Abstract:
:Many of the emerging technologies for the global evaluation of gene expression, at both the RNA and protein level, are being applied to the problem of finding biomarkers for human disease progression. These analyses can be made difficult, however, by variation between samples that arises from both technical and nondisease related physiological or genetic causes. In an effort to identify serum polypeptides whose presence or absence correlates with the clinical status of patients at high risk for hepatocellular carcinoma (HCC), we have developed a strategy that helps to focus the analysis on meaningful changes in protein levels above the background of variation. For the current study we divided the patient population into four clinically defined diagnostic groups that represent a generally increasing risk for HCC. Chronic infection with hepatitis B virus (HBV) is a major risk factor for HCC and our groups included patients with no indication of liver disease (healthy), those with inactive chronic HBV, those with active chronic HBV, and patients with a diagnosis of HCC and history of chronic HBV infection. Serum polypeptides from these patients were first analyzed in two-dimensional gels by combining the serum from patients in each of the four groups to generate composite gel profiles. Analysis of these composite gels allowed us to identify two relatively abundant features that were reduced in the HCC group as compared to the healthy group. Tryptic fragment mass fingerprinting identified the features as a carboxy terminal fragment of complement C3 and an isoform of apolipoprotein A1. These two features were examined by two-dimensional gel electrophoresis of serum from each individual in the four groups in order to verify that the inter-group differences seen in composite gels reported changes in abundance for most members of the group, rather than extreme changes for a small fraction of the group. These preliminary studies suggest that a proteomic methodology can be used for the identification of serum biomarkers for HCC and other liver disease.
journal_name
Proteomicsjournal_title
Proteomicsauthors
Steel LF,Shumpert D,Trotter M,Seeholzer SH,Evans AA,London WT,Dwek R,Block TMdoi
10.1002/pmic.200300399subject
Has Abstractpub_date
2003-05-01 00:00:00pages
601-9issue
5eissn
1615-9853issn
1615-9861journal_volume
3pub_type
杂志文章相关文献
PROTEOMICS文献大全abstract::To gain a better understanding of salt stress responses in plants, we used a proteomic approach to investigate changes in rice (Oryza sativa) root plasma-membrane-associated proteins following treatment with 150 mmol/L NaCl. With or without a 48 h salt treatment, plasma membrane fractions from root tip cells of a salt...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200800340
更新日期:2009-06-01 00:00:00
abstract::One of the major challenges facing protein analysis is the dynamic range of protein expression within massively complex samples (Corthals, G. L. et al.., Electrophoresis 2000, 21, 1104-1115). In plasma this difference is as great as ten orders of magnitude, and this is currently beyond the range of detection achievabl...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200401160
更新日期:2005-08-01 00:00:00
abstract::Changing smooth muscle phenotype and abnormal cell proliferation are important features of vascular pathology, including the failure of saphenous vein bypass grafts. We have characterised and mapped protein expression in human saphenous vein medial smooth muscle, using two-dimensional (2-D) polyacrylamide gel electrop...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/1615-9861(200111)1:11<1405::AID-PROT1405>3
更新日期:2001-11-01 00:00:00
abstract::The computational simulation of complete proteomic data sets and their utility to validate detection and interpretation algorithms, to aid in the design of experiments and to assess protein and peptide false discovery rates is presented. The simulation software has been developed for emulating data originating from da...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201000576
更新日期:2011-03-01 00:00:00
abstract::Panax ginseng is an important herb that has clear effects on the treatment of diverse diseases. Until now, the natural peptide constitution of this herb remains unclear. Here, we conduct an extensive characterization of Ginseng peptidome using MS-based data mining and sequencing. The screen on the charge states of pre...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201600183
更新日期:2016-11-01 00:00:00
abstract::Protein ubiquitination is a powerful modulator of cellular functions. Classically linked to the degradation of proteins, it also plays a role in intracellular localization, DNA damage response, vesicle fusion events, and the immune and transcriptional responses. Ubiquitin is versatile and can code for several distinct...
