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Showing 1-30 of 64 results for "UPS1" within Papers
Clarisse Gotti et al.
Data in brief, 41, 107829-107829 (2022-02-25)
In this article, we provide a proteomic reference dataset that has been initially generated for a benchmarking of software tools for Data-Independent Acquisition (DIA) analysis. This large dataset includes 96 DIA .raw files acquired from a complex proteomic standard composed
Claire Ramus et al.
Journal of proteomics, 132, 51-62 (2015-11-21)
Proteomic workflows based on nanoLC-MS/MS data-dependent-acquisition analysis have progressed tremendously in recent years. High-resolution and fast sequencing instruments have enabled the use of label-free quantitative methods, based either on spectral counting or on MS signal analysis, which appear as an
Christian J Koehler et al.
Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry, 25(1), 61-66 (2019-11-02)
Proteolytic digestion prior to LC-MS analysis is a key step for the identification of proteins. Digestion of proteins is typically performed with trypsin, but certain proteins or important protein sequence regions might be missed using this endoproteinase. Only few alternative
Wei Zhang et al.
Proteomics, 12(23-24), 3475-3484 (2012-10-20)
Database searching based methods for label-free quantification aim to reconstruct the peptide extracted ion chromatogram based on the identification information, which can limit the search space and thus make the data processing much faster. The random effect of the MS/MS
Leslie Muller et al.
Proteomics, 16(23), 2953-2961 (2016-10-18)
Sample preparation, typically by in-solution or in-gel approaches, has a strong influence on the accuracy and robustness of quantitative proteomics workflows. The major benefit of in-gel procedures is their compatibility with detergents (such as SDS) for protein solubilization. However, SDS-PAGE
Laurent Gatto et al.
Biochimica et biophysica acta, 1844(1 Pt A), 42-51 (2013-05-23)
This review presents how R, the popular statistical environment and programming language, can be used in the frame of proteomics data analysis. A short introduction to R is given, with special emphasis on some of the features that make R
Sarah R Langley et al.
Journal of proteomics, 129, 83-92 (2015-07-21)
Label-free LC-MS/MS proteomics has proven itself to be a powerful method for evaluating protein identification and quantification from complex samples. For comparative proteomics, several methods have been used to detect the differential expression of proteins from such data. We have
David L Tabb et al.
Journal of proteome research, 9(2), 761-776 (2009-11-20)
The complexity of proteomic instrumentation for LC-MS/MS introduces many possible sources of variability. Data-dependent sampling of peptides constitutes a stochastic element at the heart of discovery proteomics. Although this variation impacts the identification of peptides, proteomic identifications are far from
Aakash Chawade et al.
Journal of proteome research, 13(6), 3114-3120 (2014-04-29)
High-throughput omics data often contain systematic biases introduced during various steps of sample processing and data generation. As the source of these biases is usually unknown, it is difficult to select an optimal normalization method for a given data set.
Qi Wu et al.
The Analyst, 137(13), 3146-3153 (2012-05-15)
Although widely applied in the label-free quantification of proteomics, spectral count (SC)-based abundance measurements suffer from the narrow dynamic range of attainable ratios, leading to the serious underestimation of true protein abundance fold changes, especially when studying biological samples that
Enhanced Peptide Identification by Electron Transfer Dissociation Using an Improved Mascot Percolator.
Wright, J.C., et al.
Molecular and Cellular Proteomics, 11, 479-491 (2012)
Quentin Giai Gianetto et al.
Proteomics, 16(1), 29-32 (2015-11-18)
In MS-based quantitative proteomics, the FDR control (i.e. the limitation of the number of proteins that are wrongly claimed as differentially abundant between several conditions) is a major postanalysis step. It is classically achieved thanks to a specific statistical procedure
Laszlo Prokai et al.
Nature protocols, 9(4), 882-895 (2014-03-22)
Post-translational protein nitration has attracted interest owing to its involvement in cellular signaling, effects on protein function and potential as biomarker of nitroxidative stress. We describe a procedure for enriching nitropeptides for mass spectrometry (MS)-based proteomics that is a simple
Antonio Palomba et al.
Journal of proteome research, 20(7), 3497-3507 (2021-05-27)
MS1-based label-free quantification can compare precursor ion peaks across runs, allowing reproducible protein measurements. Among bioinformatic platforms enabling MS1-based quantification, MaxQuant (MQ) is one of the most used, while Proteome Discoverer (PD) has recently introduced the Minora tool. Here, we
Amanda G Paulovich et al.
Molecular & cellular proteomics : MCP, 9(2), 242-254 (2009-10-28)
Optimal performance of LC-MS/MS platforms is critical to generating high quality proteomics data. Although individual laboratories have developed quality control samples, there is no widely available performance standard of biological complexity (and associated reference data sets) for benchmarking of platform
Chengjian Tu et al.
