Abstract:
:Glycoproteins influence numerous indispensable biological functions, and changes in protein glycosylation have been observed in various diseases. The identification and characterization of glycoprotein and glycosylation sites by mass spectrometry (MS) remain challenging tasks, and great efforts have been devoted to the development of proteome informatics tools that facilitate the MS analysis of glycans and glycopeptides. Here we report on the development of gFinder, a web-based bioinformatics tool that analyzes mixtures of native N-glycopeptides that have been profiled by tandem MS. gFinder not only enables the simultaneous integration of collision-induced dissociation (CID) and high-energy collisional dissociation (HCD) fragmentation but also merges the spectra for high-throughput analysis. These merged spectra expedite the identification of both glycans and N-glycopeptide backbones in tandem MS data using the glycan database and a proteomic search tool (e.g., Mascot). These data can be used to simultaneously characterize peptide backbone sequences and possible N-glycan structures using assigned scores. gFinder also provides many convenient functions that make it easy to perform manual calculations while viewing the spectrum on-screen. We used gFinder to detect an additional protein (Q8N9B8) that was missed from the previously published data set containing N-linked glycosylation. For N-glycan analysis, we used the GlycomeDB glycan structure database, which integrates the structural and taxonomic data from all of the major carbohydrate databases available in the public domain. Thus, gFinder is a convenient, high-throughput analytical tool for interpreting the tandem mass spectra of N-glycopeptides, which can then be used for identification of potential missing proteins having glycans. gFinder is available publicly at http://gFinder.proteomix.org/ .
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Kim JW,Hwang H,Lim JS,Lee HJ,Jeong SK,Yoo JS,Paik YKdoi
10.1021/acs.jproteome.6b00772subject
Has Abstractpub_date
2016-11-04 00:00:00pages
4116-4125issue
11eissn
1535-3893issn
1535-3907journal_volume
15pub_type
杂志文章abstract::We aimed to evaluate neuroendocrine pulmonary tumors (NEPT) by a novel method involving map tree construction by comparing all of the protein spots. We performed a proteomics analysis to assess the similarities in protein expression between neuroendocrine pulmonary tumors (NEPT), including typical carcinoids (TC), aty...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr050460x
更新日期:2006-03-01 00:00:00
abstract::Human plasma and serum proteins are subject to intrinsic proteolytic degradation both during and after blood collection. By monitoring peptides, we investigated the stability of plasma and serum samples and the effects of anticoagulants and protease inhibitors on the plasma samples. Serum and plasma were subjected to ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr060550h
更新日期:2007-05-01 00:00:00
abstract::Starting in 2007, we have grown soybean (Glycine max [L.] Merr. variety Soniachna) and flax (Linum usitatissimum, L. variety Kyivskyi) in the radio-contaminated Chernobyl area and analyzed the seed proteomes. In the second-generation flax seeds, we detected a 12% increase in oil content. To characterize the bases for ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr400528m
更新日期:2013-11-01 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::Advancements in studies on the evolutionary mechanisms underlying bacterial antibiotic resistance are unclear. This study aimed to investigate the evolutionary mechanism underlying bacterial antibiotic resistance using isobaric tags for relative and absolute quantitation-based quantitative proteomics along with functi...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.9b00410
更新日期:2019-11-01 00:00:00
abstract::Increased throughput as well as increased multiplexing of liquid chromatography coupled to selected reaction monitoring mass spectrometry (LC-SRM-MS) assays for protein quantification challenges routine data analysis. Despite the measurement of multiple transitions from multiple peptides, for clinical applications a s...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.9b00854
更新日期:2020-06-05 00:00:00
abstract::Diabetes mellitus is a complex polygenic disease caused by gene-environment interactions with multiple complications, and metabonomic analysis is crucial for pathogenesis, early diagnosis, and timely interventions. Here, we comprehensively analyzed the dynamic metabolic changes in rat urine and plasma, which were indu...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr300280t
更新日期:2012-06-01 00:00:00
abstract::Recent advances in genome editing technologies have enabled the insertion of epitope tags at endogenous loci with relative efficiency. We describe an approach for investigation of protein interaction dynamics of the AMP-activated kinase complex AMPK using a catalytic subunit AMPKα2 (PRKAA2 gene) as the bait, based on ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.9b00378
更新日期:2019-10-04 00:00:00
abstract::After tissue or body fluid sampling, proteases and other protein-modifying enzymes can rapidly change composition of the proteome. As a direct consequence, analytical results will reflect a mix of in vivo proteome and ex vivo degradation products. Vital information about the presampling state may be destroyed or disto...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr8006446
更新日期:2009-02-01 00:00:00
abstract::Protein oxidation and nitration have been described during spinal cord injury (SCI) in animal models. Herein, mass spectrometry unambiguously identified GDP-dissociation inhibitor-2 (GDI-2) in SCI with post-translational modifications of 3-aminotyrosine (8 h post-injury) and an acrolein adduct of GDI-2 (72 h post-inju...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr060620k
更新日期:2007-04-01 00:00:00
abstract::Large-scale phosphoproteomic analysis employing liquid chromatography-tandem mass spectrometry (LC-MS/MS) often requires a significant amount of manual manipulation of phosphopeptide datasets in the post-acquisition phase. To assist in this process, we have created software, PhosphoPIC (PhosphoPeptide Identification a...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr0701153
更新日期:2007-09-01 00:00:00
abstract::A novel metabolite identification strategy is presented for the combined NMR/MS analysis of complex metabolite mixtures. The approach first identifies metabolite candidates from 1D or 2D NMR spectra by NMR database query, which is followed by the determination of the masses (m/z) of their possible ions, adducts, fragm...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.5b00184
