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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.

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At least 1,243 records · Page 69
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Quantifying the Variation in the Number of Donors in Quantum Dots Created Using Atomic Precision Advanced Manufacturing

Atomic-precision advanced manufacturing enables unique silicon quantum electronics built on quantum dots fabricated from small numbers of phosphorus dopants. The number of dopant atoms comprising a dot plays a central role in determining the behavior of charge and spin confined to the dots and thus overall device performance. Here in this work, we use both theoretical and experimental techniques to explore the combined impact of lithographic variation and stochastic kinetics on the number of P incorporations in quantum dots made using these techniques and how this variation changes as a function of the size of the dot. Using a kinetic model of PH3 dissociation augmented with novel reaction barriers, we demonstrate that for a 2 × 3 silicon dimer window the probability that no donor incorporates goes to zero, allowing for certainty in the placement of at least one donor. However, this still comes with some uncertainty in the precise number of incorporated donors (either one or two), and this variability may still impact certain applications. We also examine the impact of the size of the initial lithographic window, finding that the incorporation fraction saturates to δ-layer-like coverage as the circumference-to-area ratio decreases. We predict that this incorporation fraction depends strongly on the dosage of the precursor and that the standard deviation of the number of incorporations scales as ~√n, as would be expected for a sequence of largely independent incorporation events. Finally, we characterize an array of 36 experimentally prepared multidonor 3 × 3 nm lithographic windows with scanning tunneling microscopy, measuring the fidelity of the lithography to the desired array and the final location of PH x fragments within these lithographic windows. We use our kinetic model to examine the expected variability due to the observed lithographic error, predicting a negligible impact on incorporation statistics. We find good agreement between our model and the inferred incorporation locations in these windows from scanning tunneling microscope measurements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Interrupted DNA and Slow Silver Cluster Luminescence

A DNA–silver cluster conjugate is a hierarchical chromophore with a partly reduced silver core embedded within the DNA nucleobases that are covalently linked by the phosphodiester backbone. Specific sites within a polymeric DNA can be targeted to spectrally tune the silver cluster. Here, the repeated (C 2 A) 6 strand is interrupted with a thymine, and the resulting (C 2 A) 2 -T-(C 2 A) 4 forms only Ag 10 6+ , a chromophore with both prompt (~1 ns) green and sustained (~10 2 μs) red luminescence. Thymine is an inert placeholder that can be removed, and the two fragments (C 2 A) 2 and (C 2 A) 4 also produce the same Ag 10 6+ adduct. In relation to (C 2 A) 2 T(C 2 A) 4 , the (C 2 A) 2 + (C 2 A) 4 pair is distinguished because the red Ag 10 6+ luminescence is ~6× lower, relaxes ~30% faster, and is quenched ~2× faster with O 2 . These differences suggest that a specific break in the phosphodiester backbone can regulate how a contiguous vs broken scaffold wraps and better protects its cluster adduct.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Theoretical Investigation of the Hydrogenation of Cyclohexene Catalyzed by Supported Single-Atom Sites on Redox Noninnocent LiMn 2 O 4 and Li 2 Mn 2 O 4 Surfaces

Here, the tuning of catalyst activity via stereoelectronic modulation of the active-site structure remains a grand challenge in heterogeneous catalysis. In homogeneous catalysis, the redox noninnocent ligands can be introduced to organometallic fragments to donate electrons to the metal center and fine-tune the catalytic activity. Analogously, lithium-ion battery materials, such as lithium manganese oxide (LMO), lithium titanium oxides (LTO), etc., can serve as redox noninnocent catalyst support to modulate the electronic structures of the active site via lithiation, hence tuning the catalytic activity of supported active sites. Experimentally, the Ni single-atom site was supported on LiMn 2 O 4 via oxidative grafting and exhibited no catalytic activity toward the hydrogenation of cyclohexene. After introducing additional Li into the catalyst support forming Li 2 Mn 2 O 4 , the Ni single-atom site becomes active, with the catalytic rates increasing as a function of the lithiation for Li/Mn ratios >0.9. In this paper, density functional theory (DFT) calculations are performed to study the Ni site structure via X-ray absorption near edge structure (XANES) simulations and investigate the electronic properties of Ni single-atom site before and after the addition of intercalated lithium in the LMO spinel structure. Furthermore, the study of the reaction mechanism is also carried out to understand the thermodynamically and kinetically favored pathways. XANES simulation suggests that the Ni single-atom site is likely to stay in the Li channel of the spinel support structure and form an octahedral structure. After Li intercalation, the Ni site becomes less positively charged, indicating the partial reduction of the Ni site. The simulated reaction energy profile over the LiMn 2 O 4 support exhibits high-energy barriers (1.07 eV) for the hydrogenation of cyclohexene; however, the Li 2 Mn 2 O 4 support is able to better stabilize low-coordinated ion sites and improve ion mobility, leading to lower overall energy barriers (0.64 eV). The reduced and low-coordinated ion site, thus, can better stabilize the reaction intermediates and promote hydrogenation reaction. Similarly, other transition metal ions (Fe, Co, and Cu) are also considered over the LiMn 2 O 4 and Li 2 Mn 2 O 4 catalyst supports for hydrogenation reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Nonorthogonal Configuration Interaction for Singlet Fission: Beyond the Dimer

