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At least 127 records · Page 7

Object-Based Evaluation of Dynamical and Statistical Downscaled Precipitation Products over CONUS

High-resolution precipitation data, generated through dynamical downscaling (DD) or statistical downscaling (SD) of global climate model output, provide critical information for regional climate assessment and adaptation planning. Most downscaling development and validation have focused on accurate gridscale precipitation construction and ignored the spatial structure of precipitation across model grids and at the event scale. However, many applications, e.g., hydrologic modeling and the analysis using the downscaled precipitation, require a reasonable representation of the spatial structure of precipitation within watersheds. Therefore, a set of standard metrics to evaluate the representation of the spatial structure of individual storms across diverse downscaled precipitation products is desired. To address this need, we conducted an object-based evaluation of precipitation in decades-long DD and SD products over the contiguous United States (CONUS). Specifically, we evaluate their ability to reproduce various features of precipitation objects in the observations: total volume, precipitation area, peak intensity, and spatial structure. Multiple metrics (bias, Perkins score, and nonparametric statistical tests) are used to quantify model performance. Our evaluation reveals notable variations in performance among individual products across different climate zones and seasons, as well as between extreme and nonextreme events. In general, most DD products exhibit balanced performance across the four precipitation object features, while SD products vary more significantly in their performance across products. Based on this comprehensive evaluation, we provide guidance on choosing downscaled products for specific regions, seasons, and precipitation object features. These findings and recommendations can inform precipitation-relevant modeling and analysis over CONUS, guide future downscaling technique developments, and provide actionable information for climate impact assessment and adaptation.

Downscaling↗

A comparative analysis of YOLOv8 and U-Net image segmentation approaches for transmission electron micrographs of polycrystalline thin films

Metallic thin films offer a platform to experimentally study the dynamics of microstructural evolution, but the required transmission electron microscopy (TEM)-based imaging generates complex images that are challenging to segment and quantify. This work provides a comparative analysis of a new YOLOv8 model and an established U-Net model for bright-field TEM images of polycrystals, employing a framework leveraging physical observables to evaluate performance against two hand-traced benchmark datasets. This methodology obviates the comparison of large, diversely structured, and manually labeled datasets that are required to assess performance on a per-image/per-pixel basis. It is found that the YOLOv8 model, adapted for real-time instance segmentation, has up to 43× faster inferencing (NVIDIA GeForce RTX 4090) compared to U-Net and reconstructs hand-traced grain size distributions (GSDs) with excellent fidelity, finding mean diameter within 3% for grains near an optimal magnification; for grains that deviate from the optimal pixel-diameter, the size of small- (large)-diameter grains is systematically over- (under)-estimated. This is partially mitigated by including scale-aware augmentations during training. Moreover, when the bias is corrected post-inference by a rigid shift in distribution, the YOLOv8 model reproduces ground truth GSDs with exceptional fidelity, with statistical tests indicating <5% probability that the distributions are distinct. Based on ground truth data, calibration curves pertaining to this shift can be constructed for a given model. This issue is not present in the U-Net model’s results, indicating that for quantitative measurements where the true size of objects is of interest, special procedures must be implemented for YOLO-based models.

36 MATERIALS SCIENCE↗

The persistent shadow of the supermassive black hole of M87. II. Model comparisons and theoretical interpretations

The Event Horizon Telescope (EHT) observation of M87∗ in 2018 has revealed a ring with a diameter that is consistent with the 2017 observation. The brightest part of the ring is shifted to the southwest from the southeast. In this paper, we provide theoretical interpretations for the multi-epoch EHT observations for M87∗ by comparing a new general relativistic magnetohydrodynamics model image library with the EHT observations for M87∗ in both 2017 and 2018. The model images include aligned and tilted accretion with parameterized thermal and nonthermal synchrotron emission properties. The 2018 observation again shows that the spin vector of the M87∗ supermassive black hole is pointed away from Earth. A shift of the brightest part of the ring during the multi-epoch observations can naturally be explained by the turbulent nature of black hole accretion, which is supported by the fact that the more turbulent retrograde models can explain the multi-epoch observations better than the prograde models. The EHT data are inconsistent with the tilted models in our model image library. Assuming that the black hole spin axis and its large-scale jet direction are roughly aligned, we expect the brightest part of the ring to be most commonly observed 90 deg clockwise from the forward jet. This prediction can be statistically tested through future observations.

