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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Quality Control Analysis in Real-time (QC-ART): A Tool for Real-time Quality Control Assessment of Mass Spectrometry-based Proteomics Data

Liquid chromatography-mass spectrometry (LC-MS)-based proteomics studies of large sample cohorts can easily require from months to years to complete. Acquiring consistent, high-quality data in such large-scale studies is challenging because of normal variations in instrumentation performance over time, as well as artifacts introduced by the samples themselves, such as those due to collection, storage and processing. Existing quality control methods for proteomics data primarily focus on post-hoc analysis to remove low-quality data that would degrade downstream statistics; they are not designed to evaluate the data in near real-time, which would allow for interventions as soon as deviations in data quality are detected. In addition to flagging analyses that demonstrate outlier behavior, evaluating how the data structure changes over time can aide in understanding typical instrument performance or identify issues such as a degradation in data quality due to the need for instrument cleaning and/or re-calibration. To address this gap for proteomics, we developed Quality Control Analysis in Real-Time (QC-ART), a tool for evaluating data as they are acquired in order to dynamically flag potential issues with instrument performance or sample quality. QC-ART has similar accuracy as standard post-hoc analysis methods with the additional benefit of real-time analysis. We demonstrate the utility and performance of QC-ART in identifying deviations in data quality due to both instrument and sample issues in near real-time for LC-MS-based plasma proteomics analyses of a sample subset of The Environmental Determinants of Diabetes in the Young cohort. We also present a case where QC-ART facilitated the identification of oxidative modifications, which are often underappreciated in proteomic experiments.

Stanfill, Bryan A.↗
DOE OSTI2018

Targeted brain proteomics uncover multiple pathways to Alzheimer's dementia

Objective Previous gene expression analysis identified a network of coexpressed genes that is associated with β‐amyloid neuropathology and cognitive decline in older adults. The current work targeted influential genes in this network with quantitative proteomics to identify potential novel therapeutic targets. Methods Data came from 834 community‐based older persons who were followed annually, died, and underwent brain autopsy. Uniform structured postmortem evaluations assessed the burden of β‐amyloid and other common age‐related neuropathologies. Selected reaction monitoring quantified cortical protein abundance of 12 genes prioritized from a molecular network of aging human brain that is implicated in Alzheimer's dementia. Regression and linear mixed models examined the protein associations with β‐amyloid load and other neuropathological indices as well as cognitive decline over multiple years preceding death. Results Average age at death was 88.6 years. Overall, 349 participants (41.9%) had Alzheimer's dementia at death. A higher level of PLXNB1 abundance was associated with more β‐amyloid load ( p = 1.0 × 10 −7 ) and higher PHFtau tangle density ( p = 2.3 × 10 −7 ), and the association of PLXNB1 with cognitive decline is mediated by these known Alzheimer's disease pathologies. On the other hand, higher IGFBP5, HSPB2, and AK4 and lower ITPK1 levels were associated with faster cognitive decline, and, unlike PLXNB1, these associations were not fully explained by common neuropathological indices, suggesting novel mechanisms leading to cognitive decline. Interpretation Using targeted proteomics, this work identified cortical proteins involved in Alzheimer's dementia and begins to dissect two different molecular pathways: one affecting β‐amyloid deposition and another affecting resilience without a known pathological footprint. Ann Neurol 2018;83:78–88

Yu, Lei↗
DOE OSTI2018

Irradiation of rainbow trout at early life stages results in a proteomic legacy in adult gills. Part A; proteomic responses in the irradiated fish and in non-irradiated bystander fish

