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Benchmarking SILAC Proteomics Workflows and data Analysis Platforms

Molecular & cellular proteomics : MCP 2025年第6期24卷 100980页

作者： Ashley M Frankenfield Kevin Yang Wan Nur Atiqah Binti Mazli Jamison Shih Fengchao Yu Edwin Lo Alexey I Nesvizhskii Ling Hao Department of Chemistry the George Washington University Washington DC 20052 USA. Department of Computational Medicine and Bioinformatics University of Michigan Ann Arbor MI USA. Department of Chemistry & Biochemistry the University of Maryland College Park MD 20742 USA. Department of Pathology University of Michigan Ann Arbor MI USA. Data Science Institute the University of Chicago Chicago IL 60637 USA. Department of Computational Medicine and Bioinformatics University of Michigan Ann Arbor MI USA Department of Chemistry the George Washington University Washington DC 20052 USA Department of Chemistry & Biochemistry the University of Maryland College Park MD 20742 USA. Electronic address: linghao1@umd.edu.

Stable isotope labeling by amino acids in cell culture (SILAC) is a powerful metabolic labeling technique with broad applications and various study designs. SILAC proteomics relies on the accurate identification and quantification of all isotopic versions of proteins and peptides during both data acquisition and analysis. However, a comprehensive comparison and evaluation of SILAC data analysis platforms is currently lacking. To address this critical gap and offer practical guidelines for SILAC proteomics data analysis, we designed a comprehensive benchmarking pipeline to evaluate various in vitro SILAC workflows and commonly used data analysis software. Ten different SILAC data analysis workflows using five software packages (MaxQuant, Proteome Discoverer, FragPipe, DIA-NN, and Spectronaut) were evaluated for static and dynamic SILAC labeling with both DDA and DIA methods. For benchmarking, we used both in-house generated and repository SILAC proteomics datasets from HeLa and neuron culture samples. We assessed twelve performance metrics for SILAC proteomics including identification, quantification, accuracy, precision, reproducibility, filtering criteria, missing values, false discovery rate, protein half-life measurement, data completeness, unique software features, and speed of data analysis. Each method/software has its strengths and weaknesses when evaluated for these performance metrics. Most software reaches a dynamic range limit of 100 folds for accurate quantification of light/heavy ratios. We do not recommend using Proteome Discoverer for SILAC DDA analysis despite its wide use in label-free proteomics. To achieve greater confidence in SILAC quantification, researchers could use more than one software packages to analyze the same dataset for cross-validation. In summary, this study offers the first systematic evaluation of various SILAC data analysis platforms, providing practical guidelines to support decision-making in SILAC proteomics study design and

关键词： DDA DIA protein turnover proteomics data analysis SILAC AGC Automatic gain control DDA data-dependent acquisition DIA data-independent acquisition D-DIA direct-DIA dSILAC dynamic stable isotope labeling by amino acids in cell culture FDP false discovery proportion FDR false discovery rate H-DIA hybrid-DIA iPSC inducible pluripotent stem cells LB-DIA library based-DIA MaxIT maximum injection time MBC match between channels MBR match between runs MS mass spectrometry PD Proteome Discoverer RIA relative isotope abundance SILAC stable isotope labeling by amino acids in cell culture

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Designing an Energy Tracker and Smart Home Solutions Using Design Thinking Methodology 10

Designing an Energy Tracker and Smart Home Solutions Using D...

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10th International Conference on ICT for Smart Society, ICISS 2023

作者： Hiererra, Siti Elda Chandra, Victor Ivana, Jane Wibowo, Jessica Lynn Asadi, Faisal School of Information Systems Bina Nusantara University Information Systems Department Jakarta11480 Indonesia School of Information Systems Bina Nusantara University Business Analytics Department Jakarta11480 Indonesia School of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia School of Computer Science Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia

ISBN: (纸本)9798350339543

As energy consumption rises, finding ways to reduce energy usage in homes is crucial. This paper presents a case study using design thinking to create a daily energy tracker that helps users reduce energy consumption. We conduct user research, define the problem, brainstorm solutions (mobile app, smart thermostat, smart plug, physical tracker), and test prototypes. A mobile app that tracks energy usage in real-time and offers personalized tips emerges as the most promising solution. We develop and launch the app, partnering with an energy company. This case study showcases the effectiveness of design thinking in creating a user-centered solution for reducing energy consumption. © 2023 IEEE.

