-of-the-art methods at proteoform identification with significantly better specificity. BP-Quant is available as a MatLab ® and R packages at https://github.com/PNNL-Comp-Mass-Spec/BP-Quant.

Protein Quantitation, proteomics↗