更新日期:2015-06-05 00:00:00
abstract::POPX2 is a serine/threonine phosphatase belonging to the protein phosphatase 2C (PP2C) family that has been found to be elevated in invasive breast cancer cells. Silencing of POPX2 results in lower cell motility and invasiveness. The molecular mechanism of POPX2-regulated cell motility is not well understood. To ident...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr301113c
更新日期:2013-06-07 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::Chronic obstructive pulmonary disease (COPD) is one of the leading causes of morbidity and mortality around the world. However, the exact mechanisms leading to COPD and its progression are still poorly understood. In this study, induced sputum was analyzed by cysteine-specific two-dimensional difference gel electropho...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr2006395
更新日期:2012-02-03 00:00:00
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::The missing human proteome comprises predicted protein-coding genes with no credible protein level evidence detected so far and constitutes ~18% of the human protein coding genes (neXtProt release 19/9/2014). The missing proteins may be of pharmacological interest as many of these are membrane receptors, thus requirin...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.5b00728
更新日期:2015-12-04 00:00:00
abstract::Energy imbalance is a primary cause of obesity. While the classical approach to attenuate weight gain includes an increase in energy expenditure through exercise, dietary manipulation such as the inclusion of dairy products has also been proven effective. In the present study, we explored the potential mechanisms by w...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.9b00304
更新日期:2019-11-01 00:00:00
abstract::N-Glycans are an important source of milk oligosaccharides. In addition to free oligosaccharides found in milk, N-glycans can also be utilized by gut microbes. A potential for milk N-glycans to act as gut microbe regulators in suckling animals has attracted considerable attention; however, sow milk N-glycans and their...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.8b00789
更新日期:2019-03-01 00:00:00
abstract::Clostridioides difficile-associated infection (CDI) is a health-care-associated infection caused, as the name suggests, by obligate anaerobic pathogen C. difficile and thus mainly transmitted via highly resistant endospores from one person to the other. In vivo, the spores need to germinate into cells prior to establi...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.9b00413
更新日期:2019-11-01 00:00:00
abstract::Seasonal nitrogen (N) cycling in temperate deciduous trees involves the accumulation of bark storage proteins (BSPs) in phloem parenchyma and xylem ray cells. BSPs are anabolized using recycled N during autumn leaf senescence and later become a source of N during spring shoot growth as they are catabolized. Little is ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr501090p
更新日期:2015-02-06 00:00:00
abstract::Selective capture of glycopolypeptides followed by release and analysis of the former glycosylation-site peptides has been shown to have promise for reducing the complexity of body fluids such as blood for biomarker discovery. In this work, a protocol based on capture of polypeptides containing a N-linked carbohydrate...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr900845m
更新日期:2010-04-05 00:00:00
abstract::Investigation of how diatoms cope with the rapid fluctuations in iron bioavailability in marine environments may facilitate a better understanding of the mechanisms underlying their ecological success, in particular their ability to proliferate rapidly during favorable conditions. In this study, using in vivo biochemi...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr5004664
更新日期:2014-12-05 00:00:00
abstract::Spontaneous preterm birth (SPTB) is a major contributor to perinatal morbidity and mortality. However, the diagnosis of preterm labor (PTL) that leads to preterm birth is difficult, and there is a pressing need for improved diagnosis. We utilized multidimensional liquid chromatography-tandem mass spectrometry (LC/LC-M...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr0605421
更新日期:2007-04-01 00:00:00
abstract::Salt stress is a major abiotic factor limiting maize yield. To characterize the mechanism underlying maize salt tolerance, we compared the seedling root proteomes of salt-tolerant Jing724 and salt-sensitive D9H. The germination rate and growth parameter values (weight and length) were higher for Jing724 than for D9H u...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.7b00455
更新日期:2018-01-05 00:00:00
abstract::Isobaric tagging is the method of choice in mass-spectrometry-based proteomics for comparing several conditions at a time. Despite its multiplexing capabilities, some drawbacks appear when multiple experiments are merged for comparison in large sample-size studies due to the presence of missing values, which result fr...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.8b00110
更新日期:2018-06-01 00:00:00
abstract::Redox regulation plays an important role across a broad spectrum of biology. Accumulating evidence suggests that thioredoxin, a widely distributed redox enzyme, participates in the redox control of numerous target proteins, thus, playing a key role as a signaling intermediate that senses the metabolic state or environ...
journal_title:Journal of proteome research
pub_type: 杂志文章,评审
doi:10.1021/pr8003453
更新日期:2008-08-01 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::Phencyclidine (PCP), a noncompetitive N-methyl-D-aspartate receptor antagonist, induces psychotomimetic effects in humans and animals. Administration of PCP to rodents is used as a preclinical model for schizophrenia; however, the molecular mechanisms underlying the symptoms remain largely unknown. Acute PCP treatment...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr4010794
更新日期:2014-03-07 00:00:00
abstract::Protein biomarkers are critical for diagnosis, prognosis, and treatment of disease. The transition from protein biomarker discovery to verification can be a rate limiting step in clinical development of new diagnostics. Liquid chromatography-selected reaction monitoring mass spectrometry (LC-SRM MS) is becoming an imp...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr2006704
更新日期:2012-02-03 00:00:00