关键词： Energy utilization

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AB-Amy: machine learning aided amyloidogenic risk prediction of therapeutic antibody light chains (vol 6, pg 147, 2023)

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ANTIBODY THERAPEUTICS 2023年第3期6卷 180-180页

作者： Zhou, Yuwei Huang, Ziru Gou, Yushu Liu, Siqi Yang, Wei Zhang, Hongyu Dzisoo, Anthony Mackitz Huang, Jian School of Life Science and Technology University of Electronic Science and Technology of China Sichuan Chengdu China School of Life Science and Technology University of Electronic Science and Technology of China Sichuan Chengdu China School of Computer Science and Engineering University of Electronic Science and Technology of China Sichuan Chengdu China Research and Development Zhanyuan Therapeutics Ltd. Zhejiang Hangzhou China Bioinformatics Data and Medical Reporting Arcencsus GmbH Mecklenburg-Vorpommern Rostock Germany University of Electronic Science and Technology of China No.2006 Xiyuan Ave West Hi-Tech Zone Chengdu China

Over 120 FDA-approved antibody-based therapeutics are used to treat a variety of ***, many candidates could fail because of unfavorable physicochemical properties. Light-chain amyloidosis is one form of aggregation that can lead to severe safety risks in clinical development. Therefore, screening candidates with a less amyloidosis risk at the early stage can not only save the time and cost of antibody development but also improve the safety of antibody drugs. In this study, based on the dipeptide composition of 742 amyloidogenic and 712 non-amyloidogenic antibody light chains, a support vector machine-based model, AB-Amy, was trained to predict the light-chain amyloidogenic risk. The AUC of AB-Amy reaches 0.9651. The excellent performance of AB-Amy indicates that it can be a useful tool for the in silico evaluation of the light-chain amyloidogenic risk to ensure the safety of antibody therapeutics under clinical development. A web server is freely available at http://***/AB-Amy/.

关键词： amyloidosis developability prediction support vector machine (SVM) therapeutic antibody

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A Diversity Inventory Monitoring System of Riparian Vegetation 4

A Diversity Inventory Monitoring System of Riparian Vegetati...

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4th International Conference on Cybernetics and Intelligent System, ICORIS 2022

作者： Putra, Dian Pratama Nugraha, Nanda Satya Suparyanto, Teddy Hidayat, Alam Ahmad Sudigyo, Digdo Pardamean, Bens STIPER Agricultural Institute Faculty of Agricultural Technology Yogyakarta55282 Indonesia STIPER Agricultural Institute Yogyakarta Faculty of Agricultural Technology Faculty of Forestry Yogyakarta55282 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia Bina Nusantara University BINUS Graduate Program - Master of Computer Science Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665453950

To strengthen conservation efforts for preserving biodiversity in a conservation area, forest inventory is important to understand the natural succession process in the area and to establish a monitoring strategy. Further, tree inventory aims to monitor the output yielded in the area. More specifically, the tree inventory in the watershed area plays a key role to achieve Sustainable Development Goals (SDG), especially in riparian zones which are also vital parts of green zones in forests. However, the traditional inventory approach is time-consuming and laborious therefore the development of an expert system to assist in inventory monitoring is required. In this study, we develop a monitoring system via a mobile application to collect, analyze and visualize tree inventory data. The application includes algorithms required to compute tree biodiversity, distribution, and richness for the given input of the data of all tree species in a conservation area. For the model validation stage, we compare the traditional inventory approach with our proposed application-based approach to compute diversity inventory in two riparian locations: Klaten Conservation Park and Wonosobo Conservation Park. After the three-day data collection in the areas, we obtain that the accuracy of reading data of our proposed system can achieve more than 90% in comparison with the manual approach. This demonstrates that the system can assist forestry workers to perform more efficient tree inventories in different locations. © 2022 IEEE.

关键词： Biodiversity

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Mobile Application Implementation as Agriculture 4.0 Strategy for Sugarcane Yield Prediction 9

Mobile Application Implementation as Agriculture 4.0 Strateg...

