Abstract：
:As large-scale cross-linking data becomes available, new software tools for data processing and visualization are required to replace manual data analysis. XLink-DB serves as a data storage site and visualization tool for cross-linking results. XLink-DB accepts data generated with any cross-linker and stores them in a relational database. Cross-linked sites are automatically mapped onto PDB structures if available, and results are compared to existing protein interaction databases. A protein interaction network is also automatically generated for the entire data set. The XLink-DB server, including examples, and a help page are available for noncommercial use at http://brucelab.gs.washington.edu/crosslinkdbv1/ . The source code can be viewed and downloaded at https://sourceforge.net/projects/crosslinkdb/?source=directory .
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Zheng C,Weisbrod CR,Chavez JD,Eng JK,Sharma V,Wu X,Bruce JEdoi
10.1021/pr301162jsubject
Has Abstractpub_date
2013-04-05 00:00:00pages
1989-95issue
4eissn
1535-3893issn
1535-3907journal_volume
12pub_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：:As cellular metabolic hubs, mitochondria are the main energy producers for the cell. These organelles host essential energy producing biochemical processes, including the TCA cycle, fatty acid oxidation, and oxidative phosphorylation. An accumulating body of literature has demonstrated that a majority of mitochondrial...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/acs.jproteome.9b00086
更新日期：2019-05-03 00:00:00
abstract：:Phytopathogenic fungi are one of the most damaging plant parasitic organisms, and can cause serious diseases and important yield losses in crops. The study of the biology of these microorganisms and the interaction with their hosts has experienced great advances in recent years due to the development of moderm, holist...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/pr200873p
更新日期：2012-01-01 00:00:00
abstract：:Colorectal cancer (CRC) is a growing cause of mortality in developing countries, warranting investigation into its etiopathogenesis and earlier diagnosis. Here, we investigated the fecal metabolic phenotype of patients with advanced colorectal neoplasia and controls using (1)H-nuclear magnetic resonance (NMR) spectros...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00277
更新日期：2015-09-04 00:00:00
abstract：:Src family kinases (SFKs) are the earliest known family of tyrosine kinases and are widely thought to play essential roles in cellular signal transduction. Although numerous functional analyses have been performed, no study has analyzed the specificity of all SFKs on an equal platform. To gain a better understanding o...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100773t
更新日期：2010-11-05 00:00:00
abstract：:Campylobacter jejuni is the most common cause of bacterial gastroenteritis in the developed world. Immunoproteomics highlighted a 42-45 kDa antigen that comigrated on two-dimensional (2-DE) gels with the C. jejuni major outer membrane protein (MOMP). Predictive analysis revealed two candidates for the identity of the ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900544x
更新日期：2009-10-01 00:00:00
abstract：:Fusarium graminearum (FG) is a serious plant pathogen causing huge losses in global production of wheat and other cereals. Tri5-gene encoded trichodiene synthase is the first key enzyme for biosynthesis of trichothecene mycotoxins in FG. To further our understandings of FG metabolism which is essential for developing ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr101095t
更新日期：2011-05-06 00:00:00
abstract：:Tryptic digestion of biotinylated Lys-C peptides followed by affinity chromatography allows the selective isolation of lysine-free tryptic peptides delimited by arginine residues (RRnK peptides). In silico analysis revealed that RRnK peptides represent 87% of the whole proteomes and their specific isolation simplifies...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060003w
更新日期：2006-05-01 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：:As a recently validated reversible post translational modification, lysine malonylation regulates diverse cellular processes from bacteria to mammals, but its existence and function in photosynthetic organisms remain unknown. Cyanobacteria are the most ancient group of photosynthetic prokaryotes and contribute about 5...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00017
更新日期：2017-05-05 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：:A detailed understanding of the relationships between the distinct metabolic compartments of blood and milk would be of potential benefit to our understanding of the physiology of lactation, and potentially for development of biomarkers for health and commercially relevant traits in dairy cattle. NMR methods were used...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr301056q
更新日期：2013-03-01 00:00:00
abstract：:The development of computational strategies for the quantitative characterization of the functional mechanisms of SARS-CoV-2 spike proteins is of paramount importance in efforts to accelerate the discovery of novel therapeutic agents and vaccines combating the COVID-19 pandemic. Structural and biophysical studies have...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00654
更新日期：2020-11-06 00:00:00
abstract：:Minimal hepatic encephalopathy (MHE) reduces quality of life of cirrhotic patients, predicts overt hepatic encephalopathy, and is associated with poor prognosis. We hypothesized that MHE arises once metabolic alterations derived from the liver reach a particular threshold. Our aim was to assess whether metabolic profi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100486e
更新日期：2010-10-01 00:00:00
abstract：:For the 2018 YPIC Challenge, contestants were invited to try to decipher two unknown English questions encoded by a synthetic protein expressed in Escherichia coli. In addition to deciphering the sentence, contestants were asked to determine the three-dimensional structure and detect any post-translation modifications...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00384
