Abstract：
:Two-dimensional differential gel electrophoresis (2-D DIGE) was used to analyze human serum following the removal of albumin and five other high-abundant serum proteins. After protein removal, serum was analyzed by SDS-PAGE as a preliminary screen, and significant differences between four high-abundant protein removal methods were observed. Antibody-based albumin removal and high-abundant protein removal methods were found to be efficient and specific. To further characterize serum after protein removal, 2-D DIGE was employed, enabling multiplexed analysis of serum through the use of three fluorescent protein dyes. Comparison between crude serum and serum after removal of high-abundant proteins clearly illustrates an increase in the number of lower abundant protein spots observed. Approximately 850 protein spots were detected in crude serum whereas over 1500 protein spots were exposed following removal of six high-abundant proteins, representing a 76% increase in protein spot detection. Several proteins that showed a 2-fold increase in intensity after depletion of high-abundant proteins, as well as proteins that were depleted during abundant protein removal methods, were further characterized by mass spectrometry. This series of experiments demonstrates that high-abundant protein removal, combined with 2-D DIGE, is a practical approach for enriching and characterizing lower abundant proteins in human serum. Consequently, this methodology offers advances in proteomic characterization, and therefore, in the identification of biomarkers from human serum.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Chromy BA,Gonzales AD,Perkins J,Choi MW,Corzett MH,Chang BC,Corzett CH,McCutchen-Maloney SLdoi
10.1021/pr049921pkeywords:
subject
Has Abstractpub_date
2004-11-01 00:00:00pages
1120-7issue
6eissn
1535-3893issn
1535-3907journal_volume
3pub_type
杂志文章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：:Protein phosphorylation is essential for numerous cellular processes. Large-scale profiling of phosphoproteins continues to enhance the depth and speed at which we understand these processes. The development of effective phosphoprotein and peptide enrichment techniques and improvements to mass spectrometric instrument...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060559j
更新日期：2007-03-01 00:00:00
abstract：:In-depth, reproducible coverage of complex proteomes is challenging because the complexity of tryptic digests subjected to LC-MS/MS analysis frequently exceeds mass spectrometer analytical capacity, which results in undersampling of data. In this study, we used cancer cell lysates to systematically compare the commonl...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900927y
更新日期：2010-02-05 00:00:00
abstract：:Correct phosphorylation site assignment is a critical aspect of phosphoproteomic analysis. Large-scale phosphopeptide data sets that are generated through liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) analysis often contain hundreds or thousands of phosphorylation sites that require validation. To ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800169k
更新日期：2008-07-01 00:00:00
abstract：:Glutaredoxins (GRXs), small redox proteins that use reduced glutathione as an electron donor, are key components of the cellular antioxidant system. In this study, we used Saccharomyces cerevisiae as a model system to investigate the effects of GRX deletion on yeast chronological life span (CLS). Deletion of either Gr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00012
更新日期：2018-07-06 00:00:00
abstract：:Pancreatic cystic neoplasms represent 10-15% of primary cystic masses of the pancreas. While pancreatic cysts are detected with an increasing frequency due to the use of advanced imaging modalities in clinical practice, the diagnosis of pancreatic cystic neoplasms remains unsatisfactory because available diagnostic te...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr2000557
更新日期：2011-05-06 00:00:00
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) ex...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400884c
更新日期：2014-01-03 00:00:00
abstract：:Although some outer membrane (OM) proteins involved in antibiotic resistance have been previously reported, the OM proteins regulating chlortetracycline (CTC) resistance are largely unknown. In this study, we employed a subproteomics approach to identify altered OM proteins of Escherichia coli in response to CTC expos...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100740w
更新日期：2010-11-05 00:00:00
abstract：:Cardiovascular disease is the leading cause of diabetic morbidity with more than 10% of type 1 diabetes mellitus (T1DM) patients dying before they are 40 years old. This study utilized Akita mice, a murine model with T1DM progression analogous to that of humans. Diabetic cardiomyopathy in Akita mice presents as cardia...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4004739
更新日期：2013-09-06 00:00:00
abstract：:In pressure overload (PO), sex differences in humans and rodents have been well documented and estrogen receptor (ER) β is considered cardioprotective. However, the underlying mechanisms are poorly understood. Our aim was to investigate sex- and ERβ-specific effects in protein abundance in PO employing a 2-dimensional...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500749j
更新日期：2014-12-05 00:00:00
abstract：:Cold acclimation is the phenomenon in which plants are exposed to low, but nonfreezing, temperatures before exposure to drastic temperatures. To investigate how sunflower plants adjust their metabolism during cold treatment, a comparative proteomic approach, based on spectral counting data, was adopted to identify dif...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr101137q
更新日期：2011-05-06 00:00:00
abstract：:Ethylene has been hypothesised to be a regulator of root nodule development in legumes, but its molecular mechanisms of action remain unclear. The skl mutant is an ethylene-insensitive legume mutant showing a hypernodulation phenotype when inoculated with its symbiont Sinorhizobium meliloti. We used the skl mutant to ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0602646