Non-orthogonal configuration interaction with fragment calculations are presented for a number of compounds that show singlet fission properties: (i) four perylene-diimide derivatives, (ii) crystalline pentacene and its (B,N)-substituted variant, and (iii) a regular and a distorted stack of three indolonaphthyridine molecules. The electronic couplings between the singlet excitonic states (S 1 ) and the singlet-coupled double triplet (T 1 T 1 ), the so-called singlet fission coupling, were computed from ensembles with two and three molecules, and except for some small deviations when charge transfer states were included, results are virtually the same. Ensembles of three molecules were used to study the mechanisms of triplet separation, double triplet diffusion, and singlet and triplet exciton diffusion. The calculations show that apart from the standard mechanism for the generation of two uncoupled triplet states (S 1 → T 1 T 1 → T 1 ...T 1 ), there are two other possible pathways: the direct generation from the singlet excitonic state (S 1 → T 1 ...T 1 ) and the process in which the excitonic state evolves in a superposition of T 1 T 1 and T 1 ...T 1 states. Furthermore, the electronic coupling for triplet diffusion is in general much smaller than for singlet diffusion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

The Surface Chemistry of Methanol on TiO 2 (110): Effects of Pressure and Temperature on the Stability of C–O and C–H Bonds

Synchrotron-based ambient pressure X-ray photoelectron spectroscopy (AP-XPS) was used to study the surface chemistry of methanol on TiO 2 (110), examining the effects of methanol pressure, oxide temperature, and coadsorption with H 2 . At 300 K, the adsorption of methanol on TiO 2 (110) leads to the formation of CH 3 O on the surface with a minor amount of CH 3 OH present. The easy cleavage of the O–H bond in the alcohol agrees with the predictions of theoretical calculations, and most of the adsorbed CH 3 O was not associated with the presence of Ti 3+ sites in the oxide substrate. The adsorbed CH 3 O was removed from the TiO 2 (110) surface by heating to 600 K without the deposition of CH x fragments or C on the oxide. The results of temperature-programmed desorption (TPD) showed the evolution of methanol and formaldehyde at 360 and 490 K as a result of a disproportionation reaction: 2CH 3 O → CH 3 OH + CH 2 O. This surface chemistry, where there is no rupture of the C–O bond, and only selective cleavage of O–H and C–H bonds, is very different from that found on metals used in catalysts for methanol reforming, where massive conversion of the alcohol into CO, CH x and C species is seen. Furthermore, the TPD data indicate that any CH 3 O formed on the oxide surface can be hydrogenated and desorbed as CH 3 OH at temperatures below 550 K. In this respect, titania is an ideal support for catalysts employed to achieve methanol synthesis through CO 2 hydrogenation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Screening of Therapeutic Agents for COVID-19 Using Machine Learning and Ensemble Docking Studies

The current pandemic demands a search for therapeutic agents against the novel coronavirus SARS-CoV-2. In this work, we present an efficient computational strategy that combines machine learning (ML)-based models and high-fidelity ensemble docking studies to enable rapid screening of possible therapeutic ligands. Targeting the binding affinity of molecules for either the isolated SARS-CoV-2 S-protein at its host receptor region or the S-protein:human ACE2 interface complex, we screen ligands from drug and biomolecule data sets that can potentially limit and/or disrupt the host-virus interactions. Top scoring one hundred eighty-seven ligands (with 75 approved by the Food and Drug Administration) are further validated by all atom docking studies. Important molecular descriptors ( 2 χ n , topological surface area, and ring count) and promising chemical fragments (oxolane, hydroxy, and imidazole) are identified to guide future experiments. Overall, this work expands our knowledge of small-molecule treatment against COVID-19 and provides a general screening pathway (combining quick ML models with expensive high-fidelity simulations) for targeting several chemical/biochemical problems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Differentiating and Quantifying Gas-Phase Conformational Isomers Using Coulomb Explosion Imaging