Highlights: • The effects of early life irradiation on the trout gill proteome was investigated. • The bystander effect proteomic responses in non-irradiated fish were investigated. • Proteomic responses of embryonic irradiation were anti-tumorigenic or anti-oxidant. • Proteomic responses of larval or first feeder irradiation were “dual function”. • Bystander effect proteomic responses were anti-tumorigenic or protective. Exposure to a single 0.5 Gy X-ray dose of eggs at 48 h after fertilisation (48 h egg), eyed eggs, yolk sac larvae (YSL) and first feeders induces a legacy effect in adult rainbow trout. This includes the transmission of a bystander effect to non-irradiated adult trout which had swam with the irradiated fish. The aim of this study was to investigate this legacy by analysing the gill proteome of these irradiated and bystander fish. Irradiation at all of the early life stages resulted in changes to proteins which play a key role in development but are also known to be anti-tumorigenic and anti-oxidant: upregulation of haemoglobin subunit beta (48 h egg), haemoglobin, serum albumin 1 precursor (eyed eggs), clathrin heavy chain 1 isoform X10 (eyed eggs and first feeders), and actin-related protein 2/3 complex subunit 4 (first feeders), downregulation of pyruvate dehydrogenase, histone 1 (48 h egg), triosephosphate isomerase (TPI), collagen alpha-1(1) chain like proteins (YSL), pyruvate kinase PKM-like protein (YSL and first feeders), ubiquitin-40S ribosomal proteins S27 and eukaryotic translation initiation factor 4 A isoform 1B (first feeders). However irradiation of YSL and first feeders (post hatching early life stages) also induced proteomic changes which have a complex relationship with tumorigenesis or cancer progression; downregulation of alpha-1-antiprotease-like protein precursor, vigilin isoform X2 and nucleoside diphosphate kinase (YSL) and upregulation of hyperosmotic glycine rich protein (first feeders). In bystander fish some proteomic changes were similar to those induced by irradiation: upregulation of haemoglobin subunit beta (48 h egg), haemoglobin (eyed eggs), actin-related protein 2/3 complex subunit 4, hyperosmotic glycine rich protein (first feeders), and downregulation of alpha-1-antiprotease-like protein, vigilin isoform X2, nucleoside diphosphate kinase (YSL), pyruvate kinase PKM-like protein and ubiquitin-40S ribosomal protein S27a-like (first feeders). Other proteomic changes were unique to bystander fish; downregulation of TPI, ubiquitin-40S ribosomal protein S2 (eyed egg), cofilin-2, cold-inducible RNA-binding protein B-like isoform X3 (YSL) and superoxide dismutase (first feeder), and upregulation of haemoglobin subunit alpha, collagen 1a1 precursor, apolipoprotein A-1-1 and A-1–2 precursor (first feeders). These bystander effect proteomic changes have been shown to be overwhelmingly anti-tumorigenic or protective of the fish gill.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2020

Proximity-based proteomics reveals the thylakoid lumen proteome in the cyanobacterium Synechococcus sp. PCC 7002

Abstract Cyanobacteria possess unique intracellular organization. Many proteomic studies have examined different features of cyanobacteria to learn about the intracellular structures and their respective functions. While these studies have made great progress in understanding cyanobacterial physiology, the conventional fractionation methods used to purify cellular structures have limitations; specifically, certain regions of cells cannot be purified with existing fractionation methods. Proximity-based proteomics techniques were developed to overcome the limitations of biochemical fractionation for proteomics. Proximity-based proteomics relies on spatiotemporal protein labeling followed by mass spectrometry of the labeled proteins to determine the proteome of the region of interest. We performed proximity-based proteomics in the cyanobacterium Synechococcus sp. PCC 7002 with the APEX2 enzyme, an engineered ascorbate peroxidase. We determined the proteome of the thylakoid lumen, a region of the cell that has remained challenging to study with existing methods, using a translational fusion between APEX2 and PsbU, a lumenal subunit of photosystem II. Our results demonstrate the power of APEX2 as a tool to study the cell biology of intracellular features and processes, including photosystem II assembly in cyanobacteria, with enhanced spatiotemporal resolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Proximity-based proteomics reveals the thylakoid lumen proteome in the cyanobacterium Synechococcus sp. PCC 7002

Cyanobacteria possess unique intracellular organization. Many proteomic studies have examined different features of cyanobacteria to learn about the intracellular structures and their respective functions. While these studies have made great progress in understanding cyanobacterial physiology, the conventional fractionation methods used to purify cellular structures have limitations; specifically, certain regions of cells cannot be purified with existing fractionation methods. Proximity-based proteomics techniques were developed to overcome the limitations of biochemical fractionation for proteomics. Proximity-based proteomics relies on spatiotemporal protein labeling followed by mass spectrometry of the labeled proteins to determine the proteome of the region of interest. We performed proximity-based proteomics in the cyanobacterium Synechococcus sp. PCC 7002 with the APEX2 enzyme, an engineered ascorbate peroxidase. We determined the proteome of the thylakoid lumen, a region of the cell that has remained challenging to study with existing methods, using a translational fusion between APEX2 and PsbU, a lumenal subunit of photosystem II. Our results demonstrate the power of APEX2 as a tool to study the cell biology of intracellular features and processes, including photosystem II assembly in cyanobacteria, with enhanced spatiotemporal resolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

PPI DataHub Project Data Package: S. elongatus PCC 7942 Limited Proteolysis and Thermal Proteome Profiling Structural Proteomics (JM-PB-DP3)

