Simulated Datasets Research Articles

A Smart Secure model for Detection of DDoS Malicious Traces in Integrated LEO Satellite-Terrestrial Communications

For many researchers, defense against DDoS attacks has always been a major subject of attention. Within the LEO Satellite-Terrestrial (LSTN) network field, distributed denial of service (DDoS) attacks is considered to be one of the most potentially harmful attack techniques. For the facilitation of network protection by the detection of DDoS malicious traces inside a network of satellite devices, machine learning algorithms plays a significant role. This paper uses modern machine learning approaches on a novel benchmark Satellite dataset. The STIN and NSL-KDD datasets has been used to detect network anomalies. The pre-processing of data has been performed effectively and a host of ML methods have been applied to classify the outputs into normal, regular node or untrustable /malicious node. We have evaluated the analysis results in presence of attacks as well as without presence of attacks, supervised machine learning techniques basic measurements like accuracy, True positive, False positive etc. Our proposed trust model shows better accuracy, nearby 98% and we have shown that our proposed machine learning based security model performs better to get rid of DDoS attacks on integrated LEO satellite-terrestrial networks without compromising on the packet routing efficiency. We are able to improve routing speed and improve network security against distributed denial of service (DDoS) attacks by integrating an ensemble-based trust model trained on NSL-KDD+STIN+Exata Simulated resultant dataset with ACO for routing decisions. In dynamic network scenarios, as trustworthiness is an essential criterion in route decision-making, this proposed approach signifies resilient and adaptable routing.

A cascaded GRU-based stereoscopic matching network for precise plank measurement

Wooden plank images in industrial measurements often contain numerous textureless areas. Furthermore, due to the thin plate structure, the three-dimensional (3D) disparity of these planks is predominantly confined to a narrow range. Consequently, achieving accurate 3D matching of wooden plank images has consistently presented a challenging task within the industry. In recent years, deep learning has progressively supplanted traditional stereo matching methods due to its inherent advantages, including rapid inference and end-to-end processing. Nonetheless, the acquisition of datasets for stereo matching networks poses an additional challenge, primarily attributable to the difficulty in obtaining accurate disparity data. Thus, this paper presents a novel stereo matching method incorporating three key innovations. Firstly, an enhanced gated recurrent unit network is introduced, accompanied by a redesigned structure to achieve higher matching accuracy. Secondly, an efficient preprocessing module is proposed, aimed at improving the algorithm’s efficiency. Lastly, in response to the challenges posed by datasets acquisition, we innovatively employed image simulation software to obtain a high-quality simulated dataset of wooden planks. To assess the feasibility of our approach, we conducted both simulated and real experiments. The experiments results clearly exhibit the superiority of our method when compared to existing approaches in terms of both stability and accuracy. In the simulation experiment, our method attained a bad1.0 score of 2.1% (compared to the baseline method’s 9.76%); In the real experiment, our method achieved an average error of 0.104 mm (compared to the baseline method’s 0.268 mm). It is worth noting that our study aims to address the challenge of acquiring datasets for deep learning and bridging the gap between simulated and real data, resulting in increased applicability of deep learning in more industrial measurement domains.

Coupling the PROSAIL Model and Machine Learning Approach for Canopy Parameter Estimation of Moso Bamboo Forests from UAV Hyperspectral Data

Parameters such as the leaf area index (LAI), canopy chlorophyll content (CCH), and canopy carotenoid content (CCA) are important indicators for evaluating the ecological functions of forests. Currently, rapidly developing unmanned aerial vehicles (UAV) equipped with hyperspectral technology provide advanced technical means for the real-time dynamic acquisition of regional vegetation canopy parameters. In this study, a hyperspectral sensor mounted on a UAV was used to acquire the data in the study area, and the canopy parameter estimation model of moso bamboo forests (MBF) was developed by combining the PROSAIL radiative transfer model and the machine learning regression algorithm (MLRA), inverted the canopy parameters such as LAI, CCH, and CCA. The method first utilized the extended Fourier amplitude sensitivity test (EFAST) method to optimize the global sensitivity analysis and parameters of the PROSAIL model, and the successive projections algorithm (SPA) was used to screen the characteristic wavebands for the inversion of MBF canopy parameter inversion. Then, the optimized PROSAIL model was used to construct the ‘LAI-CCH-CCA-canopy reflectance’ simulation dataset for the MBF; multilayer perceptron regressor (MLPR), extra tree regressor (ETR), and extreme gradient boosting regressor (XGBR) employed used to construct PROSAIL_MLPR, PROSAIL_ETR, and PROSAIL_XGBR, respectively, as the three hybrid models. Finally, the best hybrid model was selected and used to invert the spatial distribution of the MBF canopy parameters. The following results were obtained: Waveband sensitivity analysis reveals 400–490 and 710–1000 nm as critical for LAI, 540–650 nm for chlorophyll, and 490–540 nm for carotenoids. SPA narrows down the feature bands to 43 for LAI, 19 for CCH, and 9 for CCA. The three constructed hybrid models were able to achieve high-precision inversion of the three parameters of the MBF, the model fitting accuracy of PROSAIL_MLRA reached more than 95%, with lower RMSE values, and the PROSAIL_XGBR model yielded the best fitting results. Our study provides a novel method for the inversion of forest canopy parameters based on UAV hyperspectral data.