Conformational isomerism plays a crucial role in defining the physical and chemical properties and biological activity of molecules ranging from simple organic compounds to complex biopolymers. However, it is often a significant challenge to differentiate and separate these isomers experimentally as they can easily interconvert due to their low rotational energy barrier. Here, we use the momentum correlation of fragment ions produced after inner-shell photoionization to distinguish conformational isomers of 1,2-dibromoethane (C 2 H 4 Br 2 ). We demonstrate that the three-body breakup channel, C 2 H 4 + + Br + + Br + , contains signatures of both sequential and concerted breakup, which are decoupled to distinguish the geometries of two conformational isomers and to quantify their relative abundance. The sensitivity of our method to quantify these yields is established by measuring the relative abundance change with sample temperature, which agrees well with calculations. Finally, our study paves the way for using Coulomb explosion imaging to track subtle molecular structural changes.

Photoionization↗
DOE OSTI2021

Ion Mobility Spectrometry Characterization of the Intermediate Hydrogen-Containing Gold Cluster Au7(PPh3)7H52+

We employ ion mobility spectrometry and density functional theory to determine the structure of Au7(PPh3)7H52+ (PPh3 = triphenylphosphine) which was recently identified by high mass resolution mass spectrometry. Experimental ion-neutral collision cross sections represent the momentum transfer between the ionic clusters and gas molecules averaged over the relative thermal velocities of the colliding pair, thereby providing structural insights. Theoretical calculations indicate the geometry of Au7(PPh3)7H52+ is similar to Au7(PPh3)7+, with three hydrogen atoms bridging two gold atoms and two hydrogen atoms forming single Au–H bonds. Collision induced dissociation products observed during IMS experiments reveal that smaller hydrogen containing clusters may be produced through fragmentation of Au7(PPh3)7H52+. Our findings indicate that hydrogen containing species like Au7(PPh3)7H52+ act as intermediates in the formation of larger phosphine ligated gold clusters. These results advance the understanding and ability to control the mechanisms of size selective cluster formation which is necessary for scalable synthesis of clusters with tailored properties. This work was supported by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. M.A.H. acknowledges support from the DOE Science Undergraduate Laboratory Internship (SULI) program. H.H. acknowledges support from the DOE Office of Workforce Development for Teachers and Scientist (WDTS) under the Visiting Faculty Program (VFP). The efforts of K.A.M. and B.H.C. were supported by the Defense Threat Reduction Agency (Grant No. HDTRA1-14-1-0023). The research was performed using EMSL, a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for DOE under Contract DE-AC05-76RL01830.

Ligare, Marshall R.↗
DOE OSTI2022

Modeling Absolute Redox Potentials of Ferrocene in the Condensed Phase

Absolute thermodynamic quantities for critical chemical reactions are needed to determine the role of solvents and reactive environments in catalysis and electrocatalysis beyond the relative scales typically employed. In principle, theoretical methods can provide such quantification but are often hindered by the innate complexity of strong electron correlation and dynamic relaxation of solvent environments. Here, we present and validate a protocol for calculating the redox potentials of ferrocene/ferrocenium redox pair in the acetonitrile. Equation-of-motion ionization potential coupled-cluster single-double (EOM-IP-CCSD) and effective fragment potential (EFP) methods are used to characterize the adiabatic and vertical ionization potentials (IP) as well as the electron affinity processes. We benchmark molecular mechanics against the EFP model to show the differences in ferrocene electronic polarizability in two redox states. Our best estimate of the redox potential (4.94 eV) agrees well with the experimental value (4.93 eV). This demonstrated the ability of modern computational methods to predict absolute redox potentials quantitatively and, more critically, quantify the correlation of dynamic effects, which underlie their origin.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Triple Excitations in Green’s Function Coupled Cluster Solver for Studies of Strongly Correlated Systems in the Framework of Self-Energy Embedding Theory