The purpose of this experiment was to investigate structural alterations in proteins involved in central carbon metabolism and photosynthetic electron transfer pathways in Synechococcus elongatus PCC 7942. Sample data was obtained from S. elongatus cell lysates using three complementary mass spectrometry (MS) techniques using limited proteolysis (LiP-MS), thermal proteome profiling (TPP-MS), and redox enrichment (Redox-MS) in evaluating alterations solvent accessibility and structural stability caused by light perturbation at the molecular level. Experimentally processed sample data for LiP and TPP proteomic datasets were derived from the same cell culture stock, prepared simultaneously in parallel, and acquired by mass spectrometry. Processed datasets are openly accessible from the download button and contain secondary processed proteomic results files, computed outputs, and supporting metadata materials. Experimental samples processed for LiP-MS label-free quantification (LFQ) or TPP-MS tandem mass tag (TMT) 10-plex were acquired using a Q-Exactive HF-X mass spectrometer and processed/compiled using either MSGF+ (v2024.03.26) or ​​​​PlexedPiper for proteome evaluation. Additional software supporting downstream proteomic analysis include FragPipe (v.4.0), MSFragger (v.22.1), and an adapted Microbial Isolate LiP Analysis Workflow (located at Zenodo). Processed proteomic data downloads include a sample naming key, normalized quantification results files, and processed protein annotated abundance files.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Irradiation of rainbow trout at early life stages results in a proteomic legacy in adult gills. Part B; the effect of a second radiation dose, after one year, on the proteomic responses in the irradiated and non-irradiated bystander fish

Highlights: • The effects of a 2nd radiation dose at one year were investigated. • The bystander effect proteomic responses in non-irradiated fish were investigated. • The effects of a 2nd radiation dose differed to those of early life irradiation only. • Proteomic responses of irradiated fish indicated tumorigenesis or cancer progression. • Bystander effect proteomic responses were tumorigenic, detrimental or uncertain. This study extends the investigation of the legacy effects of exposure to a single radiation dose at one of four early life stages, in adult rainbow trout (Part A), by examining the effects of a second identical dose after one year; i.e. egg 48 h after fertilisation (48 h egg) + 1 year, eyed egg + 1 year, yolk sac larvae (YSL) + 1 year and first feeder + 1 year. This included the induction of a bystander effect in non-irradiated trout which had swam with the irradiated fish. The second radiation dose negated any beneficial proteomic responses following early life stage irradiation only, particularly irradiation of 48 h eggs and eyed eggs (Part A). Instead the responses after early life stage + 1 year irradiation are consistently associated with tumorigenesis, cancer progression, or are otherwise damaging: upregulation of alpha-globin 1 (YSL + 1 year and first feeders + 1 year) and downregulation of histone H1, type II keratin, malate dehydrogenase 2–2, Na/K ATPase alpha subunit isoform 1b, nucleoside diphosphate kinase (48 h egg + 1 year), electron transfer flavoprotein subunit alpha (eyed egg + 1 year), 60 S ribosomal protein L30 (YSL + 1 year) and haemoglobin subunit beta-4 (first feeder + 1 year). Most significantly the second radiation dose also negated the overwhelmingly beneficial bystander effect proteomic responses induced by trout irradiated at an early life stage only (Part A). Instead the bystander effect proteomic changes induced by trout irradiated at an early life stage and again at 1 year have been associated with uncertain, with respect to tumorigenesis, or detrimental effects; upregulation of alpha-globin 1 (YSL + 1 year and first feeder + 1 year) and downregulation of malate dehydrogenase 2–2, nucleoside diphosphate kinase (48 h egg + 1 year), transferrin precursor (eyed egg + 1 year), 60 S ribosomal protein L30 (YSL + 1 year) and serine / threonine-protein phosphatase 2 A 65 kDa (first feeder + 1 year). This difference between the bystander effect induced proteomic changes following early life stage irradiation only and early life stage + 1 year irradiation may indicate a fundamental change in the non-targeted effects of radiation following multiple exposure to radiation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Mass spectrometry-based proteomics for system-level characterization of biological responses to engineered nanomaterials

The widespread applications of engineered nanomaterials or nanotechnology make the characterization of biological responses to nanomaterials as an important area of research. The applications of omics-based approaches such as mass spectrometry-based proteomics have revealed new insights into the cellular responses upon exposure to nanomaterials, including how nanomaterials interact and alter cellular pathways. For instance, a redox-dependent response is often associated with exposure of nanomaterials, which leads to the generation of reactive oxygen species. In this review, we discuss the general quantitative proteomics approaches, with an emphasis on redox proteomics and their applications for characterizing the biological responses to nanomaterials.