Journal of proteomics, 152, 276-282 (2016-12-03)
Reliable quantification of low-abundance proteins in complex proteomes is challenging largely owing to the limited number of spectra/peptides identified. In this study we developed a straightforward method to improve the quantitative accuracy and precision of proteins by strategically retrieving the
Josep Gregori et al.
Methods in molecular biology (Clifton, N.J.), 2426, 197-242 (2022-10-30)
msmsTests is an R/Bioconductor package providing functions for statistical tests in label-free LC-MS/MS data by spectral counts. These functions aim at discovering differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and
Jianqi Wang et al.
Journal of the American Society for Mass Spectrometry, 26(7), 1077-1084 (2015-04-22)
A search engine that discovers more peptides reliably is essential to the progress of the computational proteomics. We propose two new scoring functions (L- and P-scores), which aim to capture similar characteristics of a peptide-spectrum match (PSM) as Sequest and
Nkemdilim C Uwaje et al.
Electrophoresis, 28(12), 1867-1874 (2007-05-23)
In high-throughput proteomics, the bottom-up approach has become a widely used method for the identification of proteins that is based on tryptic peptide MS/MS analysis. Separation methodologies that use IEF of tryptic peptides have recently been introduced and provide an
Alexandra Zerck et al.
BMC bioinformatics, 14, 56-56 (2013-02-20)
Liquid chromatography mass spectrometry (LC-MS) maps in shotgun proteomics are often too complex to select every detected peptide signal for fragmentation by tandem mass spectrometry (MS/MS). Standard methods for precursor ion selection, commonly based on data dependent acquisition, select highly
Sven Nahnsen et al.
BMC bioinformatics, 13 Suppl 16, S8-S8 (2012-11-28)
Selected reaction monitoring (SRM)-based proteomics approaches enable highly sensitive and reproducible assays for profiling of thousands of peptides in one experiment. The development of such assays involves the determination of retention time, detectability and fragmentation properties of peptides, followed by
Kathryn S Lilley et al.
Proteomics, 11(6), 1017-1025 (2011-03-02)
Many analytical techniques have been executed by core facilities established within academic, pharmaceutical and other industrial institutions. The centralization of such facilities ensures a level of expertise and hardware which often cannot be supported by individual laboratories. The establishment of
Vincent A Fusaro et al.
Nature biotechnology, 27(2), 190-198 (2009-01-27)
Protein biomarker discovery produces lengthy lists of candidates that must subsequently be verified in blood or other accessible biofluids. Use of targeted mass spectrometry (MS) to verify disease- or therapy-related changes in protein levels requires the selection of peptides that
Matthew The et al.
Nature communications, 11(1), 3234-3234 (2020-06-28)
In shotgun proteomics, the analysis of label-free quantification experiments is typically limited by the identification rate and the noise level in the quantitative data. This generally causes a low sensitivity in differential expression analysis. Here, we propose a quantification-first approach
Ning Li et al.
Proteomics, 12(11), 1720-1725 (2012-05-25)
In this study, we presented a quality control tool named PepDistiller to facilitate the validation of MASCOT search results. By including the number of tryptic termini, and integrating a refined false discovery rate (FDR) calculation method, we demonstrated the improved
Chia-Yu Yen et al.
Molecular & cellular proteomics : MCP, 10(7), M111-M111 (2011-05-03)
The unambiguous assignment of tandem mass spectra (MS/MS) to peptide sequences remains a key unsolved problem in proteomics. Spectral library search strategies have emerged as a promising alternative for peptide identification, in which MS/MS spectra are directly compared against a
Rabah Gahoual et al.
Journal of mass spectrometry : JMS, 51(2), 150-158 (2016-02-20)
Amino acids residues are commonly submitted to various physicochemical modifications occurring at physiological pH and temperature. Post-translational modifications (PTMs) require comprehensive characterization because of their major influence on protein structure and involvement in numerous in vivo process or signaling. Mass
Jinxia Wang et al.
Scientific reports, 7(1), 3367-3367 (2017-06-15)
Considering as one of the major goals in quantitative proteomics, detection of the differentially expressed proteins (DEPs) plays an important role in biomarker selection and clinical diagnostics. There have been plenty of algorithms and tools focusing on DEP detection in
Stephane Houel et al.
Journal of proteome research, 9(8), 4152-4160 (2010-06-29)
A complicating factor for protein identification within complex mixtures by LC/MS/MS is the problem of "chimera" spectra, where two or more precursor ions with similar mass and retention time are co-sequenced by MS/MS. Chimera spectra show reduced scores due to
Jianqiu Zhang et al.
BMC genomics, 11 Suppl 3, S8-S8 (2010-12-22)
The identification and quantification of proteins using label-free Liquid Chromatography/Mass Spectrometry (LC/MS) play crucial roles in biological and biomedical research. Increasing evidence has shown that biomarkers are often low abundance proteins. However, LC/MS systems are subject to considerable noise and
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