79 ASTRONOMY AND ASTROPHYSICS↗

Emergence of robust anthropogenic increase of heat stress-related variables projected from CORDEX-CORE climate simulations

The information of when and where region-specific patterns in both mean and extreme temperatures leading to heat stress will emerge from the present-day climate variability is important to plan adaptation options, but to date studies on this issue still remain limited and fragmented. Here, we estimate the time of emergence (TOE) of temperature and wet-bulb temperature (Tw), a better indication of heat stress, using fine-scale, long-term regional climate model projections under the RCP2.6 and RCP8.5 scenarios across six different domains. Differently from previous studies, the TOE is determined using three methods applied on impact-relevant variables: two different signal-to-noise frameworks based on summer mean temperature and Tw and a statistical test to identify significant differences in daily extreme distributions. The TOE response to RCP2.6 and RCP8.5 with respect to the end of 20th century variability differs significantly regardless of which TOE metric is applied. For summer mean temperature, the land fraction reaching TOE is expected to exceed 90% by the 2050s under the RCP8.5, whereas the increase rate of land exposure to TOE tends to stagnate over time under the RCP2.6 so that more than 40% of land will not experience TOE by the end of the 21st century. Compared to temperature, the TOE of Tw is reached earlier in most of the wet tropics but is delayed in hot and dry regions because of the nonlinear response of Tw to humidity. For both temperature and Tw, the TOE appears earlier in regions with low baseline variability, such as in the tropics. Despite the uncertainties arising from the choice of TOE metrics, the vast majority of regions in Africa and southeast Asia experience TOE in the early 21st century under both the RCP2.6 and RCP8.5 scenarios, which stresses the urgent need for developing adequate adaptation strategies in these regions.

54 ENVIRONMENTAL SCIENCES↗

Analyzing the impact of design factors on solar module thermomechanical durability using interpretable machine learning techniques

Solar modules in utility-scale systems are expected to maintain decades of lifetime to rival conventional energy sources. However, cyclic thermomechanical loading often degrades their long-term performance, highlighting the importance of effective design to mitigate thermal expansion mismatches between module materials. Given the complex composition of solar modules, isolating the impact of individual components on overall durability remains a challenging task. In this work, we analyze a comprehensive data set that comprises bill-of-materials (BOM) and thermal cycling power loss from 251 distinct module designs to identify the predominant design factors and their impacts on the thermomechanical durability of modules. The methodology of our analysis combines machine learning modeling (random forest) and Shapley additive explanation (SHAP) to correlate design factors with power loss and interpret the model’s decision-making. The interpretation reveals that silicon type (monocrystalline or polycrystalline), encapsulant thickness, busbar numbers, and wafer thickness predominantly influence the degradation. With lower power loss of around 0.6% on average in the SHAP analysis, monocrystalline cells present better durability than polycrystalline cells. This finding is further substantiated by statistical testing on our raw data set. The SHAP analysis also demonstrates that while thicker encapsulants lead to reduced power loss, further increasing their thickness over around 0.6 to 0.7 mm does not yield additional benefits, particularly for the front side one. In addition, other important BOM features such as the number of busbars are analyzed. This study provides a blueprint for utilizing explainable machine learning techniques in a complex material system and can potentially guide future research on optimizing the design of solar modules.

14 SOLAR ENERGY↗

Quantifying the effect of tow architecture variability on the performance of biaxially braided composite tubes

Targeted experiments are performed with stereoscopic digital image correlation to quantify the effect of irregular braid structure on the local surface mechanical response of carbon-fiber reinforced epoxy composite tubes. Virtual models comparing both nonuniform and uniform tow structure of the outer braid of each specimen are integrated into numerical simulations similar to experiments. Experimental and numerical results agree well. Statistical tests are used to support correlations between as-manufactured braid variation ranges to local increases in stress up to 18% compared to an ideal, uniform structure in the elastic regime. Results support improved manufacturing and modeling efforts of defect sensitive braided composites.

36 MATERIALS SCIENCE↗

Systematics in the XENON1T data: The 15-keV anti-axion

The XENON1T collaboration Aprile et al. [2020] has found an excess of electron recoil events in their Science Run 1 data below ~7 keV with a spectral shape consistent with that expected from a solar-axion-induced signal. The claimed statistical significance of the solar-axion model over the null hypothesis is 3.5σ. In this work we provide suggestive evidence for mismodeling in the electron recoil data that may decrease the local significance of the axion model. To reach this conclusion, we search for a signal with the spectral template of the solar axion model, but shifted to higher (unphysical) energies above ~7 keV. We find that the distribution of significances found from this side-band analysis does not follow the expected chi-square distribution. For example, we find a high-significance feature in the data, with a global $p$-value $p≈0.026$, when the solar axion model is shifted upwards in energy by ~15 keV and allowed to have a negative normalization. We argue that such statistical tests, if performed a priori, provide a data-driven way to test and potentially account for systematic uncertainties on the background model in low-threshold dark matter experiments.

