Abstract：
:The Model Organism Protein Expression Database (MOPED, http://moped.proteinspire.org) is an expanding proteomics resource to enable biological and biomedical discoveries. MOPED aggregates simple, standardized and consistently processed summaries of protein expression and metadata from proteomics (mass spectrometry) experiments from human and model organisms (mouse, worm, and yeast). The latest version of MOPED adds new estimates of protein abundance and concentration as well as relative (differential) expression data. MOPED provides a new updated query interface that allows users to explore information by organism, tissue, localization, condition, experiment, or keyword. MOPED supports the Human Proteome Project's efforts to generate chromosome- and diseases-specific proteomes by providing links from proteins to chromosome and disease information as well as many complementary resources. MOPED supports a new omics metadata checklist to harmonize data integration, analysis, and use. MOPED's development is driven by the user community, which spans 90 countries and guides future development that will transform MOPED into a multiomics resource. MOPED encourages users to submit data in a simple format. They can use the metadata checklist to generate a data publication for this submission. As a result, MOPED will provide even greater insights into complex biological processes and systems and enable deeper and more comprehensive biological and biomedical discoveries.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Higdon R,Stewart E,Stanberry L,Haynes W,Choiniere J,Montague E,Anderson N,Yandl G,Janko I,Broomall W,Fishilevich S,Lancet D,Kolker N,Kolker Edoi
10.1021/pr400884csubject
Has Abstractpub_date
2014-01-03 00:00:00pages
107-13issue
1eissn
1535-3893issn
1535-3907journal_volume
13pub_type
杂志文章abstract：:Campylobacter jejuni, an important foodborne microorganism, poses severe and emergent threats to human health as antibiotic resistance becomes increasingly prevalent. The mechanisms of drug resistance are hard to decipher, and little is known at the metabolic level. Here we apply metabolomic profiling to discover meta...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr501061d
更新日期：2015-02-06 00:00:00
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 ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr401269z
更新日期：2014-09-05 00:00:00
abstract：:Reversible phosphorylations play a critical role in most biological pathways. Hence, in signaling studies great effort has been put into identification of a maximum number of phosphosites per experiment. Mass spectrometry (MS)-based phosphoproteomics approaches have been proven to be an ideal analytical method for map...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200092z
更新日期：2011-08-05 00:00:00
abstract：:The purpose of this study was to determine the system-wide consequences of deficiencies in two essential micronutrients, vitamins E and C, on the proteome using zebrafish (Danio rerio) as one of the few vertebrate models that similar to humans cannot synthesize vitamin C. We describe a label-free proteomics workflow t...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr401108d
更新日期：2014-03-07 00:00:00
abstract：:Mutagenesis through fast neutron (FN) radiation of soybean resulted in a mutant with a 15% increase in seed protein content. A comparative genomic hybridization analysis confirmed that the mutant is lacking 24 genes located at chromosomes 5 and 10. A tandem mass tag-based proteomic profiling of the wild type and the F...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00160
更新日期：2020-10-02 00:00:00
abstract：:High-throughput technologies, such as proteomic screening and DNA micro-arrays, produce vast amounts of data requiring comprehensive analytical methods to decipher the biologically relevant results. One approach would be to manually search the biomedical literature; however, this would be an arduous task. We developed...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0340227
更新日期：2003-07-01 00:00:00
abstract：:In this paper, we present a new purification procedure that yields a new crystalline form of rubisco and has enabled us to completely remove this most abundant protein from tobacco leaf extract. The crystals formed within 48 h after refrigeration at 4 degrees C at pH 5.6. However, these crystals were not well-ordered ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr025548e
更新日期：2002-09-01 00:00:00
abstract：:We investigated the effect of homogenization strategy and protein precipitation on downstream protein quantitation using multiple reaction monitoring mass spectrometry (MRM-MS). Our objective was to develop a workflow capable of processing disparate tissue types with high throughput, minimal variability, and maximum p...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00399
更新日期：2021-01-01 00:00:00
abstract：:Novel biomarker verification assays are urgently required to improve the efficiency of biomarker development. Benefitting from lower development costs, multiple reaction monitoring (MRM) has been used for biomarker verification as an alternative to immunoassay. However, in general MRM analysis, only one sample can be ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4005025
更新日期：2013-09-06 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：:Ribosomal proteins of the model gram-positive bacterium B. subtilis 168 were extensively characterized in a proteomic study. Mass spectra of the 52 proteins expected to be constitutive components of the 70S ribosome were recorded. Peptide MS/MS analysis with an average sequence coverage of 85% supported the identifica...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr801114k
更新日期：2009-09-01 00:00:00
abstract：:We recently developed a novel method for analysis of collagen O-glycosylations, which include galactosyl-hydroxylysine (GHL) and glucosyl-galactosyl-hydroxylysine (GGHL), using hydrazide chemistry (Taga, Y., Mol. Cell. Proteomics 2012, 11 (6), M111.010397). Here we investigated an overglycosylation model of collagen p...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400079d
