Abstract：
:Spectral library searching is a popular approach for MS/MS-based peptide identification. Because the size of spectral libraries continues to grow, the performance of searching algorithms is an important issue. This technical note introduces a strategy based on a minimum shared peak count between two spectra to reduce the set of admissible candidate spectra when issuing a query. A theoretical validation through time complexity analysis and an experimental validation based on an implementation of the candidate reduction strategy show that the approach can achieve a reduction of the set of candidate spectra by (at least) an order of magnitude, resulting in a significant improvement in the speed of the search. Meanwhile, more than 99% of the positive search results is retained. This efficient strategy to drastically improve the speed of spectral library searching with a negligible loss of sensitivity can be applied to any current spectral library search tool, irrespective of the employed similarity metric.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Vu TN,Bittremieux W,Valkenborg D,Goethals B,Lemière F,Laukens Kdoi
10.1021/pr401269zsubject
Has Abstractpub_date
2014-09-05 00:00:00pages
4175-83issue
9eissn
1535-3893issn
1535-3907journal_volume
13pub_type
杂志文章abstract：:Oligomeric amyloid-β is currently of interest in amyloid-β mediated toxicity and the pathogenesis of Alzheimer's disease. Mapping the amyloid-β interaction partners could help to discover novel pathways in disease pathogenesis. To discover the amyloid-β interaction partners, we applied a protein array with more than 8...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr1009096
更新日期：2011-04-01 00:00:00
abstract：:Rapid early triage and dose estimation is vital for limited medical resource allocation and treatment of a large number of the wounded after radiological accidents. Lipidomics has been utilized to delineate biofluid lipid signatures after irradiation. Here, high-coverage targeted lipidomics was employed to screen radi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00560
更新日期：2021-01-01 00:00:00
abstract：:As a model carcinogen in studying the mutagenicity and carcinogenicity of N-nitroso alkylating agent, N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) can induce DNA damages and many cellular defensive events, such as DNA repair, G2/M-phase arrest and apoptosis. Noticeably, diverse cellular responses were observed to occur...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900008n
更新日期：2009-06-01 00:00:00
abstract：:beta-Cell granules contain proteins involved in fuel regulation, which when altered, contribute to metabolic disorders including diabetes mellitus. We analyzed proteins present in purified granules from the INS-1E beta-cell model. Fifty-one component proteins were identified by LC-MS/MS including hormones, granins, pr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800675k
更新日期：2009-01-01 00:00:00
abstract：:A database of nonredundant structures of EF-hand domains--i.e., pairs of helix-loop-helix motifs--has been assembled, and the six angles among the four helices re-determined. A principal component analysis of these angles allows us to use two such components (PC1 and PC2) to describe the system retaining 80% of the to...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050148n
更新日期：2005-11-01 00:00:00
abstract：:Coronary artery disease remains a leading cause of death in industrialized nations, and early detection of disease is a critical intervention target to effectively treat patients and manage risk. Proteomic analysis of mixed tissue homogenates may obscure subtle protein changes that occur uniquely in underlying tissue ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00118
更新日期：2020-07-02 00:00:00
abstract：:In the framework of the C-HPP, our Franco-Swiss consortium has adopted chromosomes 2 and 14, coding for a total of 382 missing proteins (proteins for which evidence is lacking at protein level). Over the last 4 years, the French proteomics infrastructure has collected high-quality data sets from 40 human samples, incl...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr5010345
更新日期：2015-09-04 00:00:00
abstract：:The final goal of the Russian part of the Chromosome-centric Human Proteome Project (C-HPP) was established as the analysis of the chromosome 18 (Chr 18) protein complement in plasma, liver tissue and HepG2 cells with the sensitivity of 10(-18) M. Using SRM, we have recently targeted 277 Chr 18 proteins in plasma, liv...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300821n
更新日期：2013-01-04 00:00:00
abstract：:Type 1 diabetes, in human patients and NOD mice, results from an immune attack on insulin-producing beta-cells of the pancreas by autoreactive T lymphocytes. In NOD mice, genetically controlled perturbations in the signaling pathways downstream of the antigen-specific T cell receptor (TCR) may be instrumental in the a...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100035b
更新日期：2010-06-04 00:00:00
abstract：:Prostate cancer (PCa) is the second leading cause of cancer-related mortality in men. The prevalent diagnosis method is based on the serum prostate-specific antigen (PSA) screening test, which suffers from low specificity, overdiagnosis, and overtreatment. In this work, untargeted metabolomic profiling of age-matched ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500409q
更新日期：2014-07-03 00:00:00
abstract：:12-O-Tetradecanoyl-phorbol-13-acetate (TPA) is a plant derivative with multiple function as tumor promoter, differentiation revulsant or leukemia therapy drug. The molecular mechanism of its function is perplexing. Many studies have focused on the mechanism of TPA stimulation in tumor promotion of mouse models or term...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0497677
更新日期：2005-03-01 00:00:00
abstract：:Proteomic studies were performed to identify the protein species involved in copper (Cu) stress responses in common wheat. Two-week-old wheat seedlings were exposed to 100 μM CuSO4 treatment for 3 days. Growth of shoots and roots was markedly inhibited and lipid peroxidation was greatly increased. Cu was readily absor...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4008283
更新日期：2013-11-01 00:00:00
abstract：:The majority of mitochondrial preproteins are targeted via N-terminal presequences that are cleaved upon import into the organelle. The essential mitochondrial processing protease (MPP) is assumed to cleave the majority of incoming precursors; however, only a small fraction of mitochondrial precursors have been experi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00327
更新日期：2015-11-06 00:00:00