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9th International HCI and UX Conference in Indonesia, CHIuXiD 2023

作者： Mawandha, Hangger Gahara Rahutomo, Reza Suparyanto, Teddy Pardamean, Bens Institut Pertanian Stiper Faculty of Agricultural Technology Yogyakarta55282 Indonesia Bina Nusantara University School of Information Systems Information Systems Department Jakarta 11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta 11480 Indonesia Bina Nusantara University Binus Graduate Program - Master of Computer Science Computer Science Department Jakarta 11480 Indonesia

ISBN: (纸本)9798350304084

Information engineering strategies play a significant and transformative role in shaping the landscape of digital agriculture. It drives innovation and efficiency in modern farming practices, with a specific focus on enhancing the value of agricultural commodities, such as sugarcane. The application of mobile technology plays a crucial part in achieving increased sugarcane productivity. Mobile applications, equipped with advanced developer features, offer rapid and user-friendly access to vital information. Traditional methods of estimating sugarcane production relied on manual data recording on paper, followed by data transfer to computer systems, typically managed by sugar factory junior plant officers. This conventional approach presents several inherent weaknesses, including time and effort intensiveness during data recording and entry. Additionally, the potential for errors in calculation and data input is a concern. The storage capacity for paper-based documents is finite, and farmers are often unable to autonomously assess their production potential. The objective of this research is to confront these obstacles by creating a sugarcane production application for Android. This application functions as an information engineering approach focused on forecasting sugarcane yields for plantation owners and their assistants. The development procedure adhered to the systematic waterfall method, following the principles of the Software Development Life Cycle (SDLC) model. data collection was carried out through observations, while interviews with junior plant officers provided valuable insights into sugarcane estimation techniques. Analysis involved the synthesis of observational and interview data to inform the design of the application's interface and algorithmic system. The resulting application significantly simplifies the process of estimating production potential for farmers, enabling them to access sugarcane productivity data during harvest. Consequently, sugar

关键词： Forecasting

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AI-Based Ripeness Grading for Oil Palm Fresh Fruit Bunch in Smart Crane Grabber 3

AI-Based Ripeness Grading for Oil Palm Fresh Fruit Bunch in ...

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3rd International Conference on Eco Engineering Development, ICEED 2019

作者： Harsawardana Rahutomo, Reza Mahesworo, Bharuno Cenggoro, Tjeng Wawan Budiarto, Arif Suparyanto, Teddy Surya Atmaja, Don Bosco Samoedro, Bayu Pardamean, Bens Institut Pertanian STIPER Yogyakarta55281 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Mechatronics and AI Research and Development Center Biotechnic Innovation Yogyakarta55281 Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta11480 Indonesia

Indonesia is one of the biggest palm oil exporters in the world. For Indonesia to stay competitive in thepalm oil industry, the harvesting and evacuating process in its oil palm plantation need to be optimized. This research introduces machinerycalled as Smart Crane Grabber. This machinery can be used for automatic harvesting and evacuation process of oil palm fresh fruit bunch. To enable automation, Smart Crane Grabber is equipped with an Artificial Intelligencesystem for automatic ripeness sorting. TheArtificial Intelligence system developed for Smart Crane Grabber achieves 71.34% accuracy by using only 400 images as preliminary training data. © 2020 Published under licence by IOP Publishing Ltd.

关键词： Palm oil

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Emotion Detection Mastery: EEG Signal Analysis with Balanced vs. Unbalanced data

Emotion Detection Mastery: EEG Signal Analysis with Balanced...

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Brain Computer Interface & Healthcare Technologies (iCon-BCIHT), International Conference on

作者： Jadov Menaka Sreelekshmi I G Alwin Poulose School of Data Science Indian Institute of Science Education and Research Thiruvananthapuram Kerala India Department of Computational Biology and Bioinformatics University of Kerala Thiruvananthapuram Kerala India

ISBN: (数字)9798331540067

ISBN: (纸本)9798331540074

Emotion is crucial in daily life, influencing stress levels, decision-making, relationships, and overall mental health. Recognizing emotions accurately is valuable across sectors like healthcare, education, and beyond. This paper presents a comparative study on emotion recognition, applying various deep learning models with the DEAP dataset, which includes EEG recordings from 32 participants who watched 40 short music video clips. We extracted time-domain, frequency-domain, and wavelet features from the preprocessed EEG data to capture nuanced patterns within the signals. The models assessed in this study include convolutional neural networks (CNN), long short-term memory networks (LSTM), gated recurrent units (GRU), and hybrid architectures, each trained on both balanced and unbalanced datasets. To address class imbalance, data was augmented using the Synthetic Minority Oversampling Technique (SMOTE). Results indicate that the Attention GRU model achieved slightly higher performance by utilizing its attention mechanism to capture extended dependencies within the data. Additionally, model accuracy improved by 5-9% when trained on balanced datasets, underscoring the importance of data balancing in enhancing classification outcomes.