Zhang, Tong↗
DOE OSTI2025

The promising role of proteomes and metabolomes in defining the single-cell landscapes of plants

The plant community has a strong track-record of RNA sequencing technology deployment, which combined with the recent advent of spatial platforms (e.g., 10x genomics), has resulted in an explosion of outstanding single cell and nuclei datasets that can be put in an in situ context within tissues (e.g., a cell atlas)1. In the genomics era, application of proteomics technologies in the plant sciences has always trailed behind that of RNA sequencing technologies, largely due to accessibility, ease-of-use and access to expertise along with depth of analysis benefits. On the other hand, the use of early analytical tools for characterizing small molecules (metabolites) from plant systems predates nucleic acid sequencing and proteomics analysis2, as the search for plant-based natural products has played a significant role in improving human health throughout history. However, the employment of proteomics and metabolomics assays for characterizing plant cell processes now remains significantly behind transcriptional approaches, even though both provide a direct functional readout of cell states and phenotypes.

Anderton, Christopher R. [BATTELLE (PACIFIC NW LAB↗
DOE OSTI2020

Evaluation of the cytotoxic and cellular proteome impacts of food-grade TiO2 (E171) using simulated gastrointestinal digestions and a tri-culture small intestinal epithelial model

Engineered nanomaterials (ENMs) are widely used in the food industry; however, regulations for ENMs in food are still in the early stages of development due to insufficient health data. This study investigated the cytotoxicity and changes to the proteomic profile in an in vitro small intestinal epithelium model after exposure to digested food models containing the ubiquitous engineered particulate food additive, TiO2 (E171). TiO2 at 0.75% or 1.5% (w/w) concentrations in either a fasting food model (FFM) or a standardized food model (SFM) based on American diet were digested using an in vitro oral-gastric-small intestinal simulator, and the resulting digestas were applied to a small intestinal epithelium tri-culture cellular model. Effects on cell layer integrity, cytotoxicity, and oxidative stress were assessed. In order to explore impact on cellular processes beyond basic cytotoxicity, mass spectrometrybased quantitative proteomic analyses of control and exposed tri-culture cells was performed. TiO2 in FFM, but not in SFM, produced significant, dose-dependent cytotoxicity, and at the higher dose caused significant oxidative stress, indicative of a food matrix effect. No significant perturbations of the cellular proteome were observed with TiO2 in either FFM or SFM food models. However, proteins involved in the tricarboxylic acid (TCA) cycle, gluconeogenesis, and translation were up-regulated by digestas from SFM compared to those from FFM, also indicative of food matrix effects in the case of food models alone. Interestingly, the differences in profiles between the two food models was more pronounced in the presence of TiO2 indicative of food matrix effects. Together, these results indicate that TiO2 in a fasting diet may be slightly cytotoxic, and that ingested TiO2 does not significantly alter the epithelial proteome, whereas the food matrix alone can have a dramatic effect on the proteome.

Cao, Xiaoqiong↗
DOE OSTI2018

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells

Nanoscale or single cell technologies are critical for biomedical applications. However, current mass spectrometry (MS)-based proteomic approaches require samples comprising a minimum of thousands of cells to provide in-depth profiling. Here, we report the development of a nanoPOTS (Nanodroplet Processing in One pot for Trace Samples) platform as a major advance in overall sensitivity. NanoPOTS dramatically enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive LC-MS, nanoPOTS allows identification of ~1500 to ~3,000 proteins from ~10 to ~140 cells, respectively. By incorporating the Match Between Runs algorithm of MaxQuant, >3000 proteins were consistently identified from as few as 10 cells. Furthermore, we demonstrate robust quantification of ~2400 proteins from single human pancreatic islet thin sections from type 1 diabetic and control donors, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2020

The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics

Abstract While many aspects of archaeal cell biology remain relatively unexplored, systems biology approaches like mass spectrometry (MS) based proteomics offer an opportunity for rapid advances. Unfortunately, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools and field-specific biological expertise for data interpretation. Here we present the initiation of the Archaeal Proteome Project (ArcPP), a community-based effort to comprehensively analyze archaeal proteomes. Starting with the model archaeon Haloferax volcanii , we reanalyze MS datasets from various strains and culture conditions. Optimized peptide spectrum matching, with strict control of false discovery rates, facilitates identifying > 72% of the reference proteome, with a median protein sequence coverage of 51%. These analyses, together with expert knowledge in diverse aspects of cell biology, provide meaningful insights into processes such as N-terminal protein maturation, N -glycosylation, and metabolism. Altogether, ArcPP serves as an invaluable blueprint for comprehensive prokaryotic proteomics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Integrated Proteomic and Glycoproteomic Characterization of Human High-Grade Serous Ovarian Carcinoma