Joint modeling of gene-environment correlations and interactions using polygenic risk scores in case-control studies.

Polygenic risk scores (PRSs) are rapidly emerging as a way to measure disease risk by aggregating multiple genetic variants. Understanding the interplay of the PRS with environmental factors is critical for interpreting and applying PRSs in a wide variety of settings. We develop an efficient method for simultaneously modeling gene-environment correlations and interactions using the PRS in case-control studies. We use a logistic-normal regression modeling framework to specify the disease risk and PRS distribution in the underlying population and propose joint inference across the 2 models using the retrospective likelihood of the case-control data. Extensive simulation studies demonstrate the flexibility of the method in trading-off bias and efficiency for the estimation of various model parameters compared with standard logistic regression or a case-only analysis for gene-environment interactions, or a control-only analysis, for gene-environment correlations. Finally, using simulated case-control data sets within the UK Biobank study, we demonstrate the power of our method for its ability to recover results from the full prospective cohort for the detection of an interaction between long-term oral contraceptive use and the PRS on the risk of breast cancer. This method is computationally efficient and implemented in a user-friendly R package.

A New Trajectory Clustering Method for Mining Multiple Periodic Patterns from Complex Oceanic Trajectories

Oceanic trajectories frequently exhibit multiple periodic patterns across various time intervals, e.g., tidal variations, mesoscale eddies, and El Niño events correspond to diurnal, seasonal, and interannual fluctuations in environmental factors. To explore hidden spatiotemporal multiple periodic behaviors in noisy ocean data, we propose a novel trajectory clustering method, namely DTID-STFC. It first identifies dense time intervals (DTIs) in which trajectories occur frequently. Subsequently, within each DTI, it utilizes spectral embedding to project trajectories onto a latent subspace and proposes three-way fuzzy clustering to obtain results. We evaluate the proposed method on simulated datasets and compare it with traditional and state-of-the-art trajectory clustering approaches. Experimental results indicate that it outperforms other methods across all five metrics. Moreover, when applying the DTID-STFC method to the analysis of mesoscale cyclonic eddies in the South China Sea and vessel data, it demonstrates more discernible results than traditional methods, and it aligns well with physical oceanographic processes. This proposed method offers valuable insights into identifying periodic behaviors from complex and noisy spatiotemporal oceanic trajectory data.

Improved Denoising of Cryo-Electron Microscopy Micrographs with Simulation-Aware Pretraining.

Cryo-electron microscopy (cryo-EM) has emerged as a potent technique for determining the structure and functionality of biological macromolecules. However, limited by the physical imaging conditions, such as low electron beam dose, micrographs in cryo-EM typically contend with an extremely low signal-to-noise ratio (SNR), impeding the efficiency and efficacy of subsequent analyses. Therefore, there is a growing demand for an efficient denoising algorithm designed for cryo-EM micrographs, aiming to enhance the quality of macromolecular analysis. However, owing to the absence of a comprehensive and well-defined dataset with ground truth images, supervised image denoising methods exhibit limited generalization when applied to experimental micrographs. To tackle this challenge, we introduce a simulation-aware image denoising (SaID) pretrained model designed to enhance the SNR of cryo-EM micrographs where the training is solely based on an accurately simulated dataset. First, we propose a parameter calibration algorithm for simulated dataset generation, aiming to align simulation parameters with those of experimental micrographs. Second, leveraging the accurately simulated dataset, we propose to train a deep general denoising model that can well generalize to real experimental cryo-EM micrographs. Comprehensive experimental results demonstrate that our pretrained denoising model achieves excellent denoising performance on experimental cryo-EM micrographs, significantly streamlining downstream analysis.