Embedding theories became important approaches used for accurate calculations of both molecules and solids. In these theories, a small chosen subset of orbitals is treated with an accurate method, called an impurity solver, capable of describing higher correlation effects. Ideally, such a chosen fragment should contain multiple orbitals responsible for the chemical and physical behavior of the compound. Handling a large number of chosen orbitals presents a very significant challenge for the current generation of solvers used in the physics and chemistry community. Here, we develop a Green’s function coupled cluster singles doubles and triples (GFCCSDT) solver that can be used for a quantitative description in both molecules and solids. This solver allows us to treat orbital spaces that are inaccessible to other accurate solvers. At the same time, GFCCSDT maintains high accuracy of the resulting self-energy. Moreover, in conjunction with the GFCCSD solver, it allows us to test the systematic convergence of computational studies. Developing the CC family of solvers paves the road to fully systematic Green’s function embedding calculations in solids. In this paper, we focus on the investigation of GFCCSDT self-energies for a strongly correlated problem of SrMnO 3 solid. Subsequently, we apply this solver to solid MnO showing that an approximate variant of GFCCSDT is capable of yielding a high accuracy orbital resolved spectral function.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

The Surface Chemistry of Methanol on Pd(111) and H–Pd(111) Surfaces: C–O Bond Cleavage and the Effects of Metal Hydride Formation

Palladium catalysts are frequently employed in processes where methanol is an energy vector or carrier, being useful for the synthesis of methanol from mixtures of carbon dioxide and hydrogen (CO 2 /H 2 ) or its steam reforming on demand. Results of synchrotron-based ambient pressure X-ray photoelectron spectroscopy for the adsorption of methanol on a Pd(111) model catalyst show a rich surface chemistry and complex phenomena that strongly depend on pressure and temperature. At low pressures (< 10 -6 Torr) and temperatures (< 300 K), CO is the dominant decomposition product. Further, as the pressure increases, cleavage of C-H, O-H and C-O bonds is observed, and at elevated temperatures (400-600 K) the formation of CO and CH x /C fragments compete on the surface. Thus, existing reaction networks for methanol decomposition must be modified. Furthermore, surface and subsurface hydrogen (coming from PdH x ) play a significant role in the stability and removal of CH x and C species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Origin of Stabilization of Ligand-Centered Mixed Valence Ruthenium Azopyridine Complexes: DFT Insights for Neuromorphic Applications

Redox-driven conductance changes are critical processes in molecular- and coordination-complex-based memristive thin films and devices that are envisioned for neuromorphic technologies, but fundamental mechanisms of conductance switching are not fully understood. Here, we explore charge disproportionation (CD) processes in [Ru II L 2 ](PF 6 ) 2 molecular systems that intrinsically involve interfragment charge transfer (IFCT). Using a combination of ab initio molecular dynamics simulation (AIMD), time-dependent density functional theory (TD-DFT), and density functional theory (DFT) calculations, we investigate the electron transfer mechanisms and the roles of temperature and cell volumetric expansion in facilitating the counterion movements and electronic transitions required for low-cost IFCT and charge redistribution. A detailed analysis of the density of states and TD-DFT calculations highlights that unpaired electrons play a crucial role in low-energy transitions, with the azo (N=N) groups of the ligand serving as the primary sites for electronic transport between molecular fragments, further stabilizing the asymmetric state. Localization of added electrons on azo ligands occurs with negligible change at the Ru centers, supported by atomic volume expansions up to +4.74 bohr 3 , and goes along with a progressive reduction of the HOMO−LUMO gap across redox states, suggesting enhanced conductivity. The TD-DFT analysis reveals a dominant IFCT excitation at 2082.76 nm in the doubly reduced (22) state, while a stabilization energy of 1.20 eV of the asymmetric (13) state relative to the symmetric (22) state is predicted by constrained DFT. Periodic DFT and AIMD simulations emulating a molecular film show that the stabilization of the asymmetric state, relative to a symmetric one, translates in net charge separation values (order of ∼0.33 e) that are strongly linked to increased counterion mobility (average counterion displacements exceeding 0.7 Å per atom during CD events) and the involvement of azo groups in electron redistribution. These findings, which align with previously reported experimental and computational data, provide key insights into the IFCT mechanisms and electronic transport facilitated by azo groups, with important implications for redox-driven memristive and neuromorphic technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Resolving Competing Ultraviolet Photoinduced Ring-Opening and Dissociation Pathways in Iodothiophenes by Ultrafast Electron Diffraction