更新日期：2013-05-03 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：:Inspired by the availability of de novo transcriptome of horse gram (Macrotyloma uniflorum) and recent developments in systems biology studies, the first ever global protein-protein interactome (PPI) map was constructed for this highly drought-tolerant legume. Large-scale studies of PPIs and the constructed database w...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b01114
更新日期：2016-06-03 00:00:00
abstract：:The Human Proteome Project (HPP) has made great efforts to clarify the existing evidence of human proteins since 2012. However, according to the recent release of neXtProt (2019-1), approximately 10% of all human genes still have inadequate or no experimental evidence of their translation at the protein level. They we...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00355
更新日期：2019-12-06 00:00:00
abstract：:One-hundred twenty-four proteins have been identified in the soluble nuclear protein mixture from MCF-7 human breast cancer cells, of which more than 90% are classically categorized as nuclear proteins. Proteins were also studied from three drug resistant MDF-7 lines, selected previously from the same parent line by e...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0501158
更新日期：2005-09-01 00:00:00
abstract：:The protein expression pattern in the cytosol fraction of the adriamycin resistant MCF-7 cell line (MCF-7/ADR) was compared to that of the parental MCF-7 cell line using two-dimensional gel electrophoresis and mass spectrometry. Twenty proteins with altered abundances were identified and studied in MCF-7/ADR. Both up ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0340577
更新日期：2004-05-01 00:00:00
abstract：:Knowledge of the protein networks interacting with the amyloid precursor protein (APP) in vivo can shed light on the physiological function of APP. To date, most proteins interacting with the APP intracellular domain (AICD) have been identified by Yeast Two Hybrid screens which only detect direct interaction partners....
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300123g
更新日期：2012-08-03 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：: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 this Letter, we reanalyze published mass spectrometry data sets of clinical samples with a focus on determining the coinfection status of individuals infected with SARS-CoV-2 coronavirus. We demonstrate the use of ComPIL 2.0 software along with a metaproteomics workflow within the Galaxy platform to detect cohabita...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00822
更新日期：2021-01-04 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：:This report describes the application of NMR spectroscopy to the profiling of metabolites in bronchoalveolar lavage fluid (BALf) of lung transplant recipients without bronchiolitis obliterans syndrome (BOS) (stable, S, n = 10), and with BOS at different degrees of severity (BOS 0p, n = 10; BOS I, n = 10). Through the ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b01038
更新日期：2017-04-07 00:00:00
abstract：:The current technique used for microbial identification in hospitals is matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). However, it suffers from important limitations, in particular, for closely related species or when the database used for the identification lacks the appr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00351
更新日期：2021-01-01 00:00:00
abstract：:Sardinian alcohol-preferring (sP) and Sardinian alcohol-non preferring (sNP) rats have been selectively bred for opposite alcohol preference and consumption. Aiming to verify possible differences at the proteomics level between sP and sNP rats, we investigated the salivary proteome by a a liquid chromatography-mass sp...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00632
更新日期：2018-01-05 00:00:00
abstract：:We assessed proteomic patterns in breast cancer using MALDI MS and laser capture microdissected cells. Protein and peptide expression in invasive mammary carcinoma versus normal mammary epithelium and estrogen-receptor positive versus estrogen-receptor negative tumors were compared. Biomarker candidates were identifie...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr7008109
更新日期：2008-04-01 00:00:00
abstract：:We performed systematic evaluation of 38 protocols to concentrate normal human urinary proteins prior to 2D-PAGE analysis. Recovery yield and pattern of resolved protein spots were compared among different methods and intra-/inter-individual variabilities were examined. Precipitation with 90% ethanol provided the grea...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0502525
更新日期：2006-01-01 00:00:00
abstract：:The protein kinase AKT is a central kinase in the heart and has a major impact on growth/hypertrophy, survival/apoptosis, and metabolism. To gain more insight into AKT isoform-specific signaling at the molecular level, we investigated the phosphoproteome of HL-1 cardiomyocytes carrying AKT1 or AKT2 isoform-specific kn...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500131g
更新日期：2014-10-03 00:00:00
abstract：:Streptococcus agalactiae causes severe systemic infections in human and fish. In the present study, we established a pathogen-plasma interaction model by which we explored how S. agalactiae evaded serum-mediated killing. We found that S. agalactiae grew faster in the presence of yellow grouper plasma than in the absen...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00215
更新日期：2016-07-01 00:00:00
abstract：:High density lipoprotein (HDL) particles are blood-borne complexes whose plasma levels have been associated with protection from cardiovascular disease (CVD). Recent studies have demonstrated the existence of distinct HDL subspecies; however, these have been difficult to isolate and characterize biochemically. Here, w...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00419
更新日期：2015-08-07 00:00:00