Extending the CWM approach to intraspecific trait variation: how to deal with overly optimistic standard tests?

Community weighted means (CWMs) are widely used to study the relationship between community-level functional traits and environment. For certain null hypotheses, CWM-environment relationships assessed by linear regression or ANOVA and tested by standard parametric tests are prone to inflated Type I error rates. Previous research has found that this problem can be solved by permutation tests (i.e., the max test). A recent extension of the CWM approach allows the inclusion of intraspecific trait variation (ITV) by the separate calculation of fixed, site-specific, and intraspecific CWMs. The question is whether the same Type I error rate inflation exists for the relationship between environment and site-specific or intraspecific CWM. Using simulated and real-world community datasets, we show that site-specific CWM-environment relationships have also inflated Type I error rate, and this rate is negatively related to the relative ITV magnitude. In contrast, for intraspecific CWM-environment relationships, standard parametric tests have the correct Type I error rate, although somewhat reduced statistical power. We introduce an ITV-extended version of the max test, which can solve the inflation problem for site-specific CWM-environment relationships and, without considering ITV, becomes equivalent to the "original" max test used for the CWM approach. We show that this new ITV-extended max test works well across the full possible magnitude of ITV on both simulated and real-world data. Most real datasets probably do not have intraspecific trait variation large enough to alleviate the problem of inflated Type I error rate, and published studies possibly report overly optimistic significance results.

Minimal-Effect Testing, Equivalence Testing, and the Conventional Null Hypothesis Testing for the Analysis of Bi-Factor Models

A necessary step in applying bi-factor models is to evaluate the need for domain factors with a general factor in place. The conventional null hypothesis testing (NHT) was commonly used for such a purpose. However, the conventional NHT meets challenges when the domain loadings are weak or the sample size is insufficient. This article proposes using minimal-effect testing (MET) and equivalence testing (ET) to analyze bi-factor models. A key element in conducting MET and ET is the minimal size of factor loadings that can be regarded as noteworthy in practice, termed as minimal noteworthy size. This article presents two approaches to formulating the minimal noteworthy size and compares the pros and cons of MET, ET, and the conventional NHT. Analysis shows that MET, ET, and the conventional NHT are complementary. Combining them to test the noteworthiness of domain loadings can help researchers make a comprehensive judgment. Real and simulated datasets illustrate the applications of the three methods. Monte Carlo results show that MET and ET can control type I errors reasonably well while maintaining good statistical power.

Dynamical Dark Energy in Light of Cosmic Distance Measurements. I. A Demonstration Using Simulated Datasets

We develop methods to extract key dark energy information from cosmic distance measurements including the BAO scales and supernova (SN) luminosity distances. Demonstrated using simulated data sets of the complete DESI, LSST and Roman surveys designed for BAO and SN distance measurements, we show that using our method, the dynamical behavior of the energy, pressure, equation of state (with its time derivative) of dark energy and the cosmic deceleration function can all be accurately recovered from high-quality data, which allows for robust diagnostic tests for dark energy models.

An improved stochastic car-following model considering the complete state information of multiple preceding vehicles under connected vehicles environment

Studying the car-following model contributes to improving vehicle driving efficiency and traffic flow stability within the context of connected automated vehicles (CAVs). Therefore, an improved stochastic car-following model (SMLVM) is proposed in this paper, building upon the traditional FVD model and BLVD model. This new model comprehensively considers four deterministic factors: acceleration, velocity, headway, and optimal speed memory of multiple preceding vehicles, as well as the comprehensive influence of stochastic factors on car-following behavior during the traveling process. Meanwhile, weight functions are utilized to represent the varying strengths of influence from vehicles ahead with different positions and speeds on the following vehicle. The SMLVM model is categorized and discussed based on practical application scenarios in this paper. When the focus is primarily on fundamental traffic flow behavior, relative motion between vehicles, and other basic principles, the SMLVM model degenerates into the MLVM model. Through stability analysis and simulation experiments on MLVM model, critical stability conditions are derived. Comparisons with other classical models demonstrate that the MLVM model exhibits stronger stability and resistance to disturbances. When the focus is primarily on various realistic driving scenarios, through simulation experiments on SMLVM models in different scenarios, it is found that the influence of stochastic factors on SMLVM models mainly depends on the magnitude of the intensity of stochastic fluctuations, which is rarely affected by the specific functional expressions of the stochastic terms. Finally, empirical analysis is conducted by selecting five sets of processed data from the next-generation simulation (NGSIM) dataset. Based on parameter estimation using the SMLVM model, and a comparison is made with the FVD model and BLVD model. The results confirm that the model proposed in this paper fits vehicle speeds better and absorbs disturbances more effectively, and exhibiting greater stability in traffic flow.

