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Showing 1 to 15 of 15 for “"Peptide identification"”.
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Distributed Approach for Peptide Identification
<p>A crucial step in protein identification is peptide identification. The Peptide Spectrum Match (PSM) information set is enormous. Hence, it is a time-consuming procedure to work on a single machine. PSMs are situated by a cross connection, a factual score, or a probability that the match between …
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Neuropeptidomics: MS-base peptide identification and quantitation study
… approach for the investigation of neuropeptides, often under specific physiological conditions. Neuropeptides comprise a complex set of cell-to-cell signaling molecules that are important in regulatory functions and behavior in the nervous system. Neuropeptide production typically …
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Algorithms for Peptide Identification from Mixture Tandem Mass Spectra
… which, one particular challenge is that the identification rate of the MS/MS spectra collected is rather low. One significant reason that contributes to this situation is the frequently observed mixture spectra, which result from the concurrent fragmentation of multiple precursors in a single …
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An Apache Hadoop Framework for Large-Scale Peptide Identification
<p>Peptide identification is an essential step in protein identification, and Peptide Spectrum Match (PSM) data set is huge, which is a time consuming process to work on a single machine. In a typical run of the peptide identification method, PSMs are positioned by a cross correlation, a …
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classCleaner: A Quantitative Method for Validating Peptide Identification in LC-MS/MS Workflows
… (LC-MS/MS) shotgun proteomics infers the peptide sequence of each measurement, there is inherent uncertainty in the identity of each peptide and its originating protein. Removing misidentified peptides can improve the accuracy and power of downstream analyses when differences between …
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Comparison of chickpea varieties, optimization of hydrolysates production, peptide identification and evaluation of biomarkers for type 2 diabetes in the application of a value-added tortilla.
… Myles and a commercial sample), identify the peptides obtained with pepsin-pancreatin digestion, and evaluate their potential as modulators of biochemical markers for type-2 diabetes (T2D). In addition, it was aimed to produce, by the optimization in the production of hydrolysates using …
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Improving the Performance and Precision of Bioinformatics Algorithms
… alignments of comparable or better quality. Peptide identification by tandem mass spectrometry (MS/MS) is becoming the dominant high-throughput proteomics workflow for protein characterization in complex samples. Biologists currently rely on protein database search engines to identify …
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Evaluation of database search programs for accurate detection of neuropeptides in tandem mass spectrometry experiments
… experiments are not optimized to identify neuropeptides and other peptides resulting from the processing of prohormones. This is due to the unique characteristics of neuropeptides including release after complex processing of prohormones, potentially intense post-translational modifications and …
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Development and Application of Next Generation Mass Spectrometry for Protein Analysis at High-Resolution
… MS/MS platform was developed to analyze large peptides at >>50,000 resolving power along with a software suite for interpreting resolved isotopic distributions and handling all known protein modifications on a high throughput basis. Called Middle Down Proteomics, this process identified 7454 …
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Computational methods and machine learning for crosslinking mass spectrometry data analysis
… the fragmentation behavior of crosslinked peptides to design efficient database search strategies and improved acquisition settings. CLMS builds upon the preservation of distance information by crosslinking reagents, which is relayed by mass spectrometric analysis. To identify a crosslink …
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Mass spectrometry-based characterization of cell-to-cell signaling molecules in the nervous system
… within organisms. Small molecules and peptides work as neurotransmitters and neuromodulators in the nervous system and play important regulatory roles in a wide range of physiological events and animal behaviors, such as pain sensation, food intake, memory, circadian rhythm, tissue …
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Multifactorial modeling of ion abundance in tandem mass spectrometry experiments
Restriction data tranferred 2014-07-01T11:35:49-05:00 Original Data Group with Access Administrator Release Date: 2014-09-18 16:27:16 UTC Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system
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Rational Identification of Neuropilin-1 Inhibitors: From Deep-Learning to Drug Repurposing
… thesis, that gap is addressed by the rational identification of peptide and small-molecule inhibitors that can disrupt engagement at the NRP1-b1 pocket, and by the establishment of methodological principles for their discovery and validation. A multimodal framework was assembled in which …
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Click Chemistry on DNA and Targeting RNA structure with Peptide Boronic Acids
… in biotechnology and diagnostics. Interest in peptides incorporating boronic acid moieties is increasing due to their potential as therapeutics/diagnostics for a variety of diseases such as cancer. The utility of peptide boronic acids may be expanded with access to vast libraries that can be …
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Development of an Improved Proteogenomics Solution to Identify Comprehensive Catalogues of Novel Small Proteins in Prokaryotes
… complete genome sequence is known. However, the identification of the genes encoded therein is still challenging, limiting the insights that can be gained. Genes are annotated using computational tools and ideally validated experimentally, but both approaches can miss genes, especially small …