scholarly journals GproDIA enables data-independent acquisition glycoproteomics with comprehensive statistical control

2021 ◽  
Author(s):  
Yi Yang ◽  
Weiqian Cao ◽  
Guoquan Yan ◽  
Siyuan Kong ◽  
Mengxi Wu ◽  
...  
Keyword(s):  
Large Scale ◽  
Early Stage ◽  
Statistical Control ◽  
Serum Samples ◽  
Accurate Identification ◽  
Spectrum Prediction ◽  
Data Independent Acquisition ◽  
Stage Of Development ◽  
Spectral Libraries ◽  
Semi Empirical

AbstractLarge-scale profiling of intact glycopeptides is critical but challenging in glycoproteomics. Data independent acquisition (DIA) is an emerging technology with deep proteome coverage and accurate quantitative capability in proteomics studies, but is still in the early stage of development in the field of glycoproteomics. We propose GproDIA, a framework for the proteome-wide characterization of intact glycopeptides from DIA data with comprehensive statistical control by a 2-dimentional false discovery rate approach and a glycoform inference algorithm, enabling accurate identification of intact glycopeptides using wide isolation windows. We further adapt a semi-empirical spectrum prediction strategy to expand the coverage of spectral libraries of glycopeptides. We benchmark our method for N-glycopeptide profiling on DIA data of yeast and human serum samples, demonstrating that DIA with GproDIA outperforms the data dependent acquisition (DDA) based methods for glycoproteomics in terms of capacity and data completeness of identification, as well as accuracy and precision of quantification. We expect that this work can provide a powerful tool for glycoproteomic studies.

scholarly journals GproDIA enables data-independent acquisition glycoproteomics with comprehensive statistical control

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yi Yang ◽  
Guoquan Yan ◽  
Siyuan Kong ◽  
Mengxi Wu ◽  
Pengyuan Yang ◽  
...  
Keyword(s):  
Large Scale ◽  
Early Stage ◽  
Statistical Control ◽  
Serum Samples ◽  
Accurate Identification ◽  
Spectrum Prediction ◽  
Data Independent Acquisition ◽  
Stage Of Development ◽  
Spectral Libraries ◽  
Semi Empirical

AbstractLarge-scale profiling of intact glycopeptides is critical but challenging in glycoproteomics. Data independent acquisition (DIA) is an emerging technology with deep proteome coverage and accurate quantitative capability in proteomics studies, but is still in the early stage of development in the field of glycoproteomics. We propose GproDIA, a framework for the proteome-wide characterization of intact glycopeptides from DIA data with comprehensive statistical control by a 2-dimentional false discovery rate approach and a glycoform inference algorithm, enabling accurate identification of intact glycopeptides using wide isolation windows. We further utilize a semi-empirical spectrum prediction strategy to expand the coverage of spectral libraries of glycopeptides. We benchmark our method for N-glycopeptide profiling on DIA data of yeast and human serum samples, demonstrating that DIA with GproDIA outperforms the data-dependent acquisition-based methods for glycoproteomics in terms of capacity and data completeness of identification, as well as accuracy and precision of quantification. We expect that this work can provide a powerful tool for glycoproteomic studies.

scholarly journals Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology

2020 ◽  
Author(s):  
Fynn M. Hansen ◽  
Maria C. Tanzer ◽  
Franziska Brüning ◽  
Isabell Bludau ◽  
Brenda A. Schulman ◽  
...  
Keyword(s):  
Large Scale ◽  
Tnf Alpha ◽  
Circadian Cycle ◽  
Cellular Processes ◽  
Data Independent Acquisition ◽  
Protein Ubiquitination ◽  
Quantitative Accuracy ◽  
Protein Receptors ◽  
Spectral Libraries ◽  
Acquisition Method

SUMMARYProtein ubiquitination is involved in virtually all cellular processes. Enrichment strategies employing antibodies targeting ubiquitin-derived diGly remnants combined with mass spectrometry (MS) have enabled investigations of ubiquitin signaling at a large scale. However, so far the power of data independent acquisition (DIA) with regards to sensitivity in single run analysis and data completeness have not yet been explored. We developed a sensitive workflow combining diGly antibody-based enrichment and optimized Orbitrap-based DIA with comprehensive spectral libraries together containing more than 90,000 diGly peptides. This approach identified 35,000 diGly peptides in single measurements of proteasome inhibitor-treated cells – double the number and quantitative accuracy of data dependent acquisition. Applied to TNF-alpha signaling, the workflow comprehensively captured known sites while adding many novel ones. A first systems-wide investigation of ubiquitination of the circadian cycle uncovered hundreds of cycling ubiquitination sites and dozens of cycling ubiquitin clusters within individual membrane protein receptors and transporters, highlighting novel connections between metabolism and circadian regulation.

