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 identified by statistical analysis and classifiers were developed and validated in blinded test sets. Several of the m/ z features used in the classifiers were identified by LC-MS/MS and two were confirmed by immunohistochemistry.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Sanders ME,Dias EC,Xu BJ,Mobley JA,Billheimer D,Roder H,Grigorieva J,Dowsett M,Arteaga CL,Caprioli RMdoi
10.1021/pr7008109subject
Has Abstractpub_date
2008-04-01 00:00:00pages
1500-7issue
4eissn
1535-3893issn
1535-3907journal_volume
7pub_type
杂志文章abstract：:Modeling and simulation of biological networks is an effective and widely used research methodology. The Biological Network Simulator (BioNSi) is a tool for modeling biological networks and simulating their discrete-time dynamics, implemented as a Cytoscape App. BioNSi includes a visual representation of the network t...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00278
更新日期：2016-08-05 00:00:00
abstract：:A major challenge in developing cell therapies is reliable characterization of the cell product at the molecular level. Fresh autologous and passaged human bone marrow enriched for stem and mesenchymal stromal stem cells have been used to regenerate bone. We report the proteome of an innovative autologous human bone m...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr801064u
更新日期：2009-04-01 00:00:00
abstract：:In shotgun proteomics analysis, user-specified parameters are critical to database search performance and therefore to the yield of confident peptide-spectrum matches (PSMs). Two of the most important parameters are related to the accuracy of the mass spectrometer. Precursor mass tolerance defines the peptide candidat...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00028
更新日期：2017-04-07 00:00:00
abstract：:"Omics" studies reported to date have dealt with either thoroughly characterized single species or poorly explored meta-microbial communities. However, these techniques are capable of producing highly informative data for the analysis of interactions between two organisms. We examined the bacterial interaction between...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100989c
更新日期：2011-02-04 00:00:00
abstract：:Tomato fruit and seed allergens were detected by IgE-immunoblotting using sera from 18 adult tomato-sensitized patients selected based on a positive history skin prick test (SPT) and specific Immunglobulin (Ig) E-levels. Isolated tomato seed total protein showed high SPT activity comparable or even higher than tomato ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800186d
更新日期：2009-03-01 00:00:00
abstract：:Membrane proteins play a critical role in the process of neural stem cell self-renewal and differentiation. Here, we apply the SILAC (stable isotope labeling by amino acids in cell culture) approach to quantitatively compare the membrane proteome of the self-renewing and the astroglial differentiating cells. High-reso...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200677z
更新日期：2012-02-03 00:00:00
abstract：:Near-isogenic sunflower lines containing 25% (inbred RHA280) and 48% (RHA801) oil by seed dry mass were comparatively analyzed in biological triplicate at 18 days after flowering using two-dimensional (both pI 3-10 and 4-7) Difference Gel Electrophoresis. Additionally, two inbred lines varying in oleic acid content, H...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070149a
更新日期：2007-08-01 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：:Spectral libraries provide a sensitive and accurate method for identifying peptides from tandem mass spectra, complementary to searching genome-derived databases or sequencing de novo. Their application requires comprehensive libraries including peptides from low-abundant proteins. Here we describe a method for constr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4010585
更新日期：2014-03-07 00:00:00
abstract：:Clostridium difficile in recent years has undergone rapid evolution and has emerged as a serious human pathogen. Proteomic approaches can improve the understanding of the diversity of this important pathogen, especially in comparing the adaptive ability of different C. difficile strains. In this study, TMT labeling an...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr3007528
更新日期：2013-03-01 00:00:00
abstract：:Chronic kidney disease (CKD) has emerged as a major public health problem worldwide. It frequently progresses to end-stage renal disease, which is related to very high cost and mortality. Novel biomarkers can provide insight into the novel mechanism, facilitate early detection, and monitor progression of CKD and its r...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00583
更新日期：2016-10-07 00:00:00
abstract：:Gastric cancer (GC) is among the most common cancers worldwide. Gastric carcinogenesis is a multistep and multifactorial process beginning with chronic gastritis induced by Helicobacter pylori (H. pylori) infection. This process is often described via a sequence of events known as Correas's cascade, a stepwise progres...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00281
更新日期：2016-08-05 00:00:00
abstract：:The impact of low-dose ionizing radiation (IR) on the human brain has recently attracted attention due to the increased use of IR for diagnostic purposes. The aim of this study was to investigate low-dose radiation response in the hippocampus. Female B6C3F1 mice were exposed to total body irradiation with 0 (control),...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00552
更新日期：2020-01-03 00:00:00
abstract：:Formalin-fixed, paraffin-embedded (FFPE) tissues have been used to discover disease-associated protein changes using mass spectrometry. Protein post-translational modifications such as glycosylation are known to associate with disease development. In this study, we investigated whether FFPE tissues preserve such modif...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800952h