The ultraviolet photochemistry of halothiophenes is thought to proceed via competing pathways, prompt C–X (X = halogen) bond fission, and parent ring opening followed by fragmentation, yet direct structural evidence distinguishing these mechanisms is limited. Here, time-resolved gas-phase ultrafast electron diffraction (UED) has been used to directly follow the structural dynamics of 2- and 3-iodothiophene following photoexcitation at 247 nm. For both isomers, the time-resolved pair distribution functions reveal the appearance of new interatomic distances that cannot be explained by simple C–I bond cleavage and formation of C 4 SH 3 radical cofragments. The signatures, particularly those for 2-iodothiophene, are consistent with a rival ring-opening channel of the intact parent, which evolve on time scales distinct from those associated with the direct C–I bond cleavage. In addition, the extracted kinetics indicate that the ring-opening channel occurs faster in 2-iodothiophene than in the 3-isomer at this excitation wavelength. Furthermore, these measurements provide direct geometric evidence for competing pathways leading to different structures following photodissociation in a model heteroaromatic and further establish UED as a sensitive probe of complex excited-state chemistry.

Bond cleavage↗
DOE OSTI2021

TMTpro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level

Multiplexed proteomics is a powerful tool to assay cell states in health and disease, but accurate quantification of relative protein changes is impaired by interference from co-isolated peptides. Most widely, this issue is alleviated by MS3-based quantification, reducing sensitivity and requiring specialized instrumentation. An alternative approach is quantification by complementary ions, which allows accurate and precise multiplexed quantification at the MS2 level and is compatible with the most widely distributed instruments. However, complementary ions of the popular TMT tag form inefficiently and plexing is limited to five channels. In this work, we evaluate and optimize complementary ion quantification for the recently released TMTPro tag, which increases plexing capacity to 8 channels (TMTProC). We find that the beneficial fragmentation properties increase quantification signal five-fold compared to TMT. This increased sensitivity results in ~50% more proteins quantified compared to TMTPro-MS3 and even slightly outperforms TMTPro-MS2. Furthermore, TMTProC quantification is more accurate than TMTPro-MS2 and even superior to TMTPro-MS3. To demonstrate the power of TMTProC, we analyzed a human and yeast interference sample and were able to quantify 13,290 proteins in 24 fractions. Thus, TMTProC advances multiplexed proteomics data quality and widens access to accurate multiplexed proteomics beyond laboratories with MS3-capable instrumentation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection

Generating top-down tandem mass spectra (MS/MS) for complex mixtures of proteoforms has become possible through improvements in fractionation, on-line separation, dissociation, and mass analysis. The algorithms to match tandem mass spectra to sequences have undergone a parallel evolution, with both spectral alignment and peak matching being paired with diverse methods for scoring proteoform-spectral matches (PrSMs). This study assesses state-of-the-art algorithms for top-down identification through three distinct challenges. The first is identifying a large yield of PrSMs while controlling false discovery rate (FDR) in identifying thousands of proteoforms from complex cell lysates via four software workflows: ProSight Proteome Discoverer, TopPIC, Informed Proteomics, and pTop. The second is the deconvolution of data from both Thermo Orbitrap-class and Bruker maXis Q-TOF instruments to produce consistent precursor charge and mass determinations while generating fragment mass lists to optimize identification. The third attempts to detect diverse post-translational modifications (PTMs) in proteoforms from cow milk and human ovarian tissue. The data demonstrate that existing software suites produce admirable sensitivity, in some cases identifying a third of collected tandem mass spectra with FDR controlled below 2%; the overlap in these PrSMs, however, illustrates real value in searching data with multiple search engines. Differences among identification workflows seem to result from each search algorithm incorporating its own deconvolution algorithm. By transmitting deconvolution data from multiple deconvolution routes (Thermo Xtract, Bruker Auto MSn, Mascot Distiller, TopFD, and FLASHDeconv) to the downstream TopPIC search algorithm, we were able to detect common causes of deconvolution disagreement. The detection of PTMs was very inconsistent among search algorithms, with some workflows suggesting as little as 1% of PrSMs from cow’s milk were singly-phosphorylated while other workflows found that 18% of PrSMs were singly-phosphorylated. Taken together, these results make a strong argument for top-down researchers to adopt a standard practice of analyzing each MS/MS experiment with at least two different search engines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