79 ASTRONOMY AND ASTROPHYSICS↗

Machine learning-enhanced hybrid modeling approach for better identification of a building thermal network model and improved prediction

The gray-box modeling approach, which uses a semi-physical thermal network model, has been widely used in building prediction applications, such as model predictive control (MPC). However, unmeasured disturbances, such as occupants, lighting, and in/exfiltration loads, make it challenging to apply this approach to practical buildings. In this word, we propose a hybrid modeling approach that integrates the gray-box model with a model for unmeasured disturbance. After reviewing several system identification approaches, we systematically designed the unmeasured disturbance model with a model selection process based on statistical tests to make it robust. We generated data based on the building model calibrated by real operational data and then trained the hybrid model for two different weather conditions. The hybrid model approach demonstrates an RMSE reduction of approximately 0.2–0.9 °C and 0.3–2 °C on 1-day ahead temperature prediction compared to the Conventional approach for mild (Berkeley, CA) and cold (Chicago, IL) climates, respectively. In addition, this approach was applied to experimental data obtained from the laboratory building to be used for the MPC application, showing superior prediction performances.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

An update to the Sandia method for creating Typical Meteorological Years from a limited pool of calendar years

Typical Meteorological Years (TMYs) are essential for the efficient evaluation of energy system performance. Ideally, 30 years of weather data are required to generate TMYs, but significantly fewer years are typically available due to practical limitations. To address this issue, an update to the Sandia method was developed, referred to as the Argonne method, to create TMYs from a limited number of years. Furthermore, this method enhances candidate diversity by systematically shifting original candidate months forward or backward by specific days, creating an expanded pool of candidates. The effectiveness of the Argonne method was validated through statistical testing, comparison of monthly average weather parameters, and numerical simulations. The results demonstrate a high probability of identifying at least one shifted month whose cumulative distribution functions of weather parameters closely align with long-term distributions. In 67 % of all comparisons, the monthly average weather parameters in TMYs generated using the Argonne method exhibit better agreement with long-term averages than TMY3. Moreover, in 74 % of the 318 building simulation cases, the Argonne method outperforms TMY3 in estimating long-term average building heating and cooling demands. Therefore, the Argonne method effectively diversifies the candidate pool and produces typical years that provide more accurate estimations of long-term averages compared to TMY3 when only a limited pool of calendar years (10 years or fewer) is available.

Building energy modeling↗

The composition of gases from a diffusion flame above longleaf pine needle fuel beds

The gas and tar composition of a diffusion flame from longleaf pine needles is currently poorly understood and more data are needed to fill in the gap between pyrolysis data and smoke plume data, thus improving physical and chemical modeling of wildland smoke formation. A pilot experiment to measure light gas and tar composition of such a flame is described for three flame regions: persistent flame (flame base), intermittent flame, and smoke plume. Flame gases from 24 experimental fires were collected in canisters and analyzed using EPA method TO-14A for CO 2 , CO, H 2 , CH 4 , and C 2 to C 7 hydrocarbon gases. Condensed gas (tar) samples were collected and analyzed using GC/MS. Other light gases were measured using FTIR spectroscopy. Results from compositional data analysis suggest significant differences in (relative) concentration of compounds detected in the three regions of the flame. Statistical tests for differences in flame zones were performed using the canister data: Concentration of hydrocarbons relative to CO and CO 2 decreased from the persistent flame zone above the pyrolyzing needles through the intermittent flame region into the flame-free plume. This was likely due to both chemical reactions (oxidation) occurring in the flame as well as the introduction of air into the flame/plume by entrainment.