关键词： Deep learning Emotion recognition Attention mechanisms Medical services Brain modeling Feature extraction Transformers Electroencephalography data models Convolutional neural networks

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Accelerating Privacy-Preserving Medical Record Linkage: A Three-Party MPC Approach

arXiv

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arXiv 2024年

作者： Magara, Şeyma Selcan Dietrich, Noah Ünal, Ali Burak Akgün, Mete Medical Data Privacy and Privacy-Preserving ML on Healthcare Data Dept. of Computer Science University of Tübingen Germany Institute for Bioinformatics and Medical Informatics Tübingen Germany

Record linkage is a crucial concept for integrating data from multiple sources, particularly when datasets lack exact identifiers, and it has diverse applications in real-world data analysis. Privacy-Preserving Record Linkage (PPRL) ensures this integration occurs securely, protecting sensitive information from unauthorized access. This is especially important in sectors such as healthcare, where datasets include private identity information (IDAT) governed by strict privacy laws. However, maintaining both privacy and efficiency in large-scale record linkage poses significant challenges. Consequently, researchers must develop advanced methods to protect data privacy while optimizing processing performance. This paper presents a novel and efficient PPRL method based on a secure 3-party computation (MPC) framework. Our approach allows multiple parties to compute linkage results without exposing their private inputs and significantly improves the speed of linkage process compared to existing privacy-preserving solutions. We demonstrated that our method preserves the linkage quality of the state-of-the-art PPRL method while achieving up to 14 times faster performance. For example, linking a record against a database of 10,000 records takes just 8.74 seconds in a realistic network with 700 Mbps bandwidth and 60 ms latency. Even on a slower internet connection with 100 Mbps bandwidth and 60 ms latency, the linkage completes in 28 seconds, highlighting the scalability and efficiency of our solution. © 2024, CC BY.

关键词： Differential privacy

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Legal constraints on genetic data processing in European grids

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10th HealthGrid Conference and the 4th International Workshop on science Gateways for Life sciences, IWSG-Life 2012

作者： Mouw, Evert Van't Noordende, Guido Van Kampen, Antoine H.C. Louter, Baas Santcroos, Mark Olabarriaga, Silvia D. Department of Clinical Epidemiology Biostatistics and Bioinformatics Academic Medical Center University of Amsterdam Netherlands Department of Medical Informatics Academic Medical Center University of Amsterdam Netherlands Informatics Institute University of Amsterdam Netherlands Biosystems Data Analysis Swammerdam Institute for Life Science University of Amsterdam Netherlands

ISBN: (纸本)9781614990536

European laws on privacy and data security are not explicit about the storage and processing of genetic data. Especially whole-genome data is identifying and contains a lot of personal information. Is processing of such data allowed in computing grids? To find out, we looked at legal precedents in related fields, current literature, and interviews with legal experts. We found that processing of genetic data is only allowed on distributed systems with specific security measures, both technical and organizational. Informed consent, although important, offers no substitute for such requirements. © 2012 The authors and IOS Press. All rights reserved.

关键词： Digital storage

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Estimating Higher-Order Mixed Memberships via the 2,∞ Tensor Perturbation Bound

arXiv

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arXiv 2022年

作者： Agterberg, Joshua Zhang, Anru R. Departments of Electrical and Systems Engineering and Statistics and Data Science University of Pennsylvania United States Departments of Biostatistics & Bioinformatics Computer Science Mathematics and Statistical Science Duke University United States

Higher-order multiway data is ubiquitous in machine learning and statistics and often exhibits community-like structures, where each component (node) along each different mode has a community membership associated with it. In this paper we propose the tensor mixed-membership blockmodel, a generalization of the tensor blockmodel positing that memberships need not be discrete, but instead are convex combinations of latent communities. We establish the identifiability of our model and propose a computationally efficient estimation procedure based on the higher-order orthogonal iteration algorithm (HOOI) for tensor SVD composed with a simplex corner-finding algorithm. We then demonstrate the consistency of our estimation procedure by providing a per-node error bound, which showcases the effect of higher-order structures on estimation accuracy. To prove our consistency result, we develop the 2,∞ tensor perturbation bound for HOOI under independent, heteroskedastic, subgaussian noise that may be of independent interest. Our analysis uses a novel leave-one-out construction for the iterates, and our bounds depend only on spectral properties of the underlying low-rank tensor under nearly optimal signal-to-noise ratio conditions such that tensor SVD is computationally feasible. Finally, we apply our methodology to real and simulated data, demonstrating some effects not identifiable from the model with discrete community memberships. © 2022, CC BY.

关键词： Tensors

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