Large-Scale Flow Patterns and Their Influence on the Intensification Rates of Western North Pacific Tropical Storms*

2007 ◽  
Vol 135 (3) ◽  
pp. 1110-1127 ◽  
Author(s):  
Justin D. Ventham ◽  
Bin Wang
Keyword(s):  
North Pacific ◽  
Western North Pacific ◽  
Large Scale ◽  
Early Stage ◽  
Flow Patterns ◽  
Reanalysis Data ◽  
Tropical Storm ◽  
Tropical Storms ◽  
Rapid Intensification ◽  
Stage Of Development

Abstract NCEP–NCAR reanalysis data are used to identify large-scale environmental flow patterns around western North Pacific tropical storms with the goal of finding a signal for those most favorable for rapid intensification, based on the hypothesis that aspects of the horizontal flow influence tropical cyclone intensification at an early stage of development. Based on the finding that intensification rate is a strong function of initial intensity (Joint Typhoon Warning Center best track), very rapid, rapid, and slow 24-h intensification periods from a weak tropical storm stage (35 kt) are defined. By using composite analysis and scalar EOF analysis of the zonal wind around these subsets, a form of the lower-level (850 mb) combined monsoon confluence–shearline pattern is found to occur dominantly for the very rapid cases. Based on the strength of the signal, it may provide a new rapid intensification predictor for operational use. At 200 mb the importance of the location of the tropical storm under a region of flow splitting into the midlatitude westerlies to the north and the subequatorial trough to the south is identified as a common criterion for the onset of rapid intensification. Cases in which interactions with upper-level troughs occurred, prior to and during slow and rapid intensification, are studied and strong similarities to prior Atlantic studies are found.

scholarly journals In-Depth Benchmarking of DIA-type Proteomics Data Analysis Strategies Using a Large-Scale Benchmark Dataset Comprising Inter-Patient Heterogeneity

2021 ◽  
Author(s):  
Klemens Fröhlich ◽  
Eva Brombacher ◽  
Matthias Fahrner ◽  
Daniel Vogele ◽  
Lucas Kook ◽  
...  
Keyword(s):  
Data Analysis ◽  
Large Scale ◽  
Statistical Tests ◽  
Benchmark Dataset ◽  
Clinical Samples ◽  
Proteomics Data ◽  
Data Independent Acquisition ◽  
Analysis Strategies ◽  
Spectral Libraries ◽  
Differentially Abundant Proteins

Abstract An overwhelming number of proteomics software tools and algorithms have been published for different steps of Data Independent Acquisition analysis of clinical samples. Nonetheless, there is still a lack of comprehensive benchmark studies evaluating which combinations of those isolated components perform best. Here, we used 92 lymph nodes from distinct patients to create a unique benchmark dataset representing real-world inter-individual heterogeneity. The publicly available dataset comprises 118 LC-MS/MS runs with > 12 million MS2 spectra and allowed us to objectively evaluate how well different combinations of spectral libraries, DIA software, sparsity reduction, normalization and statistical tests can detect differentially abundant proteins, while also taking sample size into account. Evaluation of 2 million data analysis workflows showed that a gas phase fractionation refined spectral library in combination with DIA-NN and Significance Analysis of Microarrays reliably detected differentially abundant proteins. Furthermore, DIA-NN and Spectronaut robustly avoided the false detection of truly absent proteins.

scholarly journals ПРИМЕНЕНИЕ МЕТОДОВ ЧИСЛЕННОГО МОДЕЛИРОВАНИЯ ПРИ ЭКCПЕРИМЕНТАЛЬНОЙ ОТРАБОТКЕ ЗАБОРНЫХ УСТРОЙСТВ ЦЕНТРАЛЬНОГО ТИПА

2019 ◽  
pp. 33-42
Author(s):  
Александр Николаевич Минай ◽  
Игорь Викторович Седых ◽  
Ирина Юрьевна Кузьмич
Keyword(s):  
Numerical Modeling ◽  
Large Scale ◽  
Engineering Practice ◽  
Launch Vehicles ◽  
Stage Of Development ◽  
Initial Stage ◽  
Scale Models ◽  
Hydrodynamic Processes ◽  
Definition Of ◽  
Semi Empirical

