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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
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
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
Min-Sik Kim et al.
Journal of the American Society for Mass Spectrometry, 21(9), 1606-1611 (2010-05-21)
Shotgun proteomics has been used extensively for characterization of a number of proteomes. High-resolution Fourier transform mass spectrometry (FTMS) has emerged as a powerful tool owing to its high mass accuracy and resolving power. One of its major limitations, however
Klemens Fröhlich et al.
Nature communications, 13(1), 2622-2622 (2022-05-14)
Numerous software tools exist for data-independent acquisition (DIA) analysis of clinical samples, necessitating their comprehensive benchmarking. We present a benchmark dataset comprising real-world inter-patient heterogeneity, which we use for in-depth benchmarking of DIA data analysis workflows for clinical settings. Combining
Subina Mehta et al.
Proteomes, 8(3) (2020-07-12)
For mass spectrometry-based peptide and protein quantification, label-free quantification (LFQ) based on precursor mass peak (MS1) intensities is considered reliable due to its dynamic range, reproducibility, and accuracy. LFQ enables peptide-level quantitation, which is useful in proteomics (analyzing peptides carrying
Takashi Baba et al.
The Journal of biological chemistry, 289(16), 11497-11511 (2014-03-07)
Recent studies have suggested that phosphatidic acid (PA), a cone-shaped phospholipid that can generate negative curvature of lipid membranes, participates in mitochondrial fusion. However, precise mechanisms underling the production and consumption of PA on the mitochondrial surface are not fully
Xuepo Ma et al.
Proteome science, 9 Suppl 1, S2-S2 (2011-12-15)
Fourier Transform Mass Spectrometry coupled with Liquid Chromatography(LC-FTMS) has been widely used in proteomics. Past investigation has revealed that there exists an intensity dependent random suppression in peptide elution profiles in LC-FTMS data. The suppression is homogenous for the same
Paul A Rudnick et al.
Molecular & cellular proteomics : MCP, 13(5), 1341-1351 (2014-02-25)
Normalization is an important step in the analysis of quantitative proteomics data. If this step is ignored, systematic biases can lead to incorrect assumptions about regulation. Most statistical procedures for normalizing proteomics data have been borrowed from genomics where their
Tamar Geiger et al.
Molecular & cellular proteomics : MCP, 9(10), 2252-2261 (2010-07-09)
The orbitrap mass analyzer combines high sensitivity, high resolution, and high mass accuracy in a compact format. In proteomics applications, it is used in a hybrid configuration with a linear ion trap (LTQ-Orbitrap) where the linear trap quadrupole (LTQ) accumulates
Alexander R Ivanov et al.
Proteomics, 13(6), 904-909 (2013-01-16)
Proteomics is a rapidly transforming interdisciplinary field of research that embraces a diverse set of analytical approaches to tackle problems in fundamental and applied biology. This viewpoint article highlights the benefits of interlaboratory studies and standardization initiatives to enable investigators
Klaus Faserl et al.
Journal of chromatography. A, 1498, 215-223 (2017-02-10)
Reversed-phase high-performance liquid chromatography (RP-HPLC) in combination with mass spectrometry (MS) is typically employed for mapping modifications in proteins and peptides. Here we applied a low-flow capillary electrophoresis (CE) -electrospray ionization interface coupled to Orbitrap mass spectrometers to analyze challenging
Spectrum-to-Spectrum Searching Using a Proteome-wide Spectral Library
Yen, C.-Y., et al.
Molecular and Cellular Proteomics, 10, 1-15 (2011)
Bensheng Li et al.
Journal of proteomics, 74(11), 2510-2521 (2011-04-26)
3-nitrotyrosine (3NT) is an oxidative posttranslational modification associated with many diseases. Determining the specific sites of this modification remains a challenge due to the low stoichiometry of 3NT modifications in biological samples. Mass spectrometry-based proteomics is a powerful tool for
Daryl Wilding-McBride et al.
PloS one, 17(7), e0271025-e0271025 (2022-07-08)
For bottom-up proteomic analysis, the goal of analytical pipelines that process the raw output of mass spectrometers is to detect, characterise, identify, and quantify peptides. The initial steps of detecting and characterising features in raw data must overcome some considerable
Mark V Ivanov et al.