Many gene products exhibit great structural heterogeneity because of an array of modifications. These modifications are not directly encoded in the genomic template but often affect the functionality of proteins. Protein glycosylation plays a vital role in proper protein functions. However, the analysis of glycoproteins has been challenging compared with other protein modifications, such as phosphorylation. Here, we perform an integrated proteomic and glycoproteomic analysis of 83 prospectively collected high-grade serous ovarian carcinoma (HGSC) and 23 non-tumor tissues. Integration of the expression data from global proteomics and glycoproteomics reveals tumor-specific glycosylation, uncovers different glycosylation associated with three tumor clusters, and identifies glycosylation enzymes that were correlated with the altered glycosylation. In addition to providing a valuable resource, these results provide insights into the potentialroles of glycosylation in the pathogenesis of HGSC, with the possibility of distinguishing pathological outcomes of ovarian tumors from non-tumors, as well as classifying tumor clusters.

Hu, Yingwei↗
DOE OSTI2018

Subnanogram proteomics: Impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples

One of the greatest challenges for mass spectrometry (MS)-based proteomics is the limited ability to analyze small samples. Here we investigate the relative contributions of liquid chromatography (LC), MS instrumentation and data analysis methods with the aim of improving proteome coverage for sample sizes ranging from 0.5 ng to 50 ng. We show that the LC separations utilizing 30-µm-i.d. columns increase signal intensity by >3-fold relative to those using 75-µm-i.d. columns, leading to 32% increase in peptide identifications. The Orbitrap Fusion Lumos mass spectrometer significantly boosted both sensitivity and sequencing speed relative to earlier generation Orbitraps (e.g., LTQ-Orbitrap), leading to a ~3× increase in peptide identifications and 1.7× increase in identified protein groups for 2 ng tryptic digests of bacterial lysate. The Match Between Runs algorithm of open-source MaxQuant software further increased proteome coverage by ~ 95% for 0.5 ng samples and by ~42% for 2 ng samples. The present platform is capable of identifying >3000 protein groups from tryptic digestion of cell lysates equivalent to 50 HeLa cells and 100 THP-1 cells (~10 ng total proteins), respectively, and >950 proteins from subnanogram bacterial and archaeal cell lysates. The present ultrasensitive LC-MS platform is expected to enable deep proteome coverage for subnanogram samples, including single mammalian cells.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2023

Predicted structural proteome of Sphagnum divinum and proteome-scale annotation

Sphagnum-dominated peatlands store a substantial amount of terrestrial carbon. The genus is undersampled and under-studied. No experimental crystal structure from any Sphagnum species exists in the Protein Data Bank and fewer than 200 Sphagnum-related genes have structural models available in the AlphaFold Protein Structure Database. Tools and resources are needed to help bridge these gaps, and to enable the analysis of other structural proteomes now made possible by accurate structure prediction. We present the predicted structural proteome (25,134 primary transcripts) of Sphagnum divinum computed using AlphaFold, structural alignment results of all high-confidence models against an annotated nonredundant crystallographic database of over 90,000 structures, a structure-based classification of putative Enzyme Commission (EC) numbers across this proteome, and the computational method to perform this proteome-scale structure-based annotation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Physiological and proteomic analyses of Fe(III)-reducing co-cultures of Desulfotomaculum reducens MI-1 and Geobacter sulfurreducens PCA

We established Fe(III)-reducing co-cultures of two species of metal-reducing bacteria, the Gram-positive Desulfotomaculum reducens MI-1 and the Gram-negative Geobacter sulfurreducens PCA. Co-cultures were given pyruvate, a substrate that D. reducens can ferment and use as electron donor for Fe(III) reduction. G. sulfurreducens, which does not utilize pyruvate, relied upon products of pyruvate oxidation by D. reducens (acetate, H2) for use as electron donor in the co-culture. Fe(III) was reduced more quickly in co-cultures relative to pure cultures, and powder X-ray diffraction evidence suggests that both organisms contribute to Fe(III) reduction. Global comparative proteomic analysis was performed in order to observe differential protein abundance during co-culture versus pure culture growth. Proteins previously associated with Fe(III) reduction in G. sulfurreducens, namely c-type cytochromes and type IV pili proteins, were significantly increased in abundance in co-cultures relative to pure cultures. Dreducens ribosomal proteins were significantly increased in co-cultures, likely a reflection of faster growth rates observed for D. reducens cells while in co-culture. Furthermore, we developed multiple reaction monitoring (MRM) assays to quantitate specific biomarker peptides. The assays were validated in pure and co-cultures, and protein abundance ratios from targeted MRM and global proteomic analysis correlate strongly.

Otwell, Annie E.↗