At the design of intakes of fuel tanks of launch vehicles in engineering practice, empirical and semi-empirical dependences are used for the determination of main parameters of the movement of liquid. However, the received from skilled data, empirical dependencies are applicable for a limited circle of tasks in which conditions (initial and boundary) are similar to for what these dependencies were received. Therefore, the calculated parameters of intakes it has to be validated by the results of experimental working off. Experimental working off intakes at hydrodynamic stands is, as a rule, carried out on natural tanks and their large-scale models (skilled designs) in terrestrial conditions. For confirmation of similarity of hydrodynamic processes, experimental working off the large-scale models is carried out on several skilled designs of different scales and several model liquids. Now, with the development of computer facilities and numerical methods of the solution of the differential equations of the movement of liquid, there was an opportunity to replace almost universal use of empirical dependences with more exact computing experiment. It, in some cases, allows reducing the quantity of the used skilled designs, terms of carrying out experimental working off, and, as a result, material expenses. The article presents results of the experimental definition of the static hydraulic rest of a component of fuel in skilled designs of a tank of the first step of carrier rockets with the central selection of a component and numerical modeling on mathematical 3D and 2D models of skilled designs (similar scale) are considered. The authors developed the calculated and experimental method of verification of results of numerical modeling allowing them to conduct necessary researches with the demanded accuracy. The offered approach allows improving the existing traditional method of experimental working off of intakes, already at the initial stage of development to optimize their parameters, to reduce the volume of necessary experimental working off and to lower time and material expenditure on its carrying out.

scholarly journals The Potential Role of Direct Air Capture in the German Energy Research Program—Results of a Multi-Dimensional Analysis

Energies ◽  
2019 ◽  
Vol 12 (18) ◽  
pp. 3443 ◽  
Author(s):  
Peter Viebahn ◽  
Alexander Scholz ◽  
Ole Zelt
Keyword(s):  
Dimensional Analysis ◽  
Research Program ◽  
Large Scale ◽  
Potential Role ◽  
Early Stage ◽  
Energy Research ◽  
Stage Of Development ◽  
Direct Air Capture ◽  
Air Capture

A significant reduction in greenhouse gas emissions will be necessary in the coming decades to enable the global community to avoid the most dangerous consequences of man-made global warming. This fact is reflected in Germany’s 7th Federal Energy Research Program (EFP), which was adopted in 2018. Direct Air Capture (DAC) technologies used to absorb carbon dioxide (CO2) from the atmosphere comprise one way to achieve these reductions in greenhouse gases. DAC has been identified as a technology (group) for which there are still major technology gaps. The intention of this article is to explore the potential role of DAC for the EFP by using a multi-dimensional analysis showing the technology’s possible contributions to the German government’s energy and climate policy goals and to German industry’s global reputation in the field of modern energy technologies, as well as the possibilities of integrating DAC into the existing energy system. The results show that the future role of DAC is affected by a variety of uncertainty factors. The technology is still in an early stage of development and has yet to prove its large-scale technical feasibility, as well as its economic viability. The results of the multi-dimensional evaluation, as well as the need for further technological development, integrated assessment, and systems-level analyses, justify the inclusion of DAC technology in national energy research programs like the EFP.

scholarly journals An Ultra-Rapid Biosensory Point-of-Care (POC) Assay for Prostate-Specific Antigen (PSA) Detection in Human Serum

Sensors ◽  
2018 ◽  
Vol 18 (11) ◽  
pp. 3834 ◽  
Author(s):  
Sophie Mavrikou ◽  
Georgia Moschopoulou ◽  
Athanasios Zafeirakis ◽  
Konstantina Kalogeropoulou ◽  
Georgios Giannakos ◽  
...  
Keyword(s):  
Human Serum ◽  
Prostate Specific Antigen ◽  
High Throughput ◽  
Early Stage ◽  
Point Of Care ◽  
Low Cost ◽  
Specific Antigen ◽  
Serum Samples ◽  
Stage Of Development ◽  
Better Than

Prostate-specific antigen (PSA) is the established routine screening tool for the detection of early-stage prostate cancer. Given the laboratory-centric nature of the process, the development of a portable, ultra rapid high-throughput system for PSA screening is highly desirable. In this study, an advancedpoint-of-care system for PSA detection in human serum was developed based on a cellular biosensor where the cell membrane was modified by electroinserting a specific antibody against PSA. Thirty nine human serum samples were used for validation of this biosensory system for PSA detection. Samples were analyzed in parallel with a standard immunoradiometric assay (IRMA) and an established electrochemical immunoassay was used for comparison purposes. They were classified in three different PSA concentration ranges (0, <4 and ≥4 ng/mL). Cells membrane-engineered with 0.25 μg/mL anti-PSA antibody demonstrated a statistically lower response against the upper (≥4 ng/mL) PSA concentration range. In addition, the cell-based biosensor performed better than the immunosensor in terms of sensitivity and resolution against positive samples containing <4 ng/mL PSA. In spite of its preliminary, proof-of-concept stage of development, the cell-based biosensor could be used as aninitiative for the development of a fast, low-cost, and high-throughput POC screening system for PSA.