IsoForma: An R Package for Quantifying and Visualizing Positional Isomers in Top-Down LC-MS/MS Data

Proteoforms, the different forms of a protein with sequence variations including post-translational modifications (PTMs), execute vital functions in biological systems such as cell signaling and epigenetic regulation. Precisely defining the stoichiometry of PTMs has been challenging because, in the widely used bottom-up proteomics methods, the detection occurs at the peptide level and thus the link between peptides and their specific modification site is lost, resulting in proteoform ambiguity. Advances in top-down mass spectrometry (MS) technology have permitted the direct characterization of intact proteoforms and their exact number of modification sites, allowing for the relative quantification of positional isomers (PI). Proteins with positional isomers refers to proteoforms with identical total mass and set of modifications but varying PTM site combinations. The relative abundance of PI can be estimated by matching proteoform-specific fragment ions to top-down tandem MS (MS2) data to localize and quantify modifications. However, current approaches heavily rely on manual annotation. Here, we present IsoForma, an open-source R package for relative quantification of PI within a single tool. We benchmarked IsoForma’s performance against two existing workflows and highlight the similarity of the results and improvements in speed. Overall, IsoForma provides a streamlined process, reduces the time of conducting isoform-based analyses, and offers an essential framework for developing customized proteoform analysis workflows. Finally, the software is open source and available at https://github.com/EMSL-Computing/isoforma-lib.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Aggregation Methods for Quantifying PTM and Structural Changes in Bottom-Up Proteomics

Bottom-up proteomic workflows rely on sequential preprocessing steps, commonly including peptide-to-protein aggregation (“roll-up”), to enhance data reliability and interpretability. While roll-up is effective for protein-centered analyses, it may be suboptimal for applications focused on post-translational modifications (PTMs) or protein structural changes, such as limited proteolysis–mass spectrometry (LiP-MS). Here, we investigate how different roll-up strategies influence site-level quantification in PTM differential analysis. Moreover, we introduce a novel site-centric roll-up approach tailored for LiP-MS, which quantifies proteolytic fragments rather than solely tryptic peptides. We benchmark these methods through simulation studies, comparing their sensitivity and specificity in detecting structural and PTM-driven changes. We found that the median and mean roll-up methods outperform the sum method in both PTM and LiP proteomics, and site-level quantification in LiP outperforms peptide-level quantification. Our findings offer the first systematic, data-driven guidance for selecting roll-up techniques in site-level proteomic analyses, with implications for both PTM-focused and structural proteomics studies.

aggregation↗
DOE OSTI2020

Accurate Identification of Deamidation and Citrullination from Global Shotgun Proteomics Data Using a Dual-Search Delta Score Strategy

While proteins with deamidated/citrullinated amino acids play critical roles in the pathogenesis of many human diseases, identifying these modifications in complex biological samples has been an ongoing challenge. Herein we present a method to accurately identify these modifications from shotgun proteomics data from a deep proteome profiling study of human pancreatic islets obtained by laser capture microdissection. All MS/MS spectra were searched against database by MSGF+ twice with or without a +0.9840 Da mass shift on amino acids asparagine, glutamine, and arginine (NQR) as a dynamic modification. Consequently, for each spectrum the resulting two peptide-to-spectrum matches (PSM) with their respective MSGF+ scores were used for Delta Score calculation. It was observed that all PSMs with positive Delta Score values were clustered with mass errors around 0 ppm, while PSMs with negative Delta Score values were distributed nearly equally within the defined mass error range (20 ppm) for database searching. To estimate false discovery rate (FDR), a “pseudo-decoy” approach was applied whether datasets were searched against a database with a “real modification” mass shift (+0.9840 Da) and a “mock modification” mass shift (+1.0227 Da). FDR was controlled to ~2% with a Delta Score filter greater than zero. Manual inspection of spectra showed that PSMs with positive Delta Score value contained deamidated/citrullinated fragments in their MS/MS spectra. Finally, the results demonstrated that in-situ deamidated/citrullinated peptides can be accurately identified from shotgun tissue proteomics data by the Dual-search Delta Score Strategy.

59 BASIC BIOLOGICAL SCIENCES↗