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Comparison of different combinations of intensity power (IP) and unassigned peak scaling (UPS). The comparison is based on identification results of searching the helaDIA data set against the DDA-based spectral library using Calibr. (a) The number of validated SSMs. (b) The number of validated peptides. Validation was performed using Percolator. The largest value is marked by a black box.
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Identifying peptides and proteins from mass spectrometry (MS) data, spectral library searching has emerged as a complementary approach to the conventional database searching. However, for the spectrum-centric analysis of data-independent acquisition (DIA) data, spectral library searching has not been widely exploited because existing spectral libra...
Citations
... Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. a reduction in the size of the read head corresponding to the size of the data bits. This subsequently results in a decrease in the performance of the read head with high thermal instability, which gives rise to noisy readback signals [6][7][8]. The spin valve stack is the main component of the reader, and consists of a spacer layer (SL) sandwiched by two ferromagnets (FMs). The first FM layer, regarded as a pinned layer (PL), has a fixed magnetization due to the effect of exchange bias (EB) between the FM and antiferromagnetic (AF) material, while the magnetization direction within the second FM layer or free layer (FL) can freely change depending on the induced magnetic field from the recording media. ...
Heusler alloy has been widely utilized in the magnetoresistive sensor to enhance the device’s performance. In this work, we theoretically investigate the performance of Heusler-alloy based magnetoresistive sensor with synthetic antiferromagnet (SAF) layer. The atomistic model combined with the spin ccumulation model will be used in this work. The former is used to construct the reader stack and investigate the magnetization dynamic in the system. The latter is employed to describe the spin transport behavior at any position of the structure. We first perform simulations of the exchange bias (EB) phenomenon in the IrMn/CFS system providing high EB field. Then the realistic reader stack of IrMn/CFS/Ru/CFS/Ag/CFS is constructed via an atomistic model. Subsequently, the resistance-area product and MR ratio of the reader can be calculated by using the spin accumulation model. As a result of spin transport behavior in Huesler-alloy based reader stack including SAF structure at 0 K, it can be observed the enhancement of MR ratio up to 120% and RA < 40 mΩ· µm ² . This study shows the important role of Huesler alloy and SAF layer for the development of magnetoresistive sensors for the application of reader in HDDs with areal density beyond 2 Tb/in ² .
... as a complementary approach to database searching. Spectral library searching utilizes the intensities of fragment ions for spectrum matching, thereby enhancing sensitivity and reducing search time [14][15][16][17][18][19] . This approach has been demonstrated to improve the identification of TMT-labeled peptides by sequence database searching 20 . ...
Isobaric labeling relative quantitation is one of the dominating proteomic quantitation technologies. Traditional quantitation pipelines for isobaric-labeled mass spectrometry data are based on sequence database searching. In this study, we present a novel quantitation pipeline that integrates sequence database searching, spectral library searching, and a feature-based peptide-spectrum-match (PSM) filter using various spectral features for filtering. The combined database and spectral library searching results in larger quantitation coverage, and the filter removes PSMs with larger quantitation errors, retaining those with higher quantitation accuracy. Quantitation results show that the proposed pipeline can improve the overall quantitation accuracy at the PSM and protein levels. To our knowledge, this is the first study that utilizes spectral library searching to improve isobaric labeling-based quantitation. For users to conveniently perform the proposed pipeline, we have implemented the feature-based filter being executable on both Windows and Linux platforms; its executable files, user manual, and sample data sets are freely available at https://ms.iis.sinica.edu.tw/comics/Software_FPF.html. Furthermore, with the developed filter, the proposed pipeline is fully compatible with the Trans-Proteomic Pipeline.
... This technique embeds spectra according to similarity within a large network of public data, enabling grouping of structurally related molecules and greatly aiding metabolite annotation. Additionally, both spectrum- [20] and chromatogram-centric [21] approaches are under active development in proteomics data processing, which can serve as inspiration for continued development of metabolomics DIA data processing for both qualitative and quantitative aims. ...
The computational metabolomics field brings together computer scientists, bioinformaticians, chemists, clinicians, and biologists to maximize the impact of metabolomics across a wide array of scientific and medical disciplines. The field continues to expand as modern instrumentation produces datasets with increasing complexity, resolution, and sensitivity. These datasets must be processed, annotated, modeled, and interpreted to enable biological insight. Techniques for visualization, integration (within or between omics), and interpretation of metabolomics data have evolved along with innovation in the databases and knowledge resources required to aid understanding. In this review, we highlight recent advances in the field and reflect on opportunities and innovations in response to the most pressing challenges. This review was compiled from discussions from the 2022 Dagstuhl seminar entitled "Computational Metabolomics: From Spectra to Knowledge".
... This method has been applied to peptides, phosphopeptides, glycopeptides, as well as cross-linked peptides [78][79][80][81]. Studies have shown that some spectral library searching tools can increase the number of peptides identified by approximately 30% compared to conventional search engines that compare experiment spectra to theoretical fragment ions of putative peptides [82]. While spectral matching has been used for the analysis of metabolites for years, it is now currently becoming more popular in proteomics with the development of search tools such as SpectraST [83], COSS [84], Pepitome [85], and Calibr [86]. ...
There are probably no biological samples that did more to spur interest in proteomics than serum and plasma. The belief was that comparing the proteomes of these samples obtained from healthy and disease-affected individuals would lead to biomarkers that could be used to diagnose conditions such as cancer. While the continuing development of mass spectrometers with greater sensitivity and resolution has been invaluable, the invention of strategic strategies to separate circulatory proteins has been just as critical. Novel and creative separation techniques were required because serum and plasma probably have the greatest dynamic range of protein concentration of any biological sample. The concentrations of circulating proteins can range over twelve orders of magnitude, making it a challenge to identify low-abundance proteins where the bulk of the useful biomarkers are believed to exist. The major goals of this article are to (i) provide an historical perspective on the rapid development of serum and plasma proteomics; (ii) describe various separation techniques that have made obtaining an in-depth view of the proteome of these biological samples possible; and (iii) describe applications where serum and plasma proteomics have been employed to discover potential biomarkers for pathological conditions.
We study the influence of confinement on the dynamics of translocation of a linear polymer chain in a good solvent through a cone-shaped pore. Using the Langevin dynamics simulations, we calculate both the first attempt time and translocation time as a function of the position of the back wall and apex angle α. As the in vivo confining environment is inherently dynamic, we extended the present study to explore the consequences of a periodically driven back wall and apex angles on the translocation dynamics. Our findings reveal that the translocation time initially decreases as the driving frequency increases, but increases after a certain frequency. The frequency at which the translocation time is found to be minimum is referred to as the resonance activation. Analyzing the distribution of translocation times around this frequency renders interesting information about the translocation process. We further explore the translocation dynamics by calculating the residence time of individual monomers, shedding light on the microscopic aspects of the process.
We analyze the coexisting ordered phases that arise in the half-filled [Formula: see text]-t-U-V extended Hubbard Model on the square lattice when tackled within the Kotliar and Ruckenstein slave boson representation in the thermodynamical limit. Particular emphasis is put on the dependence of the quasi-particle dispersions, the gaps, the spin-resolved renormalization factors, and the distribution of double occupancy on the microscopical parameters of the model. Our calculations are performed in a parameter range that is most suitable for resistive switching. In particular, the main contributions to the gaps are shown to either arise from [Formula: see text] in the weak coupling regime, or from U and V when they are the largest scales. The gaps are thus from joint spin and charge origin, and so are the order parameters.