更新日期：2009-04-01 00:00:00
abstract：:Histones are subjected to extensive post-translational modifications (PTMs) that are known to play key roles in many biological processes. In this study, we report a fast, efficient, highly reproducible, and easily automated method involving ultra-high performance liquid chromatography (UHPLC) coupled to a high resolu...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100497a
更新日期：2010-10-01 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：:The deuterium, a frequently used stable isotope in isotopic labeling for quantitative proteomics, could deteriorate the accuracy and precision of proteome quantification owing to the retention time shift of deuterated peptides from the hydrogenated counterpart. We introduce a novel three-plexed peptide "diethylation" ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00775
更新日期：2019-03-01 00:00:00
abstract：:Acute kidney injury (AKI) is a frequent complication after cardiopulmonary bypass, but early detection of postoperative AKI remains challenging. Protein biomarkers predict AKI excellently in homogeneous cohorts but are less reliable in patients suffering from various comorbidities. We employed nuclear magnetic resonan...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00219
更新日期：2015-07-02 00:00:00
abstract：:Although the legume-rhizobium symbiosis is a most-important biological process, there is a limited knowledge about the protein interaction network between host and symbiont. Using interolog- and domain-based approaches, we constructed an interspecies protein interactome containing 5115 protein-protein interactions bet...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00209
更新日期：2018-09-07 00:00:00
abstract：:We aimed to determine the time-course of metabolic changes related to the early onset of insulin resistance (IR), trying to evidence breaking points preceding the appearance of the clinical IR phenotype. The model chosen was the fructose (FRU)-fed rat compared to controls fed with starch. We focused on the hepatic met...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00043
更新日期：2016-06-03 00:00:00
abstract：:Antibiotic-induced microbial perturbations alter host metabolism and affect host physiology. In this study, we aimed to investigate the effects of vancomycin (Vanc) and ciprofloxacin/metronidazole (CiMe) exposures on the gut microbiome and metabolome in the colonic content and tissue samples from advanced-stage type 1...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00402
更新日期：2019-11-01 00:00:00
abstract：:A metabonomic study was performed to investigate the biochemical perturbation of the serum samples from liver failure patients induced by hepatitis B virus (HBV; n=24) and control normal subjects (n=23). The serum metabonome was detected using gas chromatography-mass spectrometry (GC-MS) technique integrated with a co...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060591d
更新日期：2007-07-01 00:00:00
abstract：:To understand bacterial reactions to environmental stress or infection-related processes, it is necessary to identify the involved proteins. In mass spectrometry-based proteomics, the method of choice for spectra-to-peptide-match is database search, but in recent times, spectral libraries have come into focus. Here, w...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00615
更新日期：2020-04-03 00:00:00
abstract：:In this study we selected three breast cancer cell lines (SKBR3, SUM149 and SUM190) with different oncogene expression levels involved in ERBB2 and EGFR signaling pathways as a model system for the evaluation of selective integration of subsets of transcriptomic and proteomic data. We assessed the oncogene status with...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4001527
更新日期：2013-06-07 00:00:00
abstract：:Glycosylation is an abundant and important protein modification with large influence on the properties and interactions of glycoconjugates. Human plasma N-glycosylation has been the subject of frequent investigation, revealing strong associations with physiological and pathological conditions. Less well-characterized ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00071
更新日期：2016-10-07 00:00:00
abstract：:Peptide abundance estimation is generally the first step in protein quantification. In peptide abundance estimation, peptide overlapping and peak intensity variation are two challenges. The main objective of this paper is to estimate peptide abundance by taking advantage of peptide isotopic distribution and smoothness...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100181g
更新日期：2010-05-07 00:00:00
abstract：:The SwePep database is designed for endogenous peptides and mass spectrometry. It contains information about the peptides such as mass, pl, precursor protein and potential post-translational modifications. Here, we have improved and extended the SwePep database with tandem mass spectra, by adding a locally curated ver...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800036d
更新日期：2008-07-01 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：:Proteoforms containing post-translational modifications (PTMs) represent a degree of functional diversity only harnessed through analytically precise simultaneous quantification of multiple PTMs. Here we present a method to accurately differentiate an unmodified peptide from its PTM-containing counterpart through data...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00685
更新日期：2020-10-02 00:00:00
abstract：:Automated sequencing of unknowns in bottom-up proteomics makes the data produced susceptible to process control errors, which can be propagated into mistakes in analyte identification. Inclusion of an unintrusive internal standard, such as lysozyme, allows monitoring all phases of the proteomics process including samp...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr049819s
更新日期：2005-01-01 00:00:00