Toward drift-free high-throughput nanoscopy through adaptive intersection maximization.

Single-molecule localization microscopy (SMLM) often suffers from suboptimal resolution due to imperfect drift correction. Existing marker-free drift correction algorithms often struggle to reliably track high-frequency drift and lack the computational efficiency to manage large, high-throughput localization datasets. We present an adaptive intersection maximization-based method (AIM) that leverages the entire dataset's information content to minimize drift correction errors, particularly addressing high-frequency drift, thereby enhancing the resolution of existing SMLM systems. We demonstrate that AIM can robustly and efficiently achieve an angstrom-level tracking precision for high-throughput SMLM datasets under various imaging conditions, resulting in an optimal resolution in simulated and biological experimental datasets. We offer AIM as one simple, model-free software for instant resolution enhancement with standard CPU devices.

Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data.

Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2 pandemic for estimating community infection levels by qPCR. Sequencing pathogen genes or genomes from wastewater adds information about pathogen genetic diversity, which can be used to identify viral lineages (including variants of concern) that are circulating in a local population. Capturing the genetic diversity by WBS sequencing is not trivial, as wastewater samples often contain a diverse mixture of viral lineages with real mutations and sequencing errors, which must be deconvoluted computationally from short sequencing reads. In this study we assess nine different computational tools that have recently been developed to address this challenge. We simulated 100 wastewater sequence samples consisting of SARS-CoV-2 BA.1, BA.2, and Delta lineages, in various mixtures, as well as a Delta-Omicron recombinant and a synthetic 'novel' lineage. Most tools performed well in identifying the true lineages present and estimating their relative abundances and were generally robust to variation in sequencing depth and read length. While many tools identified lineages present down to 1 % frequency, results were more reliable above a 5 % threshold. The presence of an unknown synthetic lineage, which represents an unclassified SARS-CoV-2 lineage, increases the error in relative abundance estimates of other lineages, but the magnitude of this effect was small for most tools. The tools also varied in how they labelled novel synthetic lineages and recombinants. While our simulated dataset represents just one of many possible use cases for these methods, we hope it helps users understand potential sources of error or bias in wastewater sequencing analysis and to appreciate the commonalities and differences across methods.

NIPT-PG: empowering non-invasive prenatal testing to learn from population genomics through an incremental pan-genomic approach.

Non-invasive prenatal testing (NIPT) is a quite popular approach for detecting fetal genomic aneuploidies. However, due to the limitations on sequencing read length and coverage, NIPT suffers a bottleneck on further improving performance and conducting earlier detection. The errors mainly come from reference biases and population polymorphism. To break this bottleneck, we proposed NIPT-PG, which enables the NIPT algorithm to learn from population data. A pan-genome model is introduced to incorporate variant and polymorphic loci information from tested population. Subsequently, we proposed a sequence-to-graph alignment method, which considers the read mis-match rates during the mapping process, and an indexing method using hash indexing and adjacency lists to accelerate the read alignment process. Finally, by integrating multi-source aligned read and polymorphic sites across the pan-genome, NIPT-PG obtains a more accurate z-score, thereby improving the accuracy of chromosomal aneuploidy detection. We tested NIPT-PG on two simulated datasets and 745 real-world cell-free DNA sequencing data sets from pregnant women. Results demonstrate that NIPT-PG outperforms the standard z-score test. Furthermore, combining experimental and theoretical analyses, we demonstrate the probably approximately correct learnability of NIPT-PG. In summary, NIPT-PG provides a new perspective for fetal chromosomal aneuploidies detection. NIPT-PG may have broad applications in clinical testing, and its detection results can serve as a reference for false positive samples approaching the critical threshold.

PIPET: predicting relevant subpopulations in single-cell data using phenotypic information from bulk data.