abstract：:The effects of acute and chronic stress on the production of systemic metabolites were investigated in male Sprague-Dawley (SD) rats. Metabolites excreted in urine were analyzed using GC/MS in conjunction with multivariate and univariate statistical techniques. SD rats were subjected to two kinds of acute stress and c...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr801086k
更新日期：2009-05-01 00:00:00
abstract：:Difference gel electrophoresis (DiGE) allows the reliable comparison of proteome differences between two or three samples within a single gel, by way of a CyDye fluorescent labeling system. This facilitates identification of protein differences avoiding the difficulties associated with gel-to-gel variation. A drawback...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0606878
更新日期：2007-09-01 00:00:00
abstract：:Roux-en-Y gastric bypass (RYGB) is one of the most effective treatments for long-term weight loss and diabetes remission; however, the mechanisms underlying these changes are not clearly understood. In this study, the serum metabolic profiles of 23 remission and 12 nonremission patients with type 2 diabetes mellitus (...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00022
更新日期：2016-04-01 00:00:00
abstract：:The paper describes the implementation of a software system based on the Fenyö disulfide bond assignment algorithm. The system allows an investigator to enter data derived from mass spectrum peak assignments, a target protein sequence and other experimental conditions. The output of the system is the set of disulfide ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr034016a
更新日期：2003-11-01 00:00:00
abstract：:Phosphorylation is an essential post-translational modification for regulating protein function and cellular signal transduction. Mass spectrometry (MS) combined with isobaric tandem mass tags (TMTs) has become a powerful platform for simultaneous, large-scale phospho-proteome site identification and quantitation. To ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00610
更新日期：2017-11-03 00:00:00
abstract：:We investigated possible associations between sequence evolution of mammalian sperm proteins and their phosphorylation status in humans. As a reference, spermatozoa from three normozoospermic men were analyzed combining two-dimensional gel electrophoresis, immunoblotting, and mass spectrometry. We identified 99 sperm ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400228c
更新日期：2013-12-06 00:00:00
abstract：:Glioblastoma multiforme (GBM) is the most aggressive malignant primary brain tumor, with a dismal mean survival even with the current standard of care. Although in vitro cell systems can provide mechanistic insight into the regulatory networks governing GBM cell proliferation and migration, clinical samples provide a ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500418w
更新日期：2014-11-07 00:00:00
abstract：:Protein interaction networks display approximate scale-free topology, in which hub proteins that interact with a large number of other proteins determine the overall organization of the network. In this study, we aim to determine whether hubs are distinguishable from other networked proteins by specific sequence featu...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060171o
更新日期：2006-11-01 00:00:00
abstract：:Defined as proteins actively transported via secretion systems, secreted proteins can have radically different subcellular destinations in monoderm (Gram-positive) bacteria. From degradative enzymes in saprophytes to virulence factors in pathogens, secreted proteins are the main tools used by bacteria to interact with...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr1003642
更新日期：2010-10-01 00:00:00
abstract：:RelA (NF-kappaB) is a transcription factor inducible by distinct stimuli in many different cell types. To find new cell type specific cofactors of NF-kappaB dependent transcription, we isolated RelA transcription activation domain binding proteins from the nuclear extracts of three different cell types. Analysis by el...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0500713
更新日期：2005-07-01 00:00:00
abstract：:Populations around the world are aging rapidly. Age-related loss of physiological functions negatively affects quality of life. A major contributor to the frailty syndrome of aging is loss of skeletal muscle. In this study we assessed the skeletal muscle biopsy metabolome of healthy young, healthy older and frail olde...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00840
更新日期：2016-02-05 00:00:00
abstract：:MHC molecules present protein-derived peptides to T lymphocytes. By developing TiO2-based microcentrifugation columns, we identified the first phosphorylated MHC class I ligands from tumor tissue (renal cell carcinoma) and, by comparison to healthy renal tissue, found one Brf1-derived ligand as potentially tumor-assoc...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800937k
更新日期：2009-07-01 00:00:00
abstract：:Breast cancer is a leading cancer in women and is considered to be the second-most common metastatic cancer following lung cancer. An estimated 10-16% of breast cancer patients are suffering from brain metastasis, and the diagnostic cases of breast cancer brain metastasis are increasing. Nevertheless, the mechanisms b...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00429
更新日期：2019-10-04 00:00:00
abstract：:Herein, we report on the venom proteome of Vipera anatolica senliki, a recently discovered and hitherto unexplored subspecies of the critically endangered Anatolian meadow viper endemic to the Antalya Province of Turkey. Integrative venomics, including venom gland transcriptomics as well as complementary bottom-up and...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00869
更新日期：2020-04-03 00:00:00
abstract：:Equine grass sickness (EGS) is a frequently fatal disease of horses, responsible for the death of 1 to 2% of the U.K. horse population annually. The etiology of this disease is currently uncharacterized, although there is evidence it is associated with Clostridium botulinum neurotoxin in the gut. Prevention is current...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00784
更新日期：2018-03-02 00:00:00
abstract：:Proteins are involved in all tasks of life, and their characterization is essential to understand the underlying mechanisms of biological processes. We present a method called "differential visual proteomics" geared to study proteome-wide structural changes of proteins and protein-complexes between a disturbed and an ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00447
更新日期：2019-09-06 00:00:00
abstract：:Aquaporin (AQP) family plays a pivotal role in fluid secretion and absorption, especially in the digestive system and secretory glands. Within this family, AQP8 was reported to be widely expressed in the epithelia of the digestive tract, liver, and pancreas. In two parallel experimental platforms with different analyt...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100789v
更新日期：2010-12-03 00:00:00