更新日期：2019-11-01 00:00:00
abstract：:Broadly neutralizing antibodies (bNAbs) that target the trimeric HIV-1 envelope glycoprotein spike (Env) are tools that can guide the design of recombinant Env proteins intended to engage the predicted human germline precursors of bNAbs (gl-bNAbs). The protein components of gl-bNAb epitopes are often masked by glycans...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00639
更新日期：2018-03-02 00:00:00
abstract：:Since 2012, missing proteins (MPs) investigation has been one of the critical missions of Chromosome-Centric Human Proteome Project (C-HPP) through various biochemical strategies. On the basis of our previous testis MPs study, faster scanning and higher resolution mass-spectrometry-based proteomics might be conducive ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00390
更新日期：2016-11-04 00:00:00
abstract：:Genetically identical cloned pigs should in principle eliminate biological variation and provide more pronounced effects when subjected to, e.g., dietary interventions, but little is known about how phenotype and phenotypic variation is affected by cloning. Therefore, an investigation of the metabolome of cloned pigs ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr201253h
更新日期：2012-07-06 00:00:00
abstract：:We compared the metabolomic profile of aqueous humor from patients with primary open-angle glaucoma (POAG; n = 26) with that of a group of age- and sex-matched non-POAG controls (n = 26), all participants undergoing cataract surgery. Supervised paired partial least-squares discriminant analysis showed good predictive ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00915
更新日期：2019-03-01 00:00:00
abstract：:Numerous reports have predicted/hypothesized a role for probenazole-induced protein (PBZ1) as a molecular marker in rice self-defense mechanism. However, the precise function of PBZ1 remains unknown. In the present study, we examined PBZ1 as a putative cell death marker in rice. For this, we focused our attention on a...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr700878t
更新日期：2008-04-01 00:00:00
abstract：:Analysis of the cerebrospinal fluid (CSF) proteome has proven valuable to the study of neurodegenerative disorders. To identify new protein/pathway alterations and candidate biomarkers for amyotrophic lateral sclerosis (ALS), we performed comparative proteomic profiling of CSF from sporadic ALS (sALS), healthy control...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00804
更新日期：2015-11-06 00:00:00
abstract：:Staphylococcus aureus with spa-type t437 has been identified as a predominant community-associated methicillin-resistant S. aureus clone from Asia, which is also encountered in Europe. Molecular typing has previously shown that t437 isolates are highly similar regardless of geographical regions or host environments. T...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00179
更新日期：2019-07-05 00:00:00
abstract：:The Biology/Disease-driven (B/D) working groups of the Human Proteome Project are alliances of research groups aimed at developing or improving proteomic tools to support specific biological or disease-related research areas. Here, we describe the activities and progress to date of the B/D working group focused on pro...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/acs.jproteome.8b00401
更新日期：2018-12-07 00:00:00
abstract：:We report the use of chemical derivatization with MALDI-MS/MS analysis for de novo sequence analysis. Using three frequently used homology-based search algorithms, we were able to identify more than 40 proteins from banana, a nonmodel plant with unsequenced genome. Furthermore, this approach allowed the identification...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0601943
更新日期：2007-01-01 00:00:00
abstract：:Proteomics by mass spectrometry (MS) allows the large-scale identification and quantitation of the cellular proteins in a given biological context. Systems biology studies from proteomics data are largely limited by the accuracy and coverage of quantitative proteomics along with missing values. Toward this end, statis...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/acs.jproteome.9b00228
更新日期：2019-06-07 00:00:00
abstract：:Tyrosine phosphorylation plays a major role in regulating cell signaling pathways governing diverse biological functions such as proliferation and differentiation. Systemically mapping phosphotyrosine (pTyr) sites is the key to understanding molecular mechanisms underlining pTyr-dependent signaling. Although mass spec...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00045
更新日期：2019-04-05 00:00:00
abstract：:Early pathogenic events in Alzheimer's disease (AD) involve increased production and/or reduced clearance of beta-amyloid (Abeta), especially the 42 amino acid fragment Abeta1-42. The Abeta1-42 peptide is generated through cleavage of the amyloid precursor protein by beta- and gamma-secretase and is catabolised by a v...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050475v
更新日期：2006-04-01 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：:To cope with sudden changes in the external environment, the budding yeast Saccharomyces cerevisiae orchestrates a multifaceted response that spans many levels of physiology. Several studies have interrogated the transcriptome response to endoplasmic reticulum (ER) stress and the role of regulators such as the Ire1 ki...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00253
更新日期：2020-08-07 00:00:00
abstract：:The identification and the present wide acceptance of cardiovascular risk factors such as age, sex, hypertension, hyperlipidemia, smoking, obesity, diabetes, and physical inactivity have led to dramatic reductions in cardiovascular morbidity and mortality. However, novel risk predictors present opportunities to identi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200452j
更新日期：2011-11-04 00:00:00