Journal of proteome research, 13(4), 1911-1920 (2014-02-28)
Data-dependent tandem mass spectrometry (MS/MS) is one of the main techniques for protein identification in shotgun proteomics. In a typical LC-MS/MS workflow, peptide product ion mass spectra (MS/MS spectra) are compared with those derived theoretically from a protein sequence database.
Henrik Molina et al.
Analytical chemistry, 80(13), 4825-4835 (2008-06-11)
Electron transfer dissociation (ETD) is a recently introduced mass spectrometric technique which has proven to be an excellent tool for the elucidation of labile post-translational modifications such as phosphorylation and O-GlcNAcylation of serine and threonine residues. However, unlike collision induced
Chia-Yu Yen et al.
Molecular & cellular proteomics : MCP, 8(4), 857-869 (2008-12-25)
Identifying peptides from mass spectrometric fragmentation data (MS/MS spectra) using search strategies that map protein sequences to spectra is computationally expensive. An alternative strategy uses direct spectrum-to-spectrum matching against a reference library of previously observed MS/MS that has the advantage
Robert Winkler
Journal of proteomics, 230, 103985-103985 (2020-09-22)
Comparing multiple label-free shotgun proteomics datasets requires various data processing and formatting steps, including peptide-spectrum matching, protein inference, and quantification. Finally, the compilation of results files into a format that allows for downstream analyses. ProtyQuant performs protein inference and quantification
Markus Brosch et al.
Molecular & cellular proteomics : MCP, 7(5), 962-970 (2008-01-25)
It is a major challenge to develop effective sequence database search algorithms to translate molecular weight and fragment mass information obtained from tandem mass spectrometry into high quality peptide and protein assignments. We investigated the peptide identification performance of Mascot
Attila Kertész-Farkas et al.
Bioinformatics (Oxford, England), 30(2), 234-241 (2013-11-12)
Tandem mass spectrometry has become a standard tool for identifying post-translational modifications (PTMs) of proteins. Algorithmic searches for PTMs from tandem mass spectrum data (MS/MS) tend to be hampered by noisy data as well as by a combinatorial explosion of
W Sean Davidson et al.
Arteriosclerosis, thrombosis, and vascular biology, 29(6), 870-876 (2009-03-28)
Recent proteomic studies have identified multiple proteins that coisolate with human HDL. We hypothesized that distinct clusters of protein components may distinguish between physicochemically-defined subpopulations of HDL particles, and that such clusters may exert specific biological function(s). We investigated the
David Bouyssié et al.
Bioinformatics (Oxford, England), 36(10), 3148-3155 (2020-02-26)
The proteomics field requires the production and publication of reliable mass spectrometry-based identification and quantification results. Although many tools or algorithms exist, very few consider the importance of combining, in a unique software environment, efficient processing algorithms and a data
Olli Kannaste et al.
Journal of proteome research, 13(4), 1957-1968 (2014-03-13)
The measurement of change in biological systems through protein quantification is a central theme in modern biosciences and medicine. Label-free MS-based methods have greatly increased the ease and throughput in performing this task. Spectral counting is one such method that
David L Tabb et al.
Journal of proteome research, 6(2), 654-661 (2007-02-03)
Shotgun proteomics experiments are dependent upon database search engines to identify peptides from tandem mass spectra. Many of these algorithms score potential identifications by evaluating the number of fragment ions matched between each peptide sequence and an observed spectrum. These
Hiromi W L Koh et al.
Proteomics, 15(15), 2580-2591 (2015-04-29)
Labeling-based proteomics is a powerful method for detection of differentially expressed proteins (DEPs). The current data analysis platform typically relies on protein-level ratios, which is obtained by summarizing peptide-level ratios for each protein. In shotgun proteomics, however, some proteins are
Sean McIlwain et al.
BMC bioinformatics, 13, 308-308 (2012-11-21)
Spectral counting methods provide an easy means of identifying proteins with differing abundances between complex mixtures using shotgun proteomics data. The crux spectral-counts command, implemented as part of the Crux software toolkit, implements four previously reported spectral counting methods, the
Isma Belouah et al.
Journal of proteomics, 193, 131-141 (2018-10-13)
In bottom-up proteomics, data are acquired on peptides resulting from proteolysis. In XIC-based quantification, the quality of the estimation of protein abundance depends on how peptide data are filtered and on which quantification method is used to express peptide intensity
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