Biomass↗

On the transferability of residence time distributions in two 10-km long river sections with similar hydromorphic units

Quantifying hydrologic exchange fluxes (HEFs) at the stream-groundwater interface and their residence time distributions (RTDs) in the subsurface are important for managing the water quality and ecosystem health in dynamic river corridors. However, direct simulating high-spatial resolution HEFs and RTDs can be time-consuming, especially for watershed-scale modeling. Efficient surrogate models linking RTDs to hydromorphic units (HUs) can be alternatives for simulating RTDs in large-scale models. A common concern of these surrogate models, though, is the transferability of the relationship between the RTDs and HUs from one river corridor to another. To address this issue, this work evaluates the HEFs and resulting RTD-HU relationships for two 10-km long river corridors along the Columbia River leveraging a one-way coupled three-dimensional transient surface-subsurface water transport modeling framework we previously developed. Applying such a framework at the two river corridors with similar HUs allows for quantitative comparisons of HEFs and RTDs using both statistical tests and machine learning classification models. Finally, our comparison shows that the similarity and transferability of the RTD-HU relationship is very low for the two investigated river sections, which suggests that devising a general algorithm to estimate RTDs based solely on surface water hydrodynamics and short-distance river channel topography data, as well as HU classification, might be nearly impossible.

54 ENVIRONMENTAL SCIENCES↗

Irradiation creep measurement and microstructural analysis of chromium nitride–coated zirconium alloy using pressurized tubes

Environmental barrier coatings for Zr-based materials are currently under development to reduce oxidation and embrittlement in light-water reactors. Chromium nitride is one such candidate for this application, particularly as accident-tolerant fuel cladding. However, quantifying the impact of coatings on the irradiation-induced creep of zircaloy (Zry) is critical as this mechanism often exceeds thermal creep rates under light-water reactor operating conditions and can be a limiting design characteristic. Additionally, examining irradiation effects in the microstructure at the coating interface is key to understanding the compatibility of the material system. Here, to accelerate the experimental measurement of irradiation creep and microstructure evolution in CrN-Zry, compact, pressurized creep tubes were fabricated and irradiated in the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory. Miniature, thin-walled rodlets fabricated from annealed Zr-Sn barstock were coated with CrN using physical vapor deposition (PVD) to nominal thicknesses of 4 and 8 μm. Coated and uncoated rodlet specimens were internally pressurized and welded, generating nominal circumferential hoop stresses of 0, 90, or 180 MPa under 300°C irradiation conditions. Twelve specimens were measured diametrically prior to irradiation using a low-cost, automated, contactless laser profilometer developed for this work. Specimens were irradiated in sealed capsules for one 25-day HFIR cycle, accumulating approximately 1.8 $\times$ 10 21 n/cm 2 fast fluence (E n > 10 MeV). The irradiated samples were retrieved and remeasured using the same profilometry system in a shielded hot cell facility. Irradiation creep between specimens was compared using standard statistical tests and showed that both thicknesses of CrN coating had a negligible effect on the irradiation creep strain of the Zry material. Microstructure characterization of pre- and post-irradiated CrN-Zry specimens showed minimal changes due to irradiation but did show a substantial O-rich region at the Zry-CrN interface.

36 MATERIALS SCIENCE↗

Shared micromobility as a first- and last-mile transit solution? Spatiotemporal insights from a novel dataset

The first- and last-mile (FM/LM) problem is a major deterrent to public transit use. With the rise of shared micromobility options such as shared e-scooters in recent years, there is a growing interest in understanding their potential to serve as a last-mile transit solution. However, empirical data regarding the integrated use of shared micromobility and public transit have been limited so far. As a result, much is unknown regarding the spatiotemporal patterns and characteristics of shared micromobility trips serving as an FM/LM connection to transit. Here, this paper addresses these knowledge gaps by leveraging a novel dataset (i.e., the Spin post-ride survey dataset) that records thousands of transit-connecting shared e-scooter trips in Washington DC. Specifically, we used the dataset to reveal the spatiotemporal patterns of transit-connecting shared e-scooter trips in Washington DC, resulting in some major policy insights regarding the integral use of shared e-scooters and public transit. We further leveraged the dataset to validate if and to what extent a commonly applied buffer-zone approach can infer FM/LM micromobility trips accurately. Statistical tests showed that the actual FM/LM Spin e-scooter trips differ from inferred FM/LM Spin e-scooter trips in both spatial and temporal dimensions. This indicates that the common practice of inferring FM/LM micromobility trips with a buffer-zone approach can lead to inaccurate estimates of transit-connecting micromobility trips.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Identifying paleowater in California drinking water wells