更新日期：2006-11-01 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：:MSI is a molecular imaging technique that allows for the generation of topographic 2D maps for various endogenous and some exogenous molecules without prior specification of the molecule. In this paper, we start with the premise that a region of interest (ROI) is given to us based on preselected morphological criteria...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr101159e
更新日期：2011-04-01 00:00:00
abstract：:Akt1 is a serine/threonine kinase that promotes cell growth and survival. Previously, Akt1 activation in a double transgenic (DTG) mouse model fed a high-fat/high-sucrose (HF/HS) diet was found to promote type IIb muscle growth and to lead to a significant reduction in obesity. Here, we have used metabolomics to exami...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500756u
更新日期：2015-01-02 00:00:00
abstract：:Epithelial ovarian carcinoma has in general a poor prognosis since the vast majority of tumors are genomically unstable and clinically highly aggressive. This results in rapid progression of malignancy potential while still asymptomatic and thus in late diagnosis. It is therefore of critical importance to develop meth...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr201258q
更新日期：2012-05-04 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：:In Ralstonia eutropha H16, seven genes encoding proteins being involved in the phosphoenolpyruvate-carbohydrate phosphotransferase system (PEP-PTS) were identified. In order to provide more insights into the poly(3-hydroxybutyrate) (PHB)-leaky phenotype of the HPr/EI deletion mutants H16ΔptsH, H16ΔptsI, and H16ΔptsHI ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300042f
更新日期：2012-07-06 00:00:00
abstract：:Phospholipase C gamma 1 (PLC-γ1) occupies a critically important position in the T-cell signaling pathway. While its functions as a regulator of both Ca2+ signaling and PKC-family kinases are well characterized, PLC-γ1's role in the regulation of early T-cell receptor signaling events is incompletely understood. Activ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b01026
更新日期：2017-08-04 00:00:00
abstract：:Reliable statistical validation of peptide and protein identifications is a top priority in large-scale mass spectrometry based proteomics. PeptideProphet is one of the computational tools commonly used for assessing the statistical confidence in peptide assignments to tandem mass spectra obtained using database searc...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr7006818
更新日期：2008-01-01 00:00:00
abstract：:The energy-dissipating alternative oxidase (AOX) from Hansenula anomala was expressed in Saccharomyces cerevisiae. The recombinant AOX was functional. A comparative analysis by two-dimensional differential in-gel electrophoresis (2D-DIGE) of mitochondrial protein patterns found in wild-type and recombinant AOX strains...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050346e
更新日期：2006-02-01 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：:Gram-negative and -positive bacteria elicit different response patterns by the host. The proteomic profiles of milk whey samples from cows naturally infected with Escherichia coli or Staphyloccocus aureus as compared to whey from healthy cows were determined by one-dimensional, liquid chromatography-tandem mass spectr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100336e
更新日期：2010-09-03 00:00:00
abstract：:Proteogenomic searching is a useful method for identifying novel proteins, annotating genes and detecting peptides unique to an individual genome. The approach, however, can be laborious, as it often requires search segmentation and the use of several unintegrated tools. Furthermore, many proteogenomic efforts have be...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400208w
更新日期：2013-06-07 00:00:00
abstract：:Prediction of the types of membrane proteins is of great importance both for genome-wide annotation and for experimental researchers to understand proteins' functions. We describe a new strategy for the prediction of the types of membrane proteins using the Nearest Neighbor Algorithm. We introduced a bipartite feature...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr700715c
更新日期：2008-03-01 00:00:00
abstract：:Pathogenesis of Staphylococcus aureus, an opportunistic human pathogen, is complex and involves many virulence factors including an array of surface proteins (adhesins) that promote bacterial interactions with extracellular matrix components. A better understanding of these interactions can be achieved by studying the...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr049866k
更新日期：2005-03-01 00:00:00
abstract：:Sperm proteomes have emerged for several species; however, the extent of species similarity is unknown. Sheep are an important agricultural species for which a comprehensive sperm proteome has not been produced. In addition, potential proteomic factors from seminal plasma that may contribute to improved fertility afte...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00530
更新日期：2016-10-07 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：:Sulfur trafficking systems are multiprotein systems that synthesize sulfur-containing cofactors such as iron-sulfur clusters. The sulfur is derived enzymatically from cysteine and transferred between nucleophilic cysteine residues within proteins until incorporation into the relevant cofactor. As these systems are poo...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100920r
更新日期：2010-12-03 00:00:00
abstract：:Protein lysine acylation, including acetylation and succinylation, has been found to be a major post-translational modification (PTM) and is associated with the regulation of cellular processes that are widespread in bacteria. Vibrio parahemolyticus is a model marine bacterium that causes seafood-borne illness in huma...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00485
更新日期：2015-10-02 00:00:00