journal_title:Proteomics
pub_type: 杂志文章,评审
doi:10.1002/pmic.201500290
更新日期:2016-01-01 00:00:00
abstract::Identification of differential proteomic responses to cadmium (Cd) would provide a means for better understanding the survival mechanisms of the earthworm, Eisenia fetida, living in a Cd-polluted environment, and the stress responses can be assessed by ecotoxiptoromics approaches. Extracts of whole earthworm collected...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201000209
更新日期:2010-12-01 00:00:00
abstract::Embryo implantation into maternal endometrium is critical for initiation and establishment of pregnancy, requiring developmental synchrony between endometrium and blastocyst. However, factors regulating human endometrial-embryo cross talk and facilitate implantation remain largely unknown. Extracellular vesicles (EVs)...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201800423
更新日期:2019-12-01 00:00:00
abstract::Despite increasing evidence of behavioural manipulation of their vectors by pathogens, the underlying mechanisms causing infected vectors to act in ways that benefit pathogen transmission remain enigmatic in most cases. Here, 2-D DIGE coupled with MS were employed to analyse and compare the head proteome of mosquitoes...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200601021
更新日期:2007-06-01 00:00:00
abstract::Identification of mucin-type O-glycosylated proteins with known functions in model organisms like Drosophila could provide keys to elucidate functions of the O-glycan moiety and proteomic analyses of O-glycoproteins in higher eukaryotes remain a challenge due to structural heterogeneity and a lack of efficient tools f...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200600793
更新日期:2007-09-01 00:00:00
abstract::Renal cell carcinoma (RCC) originates in the renal cortex. It accounts for 2-3 percent of all cancers occurring in adults and it is characterised by lack of early clinical manifestations, unpredictable outcome, and absence of effective treatment modalities except early surgery. RCC comprises a heterogeneous group of t...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/1615-9861(200110)1:10<1288::AID-PROT1288>3
更新日期:2001-10-01 00:00:00
abstract::Shewanella inhabit a wide variety of niches in nature and can utilize a broad spectrum of electron acceptors under anaerobic conditions. How they modulate their gene expression to adapt is poorly understood. ArcA, homologue of a global regulator controlling hundreds of genes involved in aerobic and anaerobic respirati...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201100651
更新日期:2012-06-01 00:00:00
abstract::In 2001, the German Federal Ministry of Education and Research (BMBF) initiated the National Genome Research Network (NGFN; www.ngfn.de) as a nation-wide multidisciplinary networking platform aiming at the analysis of common human diseases and aging. Within the NGFN the Human Brain Proteome Project (HBPP; www.smp-prot...
journal_title:Proteomics
pub_type: 杂志文章,评审
doi:10.1002/pmic.200700980
更新日期:2008-03-01 00:00:00
abstract::MS/MS has been used to improve genome annotation in various organisms. The classical approach is to construct comprehensive theoretical peptide database with six frame translation model from the whole ORF of a genome and search against this database with real MS/MS spectra. In this work we took a more focused approach...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201400174
更新日期:2014-12-01 00:00:00
abstract::As mass-spectrometry-based proteomics has matured during the past decade, a growing emphasis has been placed on quality control. For this purpose, multiple computational quality control tools have been introduced. These tools generate a set of metrics that can be used to assess the quality of a mass spectrometry exper...