Single-cell RNA sequencing has revealed cellular heterogeneity in complex tissues, notably benefiting research on diseases such as cancer. However, the integration of single-cell data from small samples with extensive clinical features in bulk data remains underexplored. In this study, we introduce PIPET, an algorithmic method for predicting relevant subpopulations in single-cell data based on multivariate phenotypic information from bulk data. PIPET generates feature vectors for each phenotype from differentially expressed genes in bulk data and then identifies relevant cellular subpopulations by assessing the similarity between single-cell data and these vectors. Subsequently, phenotype-related cell states can be analyzed based on these subpopulations. In simulated datasets, PIPET showed robust performance in predicting multiclassification cellular subpopulations. Application of PIPET to lung adenocarcinoma single-cell RNA sequencing data revealed cellular subpopulations with poor survival and associations with TP53 mutations. Similarly, in breast cancer single-cell data, PIPET identified cellular subpopulations associated with the PAM50 clinical subtypes and triple-negative breast cancer subtypes. Overall, PIPET effectively identified relevant cellular subpopulations in single-cell data, guided by phenotypic information from bulk data. This approach comprehensively delineates the molecular characteristics of each cellular subpopulation, offering insights into disease-related subpopulations and guiding personalized treatment strategies.

Comparative analysis of integrative classification methods for multi-omics data.

Recent advances in sequencing, mass spectrometry, and cytometry technologies have enabled researchers to collect multiple 'omics data types from a single sample. These large datasets have led to a growing consensus that a holistic approach is needed to identify new candidate biomarkers and unveil mechanisms underlying disease etiology, a key to precision medicine. While many reviews and benchmarks have been conducted on unsupervised approaches, their supervised counterparts have received less attention in the literature and no gold standard has emerged yet. In this work, we present a thorough comparison of a selection of six methods, representative of the main families of intermediate integrative approaches (matrix factorization, multiple kernel methods, ensemble learning, and graph-based methods). As non-integrative control, random forest was performed on concatenated and separated data types. Methods were evaluated for classification performance on both simulated and real-world datasets, the latter being carefully selected to cover different medical applications (infectious diseases, oncology, and vaccines) and data modalities. A total of 15 simulation scenarios were designed from the real-world datasets to explore a large and realistic parameter space (e.g. sample size, dimensionality, class imbalance, effect size). On real data, the method comparison showed that integrative approaches performed better or equally well than their non-integrative counterpart. By contrast, DIABLO and the four random forest alternatives outperform the others across the majority of simulation scenarios. The strengths and limitations of these methods are discussed in detail as well as guidelines for future applications.

DeepGRNCS: deep learning-based framework for jointly inferring gene regulatory networks across cell subpopulations.

Inferring gene regulatory networks (GRNs) allows us to obtain a deeper understanding of cellular function and disease pathogenesis. Recent advances in single-cell RNA sequencing (scRNA-seq) technology have improved the accuracy of GRN inference. However, many methods for inferring individual GRNs from scRNA-seq data are limited because they overlook intercellular heterogeneity and similarities between different cell subpopulations, which are often present in the data. Here, we propose a deep learning-based framework, DeepGRNCS, for jointly inferring GRNs across cell subpopulations. We follow the commonly accepted hypothesis that the expression of a target gene can be predicted based on the expression of transcription factors (TFs) due to underlying regulatory relationships. We initially processed scRNA-seq data by discretizing data scattering using the equal-width method. Then, we trained deep learning models to predict target gene expression from TFs. By individually removing each TF from the expression matrix, we used pre-trained deep model predictions to infer regulatory relationships between TFs and genes, thereby constructing the GRN. Our method outperforms existing GRN inference methods for various simulated and real scRNA-seq datasets. Finally, we applied DeepGRNCS to non-small cell lung cancer scRNA-seq data to identify key genes in each cell subpopulation and analyzed their biological relevance. In conclusion, DeepGRNCS effectively predicts cell subpopulation-specific GRNs. The source code is available at https://github.com/Nastume777/DeepGRNCS.

Transferable deep generative modeling of intrinsically disordered protein conformations.

Intrinsically disordered proteins have dynamic structures through which they play key biological roles. The elucidation of their conformational ensembles is a challenging problem requiring an integrated use of computational and experimental methods. Molecular simulations are a valuable computational strategy for constructing structural ensembles of disordered proteins but are highly resource-intensive. Recently, machine learning approaches based on deep generative models that learn from simulation data have emerged as an efficient alternative for generating structural ensembles. However, such methods currently suffer from limited transferability when modeling sequences and conformations absent in the training data. Here, we develop a novel generative model that achieves high levels of transferability for intrinsically disordered protein ensembles. The approach, named idpSAM, is a latent diffusion model based on transformer neural networks. It combines an autoencoder to learn a representation of protein geometry and a diffusion model to sample novel conformations in the encoded space. IdpSAM was trained on a large dataset of simulations of disordered protein regions performed with the ABSINTH implicit solvent model. Thanks to the expressiveness of its neural networks and its training stability, idpSAM faithfully captures 3D structural ensembles of test sequences with no similarity in the training set. Our study also demonstrates the potential for generating full conformational ensembles from datasets with limited sampling and underscores the importance of training set size for generalization. We believe that idpSAM represents a significant progress in transferable protein ensemble modeling through machine learning.