scholarly journals Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses

2017 ◽  
Vol 14 (9) ◽  
pp. 921-927 ◽  
Author(s):  
George Rosenberger ◽  
Isabell Bludau ◽  
Uwe Schmitt ◽  
Moritz Heusel ◽  
Christie L Hunter ◽  
...  
Keyword(s):  
Large Scale ◽  
Error Rates ◽  
Statistical Control ◽  
Data Independent Acquisition

scholarly journals Serum proteomic profiling in patients with advanced Schistosoma japonicum-induced hepatic fibrosis

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Jing Huang ◽  
Xinguang Yin ◽  
Lifang Zhang ◽  
Ming Yao ◽  
Dahai Wei ◽  
...  
Keyword(s):  
Schistosoma Japonicum ◽  
Hepatic Fibrosis ◽  
Large Scale ◽  
Differentially Expressed ◽  
Control Group ◽  
Rapid Progression ◽  
Proteomic Profiling ◽  
Serum Samples ◽  
Data Independent Acquisition ◽  
Fundamental Information

Abstract Background Schistosoma japonicum is a parasitic flatworm that is the aetiological agent of human schistosomiasis, an important cause of hepatic fibrosis. Schistosomiasis-induced hepatic fibrosis is a consequence of the highly fibrogenic nature of egg-induced granulomatous lesions, which are the main pathogenic features of schistosomiasis. Although global awareness of the association between schistosomiasis-induced hepatic fibrosis and S. japonicum infection is increasing, little is known about the molecular differences associated with rapid progression to schistosomiasis in cirrhotic patients. Methods We systematically used data-independent acquisition (DIA)-based liquid chromatography-mass spectrometry to identify differentially expressed proteins in serum samples from patients with advanced S. japonicum-induced hepatic fibrosis. Results Our analysis identified 1144 proteins, among which 66 were differentially expressed between the healthy control group and the group of patients with advanced S. japonicum-induced hepatic fibrosis stage F2 (SHF-F2) and 214 were differentially expressed between the SHF-F2 and SHF-F4 groups (up- or downregulation of at least 1.5-fold in serum samples). The results also indicated that two selected proteins (C1QA and CFD) are potential biomarkers for distinguishing between patients with SHF-F2 and those with SHF-F4 due to S. japonicum infection. Conclusions We provide here the first global proteomic profile of serum samples from patients with advanced S. japonicum-induced hepatic fibrosis. The proteins C1QA and CFD are potential diagnostic markers for patients with SHF-F2 and SHF-F4 due to S. japonicum infection, although further large-scale studies are needed. Our DIA-based quantitative proteomic analysis revealed molecular differences among individuals at different stages of advanced S. japonicum-induced hepatic fibrosis and may provide fundamental information for further detailed investigations. Graphic Abstract

scholarly journals DIAproteomics: A multi-functional data analysis pipeline for data-independent-acquisition proteomics and peptidomics

2020 ◽  
Author(s):  
Leon Bichmann ◽  
Shubham Gupta ◽  
George Rosenberger ◽  
Leon Kuchenbecker ◽  
Timo Sachsenberg ◽  
...  
Keyword(s):  
Data Analysis ◽  
Large Scale ◽  
Dynamic Range ◽  
Expert Knowledge ◽  
Data Sets ◽  
Data Independent Acquisition ◽  
Large Scale Data ◽  
False Discovery ◽  
Spectral Libraries ◽  
Scale Data

ABSTRACTData-independent acquisition (DIA) is becoming a leading analysis method in biomedical mass spectrometry. Main advantages include greater reproducibility, sensitivity and dynamic range compared to data-dependent acquisition (DDA). However, data analysis is complex and often requires expert knowledge when dealing with large-scale data sets. Here we present DIAproteomics a multi-functional, automated high-throughput pipeline implemented in Nextflow that allows to easily process proteomics and peptidomics DIA datasets on diverse compute infrastructures. Central components are well-established tools such as the OpenSwathWorkflow for DIA spectral library search and PyProphet for false discovery rate assessment. In addition, it provides options to generate spectral libraries from existing DDA data and carry out retention time and chromatogram alignment. The output includes annotated tables and diagnostic visualizations from statistical post-processing and computation of fold-changes across pairwise conditions, predefined in an experimental design. DIAproteomics is open-source software and available under a permissive license to the scientific community at https://www.openms.de/diaproteomics/.

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