Identification of paleowater in aquifers tapped for the public water supply is important both for sound water management, because paleowater is likely to be withdrawn unsustainably in high demand regions in the absence of large scale artificial recharge operations, and for contamination susceptibility assessment, because paleowater is typically isolated from contamination sources. In this study, paleowater, which herein includes pre-Holocene groundwater and also water that recharged well before the onset of significant human alteration of the hydrologic system in California, is identified using three key isotopic indicators of groundwater residence time: tritium ( 3 H), radiocarbon ( 14 C), and radiogenic helium-4 ( 4 He rad ). In this work, we compared results of these three tracers from a unique data set of more than 2000 wells that are predominantly long-screened drinking water production wells. Although considerable uncertainty is associated with calculated apparent ages for individual samples, non-parametric statistical tests indicate that the composite set of isotopic indicators support classification of samples into categories that allow identification of wells most likely to produce paleowater. Approximately 7% of the wells included in the study show strong evidence for producing paleowater, with screens extending greater than 146 m below ground surface, in which 3 H activity is less than 1 pCi/L, 14C activity is less than 40.9 pmC, and 4Herad concentration exceeds 7.4 × 10 –8 cm 3 STP/g water . An additional 22% of wells produce mixed-age water with a component of paleowater, with screens extending greater than 95 m below ground surface, in which 3 H is less than 5 pCi/L, and 14C activity is less than 95.91 pmC. Wells in desert basins of southeastern California and wells in the southwestern quadrant of the Central Valley are most likely to produce paleowater that is pre-Holocene in age. Very few wells in the northwestern portion of the state, the foothills and Sierra Nevada regions, and coastal basins with intensive artificial recharge activities are categorized as producing paleowater. Climate is the primary control on paleowater occurrence, with arid portions of the state that were wetter during the Pleistocene having the largest number of wells categorized as producing paleowater. Secondarily, paleowater is found at the end of very long flow paths in confined aquifers, e.g., in the center of the Northern Sacramento Valley. In contrast, paleowater may be masked in areas where unconfined or semi-confined conditions allow substantial mixing between modern recharge and paleowater. Modern, artificially recharged water has replaced very old groundwater on a large scale in urban coastal basins.

54 ENVIRONMENTAL SCIENCES↗

Detecting Thermally Induced Spinodal Decomposition with Picosecond Ultrasonics in Cast Austenitic Stainless Steels

Given the existential climate crisis faced by mankind and the world, the lifetime and sustainability of nuclear reactors as a carbon-free source of renewable energy depend on the susceptibility of their structural components to environmental degradation. In particular, critical components for light water reactors (LWRs) evolve over decades in service, losing ductility and toughness due to thermal and irradiation aging. Techniques to monitor their health cannot be easily applied in the field due to their destructive, expensive, or immobile nature. Thus, non-destructive evaluation (NDE) methods are sought to monitor and evaluate the health of major LWR components such as core barrels, steam generator tubes, or primary coolant pipes and are often required by policy, such as NRC policy #10-CFR-50.65. In this work we demonstrate the use of gigahertz, non-contact ultrasonics to gauge the state of cast austenitic stainless steels (CASS), used in some of the largest components in LWR primary systems. We do so by linking changes in their surface acoustic wave (SAW) characteristics using transient grating spectroscopy (TGS) to transmission electron microscopy (TEM)-verified evidence of spinodal decomposition and G-phase precipitation. In this thesis, thermal aging is shown to induce SAW peak splitting in spinodally decomposed CASS alloys, correlated strongly with lowered toughness and decreased ductility. Furthermore, statistical testing on the number of SAW peak splits observed show that the second SAW peak significantly appears more frequently and is significantly different in frequency in comparison to counts and frequencies measured in unaged specimens. The ability of this technique to non-destructively detect microstructural degradation at a distance in a predictive manner in the case of CASS motivates extending gigahertz ultrasonics to detect other LWR material degradation modes as an in-vessel inspection technique, such as reactor pressure vessel (RPV) embrittlement. This allows for the greater use of NDE techniques for confident monitoring of LWR structural material health to 80 years and beyond, saving costs by minimizing structural replacements until needed and maximizing energy production by preventing early decommission until necessary.