journal_title:Proteomics
pub_type: 杂志文章,评审
doi:10.1002/pmic.201600159
更新日期:2017-02-01 00:00:00
abstract::CID has become a routine method for fragmentation of peptides in shotgun proteomics, whereas electron transfer dissociation (ETD) has been described as a preferred method for peptides carrying labile PTMs. Though both of these fragmentation techniques have their obvious advantages, they also have their own drawbacks. ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201000547
更新日期:2011-06-01 00:00:00
abstract::Many cancer cells show unique protein expression patterns. We used proteome technology including MS, free flow isoelectric focusing and Western blotting to determine current concentrations of metabolic enzymes in healthy and malignant human thyroid cells. Three different types of human thyroid cells were investigated ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201200070
更新日期:2012-08-01 00:00:00
abstract::2-D analysis of plant proteomes containing thousands of proteins has limited dynamic resolution because only abundant proteins can be detected. Proteomic assessment of the non-abundant proteins within seeds is difficult when 60-80% is storage proteins. Resolution can be improved through sample fractionation using sepa...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200800875
更新日期:2009-06-01 00:00:00
abstract::Carcinoma of the prostate (CaP) is the second leading cause of cancer-related mortality among American men. While high cure rates are associated with localized CaP, no cure exists for advanced recurrent disease. At present there are no known serologic biomarkers specific to this stage of the disease. Several groups ha...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200401165
更新日期:2005-07-01 00:00:00
abstract::RNAi experiments are ubiquitously used in cell biology and are achieved by transfection of small interfering RNAs (siRNAs) into cells using a transfection reagent. These results in knock-down of proteins of interest, and the phenotypic consequences are then analyzed. It is reported here that two common RNA interferenc...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201800298
更新日期:2019-07-01 00:00:00
abstract::SELDI-TOF-MS is rapidly gaining popularity as a screening tool for clinical applications of proteomics. Application of adequate statistical techniques in all the stages from measurement to information is obligatory. One of the statistical methods often used in proteomics is classification: the assignment of subjects t...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200700046
更新日期:2007-10-01 00:00:00
abstract::Most information on molecular processes accompanying and driving adipocyte differentiation are derived from rodent models. Here, we provide a comprehensive analysis of combined transcriptomic and proteomic alterations during adipocyte differentiation in Simpson-Golabi-Behmel Syndrome (SGBS) cells. The SGBS cells are a...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201900405
更新日期:2020-05-08 00:00:00
abstract::We have used MALDI-MS imaging (MALDI-MSI) to monitor the time dependent appearance and loss of signals when tissue slices are brought rapidly to room temperature for short to medium periods of time. Sections from mouse brain were cut in a cryostat microtome, placed on a MALDI target and allowed to warm to room tempera...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200800201
更新日期:2008-09-01 00:00:00
abstract::Antibiotics disturb the physiological homeostasis of bacterial cells by interfering with essential cellular functions or structures. The bacterial proteome adjusts quickly in response to antibiotic challenge. This physiological response is specifically tailored to overcome the inflicted damage and, thus, closely linke...
journal_title:Proteomics
pub_type: 杂志文章,评审
doi:10.1002/pmic.201100046
更新日期:2011-08-01 00:00:00
abstract::Deciphering a complete landscape of protein-RNA interactions in the human proteome remains an elusive challenge. We computationally elucidate RNA binding proteins (RBPs) using an approach that complements previous efforts. We employ two modern complementary sequence-based methods that provide accurate predictions from...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201800064
更新日期:2018-11-01 00:00:00
abstract::Helicobacter pylori is one of the most common bacterial pathogens and causes a variety of diseases, such as peptic ulcer or gastric cancer. Despite intensive study of this human pathogen in the last decades, knowledge about its membrane proteins and, in particular, those which are putative components of the type IV se...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200401019
更新日期:2005-04-01 00:00:00
abstract::Soil salinity is a major abiotic constraint to agricultural productivity. We successfully bred a new common wheat (Triticum aestivum L.) introgression variety (Shanrong No. 3) with high salt-tolerance via asymmetric somatic hybridization between common wheat cultivar (Jinan 177) and UV-irradiated Agropyron elongatum (...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200700569
更新日期:2008-04-01 00:00:00
abstract::Cardiac conduction defects were found in transgenic mice deficient in urea transporter UT-B. To investigate the molecular mechanisms of the conduction defects caused by UT-B deletion, we studied the protein expression profiles of heart tissue (comprising most conduction system) in wild-type versus UT-B null mice at di...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200701079
更新日期:2009-02-01 00:00:00
abstract::A novel proteolysis approach was developed by using infrared (IR) radiation and trypsin-immobilized silica microspheres. Protein solutions containing trypsin-immobilized microspheres in sealed transparent Eppendorf tubes were allowed to digest under an IR lamp at 37 degrees C. The feasibility and performance of the pr...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200800659
更新日期:2009-02-01 00:00:00
abstract::Until now, no data are available on the outer membrane (OM) proteome of Erwinia amylovora, a Gram-negative plant pathogen, causing fire blight in most of the members of the Rosaceae family. Since the OM forms the interface between the bacterial cell and its environment it is in direct contact with the host. Additional...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201500513
更新日期:2016-09-01 00:00:00