Comparing full variation profile analysis with the conventional consensus method in SARS-CoV-2 phylogeny.

This study proposes a novel approach to studying severe acute respiratory syndrome coronavirus 2 virus mutations through sequencing data comparison. Traditional consensus-based methods, which focus on the most common nucleotide at each position, might overlook or obscure the presence of low-frequency variants. Our method, in contrast, retains all sequenced nucleotides at each position, forming a genomic matrix. Utilizing simulated short reads from genomes with specified mutations, we contrasted our genomic matrix approach with the consensus sequence method. Our matrix methodology, across multiple simulated datasets, accurately reflected the known mutations with an average accuracy improvement of 20% over the consensus method. In real-world tests using data from GISAID and NCBI-SRA, our approach demonstrated an increase in reliability by reducing the error margin by approximately 15%. The genomic matrix approach offers a more accurate representation of the viral genomic diversity, thereby providing superior insights into virus evolution and epidemiology.

Empirical uncertainty evaluation for the pose of a kinematic LiDAR-based multi-sensor system

Abstract Kinematic multi-sensor systems (MSS) describe their movements through six-degree-of-freedom trajectories, which are often evaluated primarily for accuracy. However, understanding their self-reported uncertainty is crucial, especially when operating in diverse environments like urban, industrial, or natural settings. This is important, so the following algorithms can provide correct and safe decisions, i.e. for autonomous driving. In the context of localization, light detection and ranging sensors (LiDARs) are widely applied for tasks such as generating, updating, and integrating information from maps supporting other sensors to estimate trajectories. However, popular low-cost LiDARs deviate from other geodetic sensors in their uncertainty modeling. This paper therefore demonstrates the uncertainty evaluation of a LiDAR-based MSS localizing itself using an inertial measurement unit (IMU) and matching LiDAR observations to a known map. The necessary steps for accomplishing the sensor data fusion in a novel Error State Kalman filter (ESKF) will be presented considering the influences of the sensor uncertainties and their combination. The results provide new insights into the impact of random and systematic deviations resulting from parameters and their uncertainties established in prior calibrations. The evaluation is done using the Mahalanobis distance to consider the deviations of the trajectory from the ground truth weighted by the self-reported uncertainty, and to evaluate the consistency in hypothesis testing. The evaluation is performed using a real data set obtained from an MSS consisting of a tactical grade IMU and a Velodyne Puck in combination with reference data by a Laser Tracker in a laboratory environment. The data set consists of measurements for calibrations and multiple kinematic experiments. In the first step, the data set is simulated based on the Laser Tracker measurements to provide a baseline for the results under assumed perfect corrections. In comparison, the results using a more realistic simulated data set and the real IMU and LiDAR measurements provide deviations about a factor of five higher leading to an inconsistent estimation. The results offer insights into the open challenges related to the assumptions for integrating low-cost LiDARs in MSSs.

PIPI2: Sensitive Tag-Based Database Search to Identify Peptides with Multiple Post-translational Modifications.

Peptide identification is important in bottom-up proteomics. Post-translational modifications (PTMs) are crucial in regulating cellular activities. Many database search methods have been developed to identify peptides with PTMs and characterize the PTM patterns. However, the PTMs on peptides hinder the peptide identification rate and the PTM characterization precision, especially for peptides with multiple PTMs. To address this issue, we present a sensitive open search engine, PIPI2, with much better performance on peptides with multiple PTMs than other methods. With a greedy approach, we simplify the PTM characterization problem into a linear one, which enables characterizing multiple PTMs on one peptide. On the simulation data sets with up to four PTMs per peptide, PIPI2 identified over 90% of the spectra, at least 56% more than five other competitors. PIPI2 also characterized these PTM patterns with the highest precision of 77%, demonstrating a significant advantage in handling peptides with multiple PTMs. In the real applications, PIPI2 identified 30% to 88% more peptides with PTMs than its competitors.