36 MATERIALS SCIENCE↗

Proteomic Profiling of the Substantia Nigra to Identify Determinants of Lewy Body Pathology and Dopaminergic Neuronal Loss

Proteinaceous aggregates containing ?-synuclein protein called Lewy bodies in the substantia nigra is a hallmark of Parkinson’s disease. The molecular mechanisms of Lewy body formation and associated neuronal loss remain largely unknown. To gain insights on proteins and pathways associated with Lewy body pathology, we performed quantitative profiling of the proteome. We analyzed substantia nigra tissue from 51 subjects arranged into three groups: cases with Lewy body pathology, Lewy body-negative controls with matching neuronal loss and controls with no neuronal loss. Using label-free LC-MS/MS approach we quantified the 2,963 most abundant proteins. Statistical testing for differential protein abundance, followed by pathway enrichment and Bayesian learning of the causal network structure were performed to identify likely drivers of Lewy body formation and dopaminergic neuronal loss. The identified pathways include (1) Arp2/3 complex-mediated actin nucleation; (2) synaptic function; (3) poly(A) RNA binding; (4) basement membrane and endothelium; and (5) hydrogen peroxide metabolic process. According to the data, the endothelial/basement membrane pathway is tightly connected with both pathologies and likely to be one of the drivers of the neuronal loss. The poly(A) RNA-binding proteins, including the ones relevant to other neurodegenerative disorders (e.g. TDP-43 and FUS) have strong inverse correlation with Lewy bodies and may reflect alternative mechanism of nigral neurodegeneration.

Petyuk, Vladislav A.↗

Rapidly Assessing the Quality of Targeted Proteomics Experiments through Monitoring Stable-Isotope Labeled Standards

Selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), is a data acquisition technique used in targeted analysis of molecules, including targeted proteomic studies. It exploits the unique capability of triple-quadrupole (QQQ) mass spectrometers to monitor the predefined precursor and fragment ion pairs of specific molecules of interest throughout a liquid chromatography (LC) elution profile. Compared to shotgun proteomics, targeted proteomics using SRM has high selectivity, high sensitivity, and a wide linear dynamic range,(1-3) which makes it especially useful in the accurate and reproducible quantification of low-abundance proteins in highly complex biological samples. SRM has been widely used in the fields of biomarker discovery,(4-7) analysis of protein post-translational modifications(8) and characterization of biological protein networks.(4,9) In the recent years, multiple technical advances have greatly improved the throughput of SRM analyses, allowing for the quantification of hundreds of peptides in a single analysis.(6,7,10) For example, a single 800-plex SRM assay (e.g., 400 unlabeled and heavy-labeled peptide pairs and 2400 transitions with retention time scheduling) using ultrahigh-performance liquid chromatography (UHPLC) has been developed to quantify proteins in plasma.(11) Advanced labeling techniques utilizing in vitro proteome-assisted MRM for protein absolute quantification (iMPAQT) demonstrated the capability of SRM in genome-wide protein quantification of over 18?000 human proteins.(12) Moreover, the scan speed of QQQ instrumentation has been greatly improved in recent releases of commercial instrumentation. The newly developed TSQ Altis (released in 2017) can scan more than 600 transitions per second, which is 6 times more than a traditional QQQ scan speed of 100 transitions per second. The breadth of measurement enabled by these technological improvements to QQQ mass spectrometry has increased the feasibility and popularity of large scale targeted proteomics studies,(13) a major application of which will be in clinical studies in which up to hundreds of protein candidates need to be quantified in hundreds of clinical specimens.(14) Quantitative accuracy is a primary motivating factor for utilizing a targeted proteomics protocol. The precise and reproducible absolute quantification produced by SRM assays is essential to many clinical and laboratory experiments.(15,16) Because the abundance of an endogenous peptide is calculated from the measurement of the spiked-in reference standard, it is essential to assess the data quality of these references.(17) In early applications of targeted proteomics, when instrument speed greatly limited the number of transitions that could be monitored, much of this quality assessment was done manually. However, recent improvements in instrument performance and experimental design have enabled a dramatic increase in the number of target peptides and associated SRM transitions, which makes manual quality assessment an untenable and laborious task. A variety of computational tools assist in SRM experiment design and data analysis. The first task in creating an SRM experiment is the choice of proteins and representative peptides to monitor. Achieving a reliable protein abundance requires appropriately choosing peptides that have a strong signal and are free from interferences in the biological matrix. Numerous computational tools exist to facilitate assay design by identifying peptides and refining SRM transitions.(18-21) To help share these assays and eliminate time spent designing the same transitions at multiple institutions, community portals have begun to host well-designed and vetted assays.(22-24) Analyzing the experimental data requires significant computational effort to align files across replicates and experimental conditions, pick peaks and produce quantitative values, normalize data and perform statistical tests, etc.(25-27)

Gibbons, Bryson C.↗