Abstract：
:In this report, we describe an integrated fluidic platform composed of tandem affinity columns for the depletion of high-abundance proteins from human serum and on-line fractionation/concentration of medium- and low-abundance proteins by tandem immobilized metal-ion affinity chromatography (IMAC) columns and reversed phase (RP) column for in-depth proteomics analysis. The depletion columns were based on monolithic polymethacrylate with surface immobilized protein A, protein G', and antibodies for depleting the top 8 high-abundance proteins. The IMAC fractionation/concentration columns consisted of monolithic stationary phases with surface bound iminodiacetic acid (IDA) chelated with Zn2+, Ni2+ and Cu2+, while the RP column was packed with nonpolar polymer beads. The integrated multicolumn fluidic platform was very effective in reducing simultaneously both the dynamic range differences among the protein constituents of serum and the complexity of the proteomics samples, thus, facilitating the in-depth proteomics analysis by 2-DE followed by MALDI-TOF and LC-MS/MS. In fact, the number of detected spots was approximately 1450 using SYPRO fluorescent stain from which 384 spots were subsequently detected by Coomassie Blue. Since the investigation was simply a proof of concept, 295 proteins were readily identified in some selected spots by MALDI-TOF and LC-MS/MS.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Jmeian Y,El Rassi Zdoi
10.1021/pr900399qsubject
Has Abstractpub_date
2009-10-01 00:00:00pages
4592-603issue
10eissn
1535-3893issn
1535-3907journal_volume
8pub_type
杂志文章abstract：:Pancreas ductal adenocarcinoma (PDAC) remains a deadly malignancy with poor early diagnostic and no effective therapy. Although several proteomic studies have performed comparative analysis between normal and malignant tissues, there is a lack of clear characterization of proteins that could be of clinical value. Syst...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200527z
更新日期：2011-09-02 00:00:00
abstract：:We propose a method for finding features in liquid chromatography mass spectrometry data that is based on the isotopic pattern of peaks. Our interactive approach to feature finding is carried out across many samples simultaneously and aligns features concurrently. Our scale-independent approach prioritises potential f...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060226m
更新日期：2006-11-01 00:00:00
abstract：:The insulin/insulin-like growth factor-1 (IGF-1) signaling system is a public regulator of aging in the model animals Caenorhabditis elegans, Drosophila melanogaster, and Mus musculus. For the first time, proteomic analyses of the environmentally resistant and 'nonaging' C. elegans dauer stage and long-lived daf-2 mut...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr9009639
更新日期：2010-06-04 00:00:00
abstract：:Ceramides are central molecules in sphingolipid metabolism. They are involved in the regulation of cancer-cell growth, differentiation, senescence and apoptosis. To better understand how these secondary messengers induce their biological effects, adenocarcinoma cells (HCT116) were treated with exogenous long-chain cer...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr9005316
更新日期：2009-10-01 00:00:00
abstract：:The field of computational proteomics is approaching the big data age, driven both by a continuous growth in the number of samples analyzed per experiment as well as by the growing amount of data obtained in each analytical run. In order to process these large amounts of data, it is increasingly necessary to use elast...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00328
更新日期：2020-01-03 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：:Tandem mass spectrometry has become the method of choice for high-throughput, quantitative analysis in proteomics. Peptide spectrum matching algorithms score the concordance between the experimental and the theoretical spectra of candidate peptides by evaluating the number (or proportion) of theoretically possible fra...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00499
更新日期：2019-06-07 00:00:00
abstract：:The use of matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) to acquire spectral profiles has become a common approach to detect proteomic biomarkers of disease. MALDI-MS signals may represent both intact proteins as well as proteolysis products. Liquid chromatography-tandem mass spectrometry (L...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050138m
更新日期：2005-09-01 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：: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：: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：:Salt stress is a major abiotic factor limiting maize yield. To characterize the mechanism underlying maize salt tolerance, we compared the seedling root proteomes of salt-tolerant Jing724 and salt-sensitive D9H. The germination rate and growth parameter values (weight and length) were higher for Jing724 than for D9H u...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00455
更新日期：2018-01-05 00:00:00
abstract：:A simple and site-specific nonenzymatic method based on pyrolysis has been developed to cleave peptides and proteins. Pyrolytic cleavage was found to be specific and rapid as it induced a cleavage at the C-terminal side of aspartic acid in the temperature range of 220-250 degrees C in 10 s. Electrospray ionization (ES...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060648w
更新日期：2007-05-01 00:00:00
abstract：:Trypanosoma cruzi is a protozoan that causes Chagas' disease, a neglected infectious illness that affects millions of people, mostly in Latin America. Here, the cell surface subproteome of the T. cruzi epimastigote life form was characterized. In order to prepare samples enriched in epimastigote plasma membrane protei...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400110h
更新日期：2013-07-05 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：:The time course of the thylakoid membranes proteomic profile changes upon cadmium (Cd) addition to hydroponic Spinacia oleracea L. plants has been investigated. Two different proteomic approaches have been used: blue native gel electrophoresis followed by SDS-PAGE (2D BN-SDS-PAGE) and sucrose density gradient ultracen...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800507x
更新日期：2009-01-01 00:00:00
abstract：:Proteomics has been applied to study intracellular bacteria and phagocytic vacuoles in different host cell lines, especially macrophages (Mφs). For mycobacterial phagosomes, few studies have identified over several hundred proteins for systems assessment of the phagosome maturation and antigen presentation pathways. M...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr101245u
更新日期：2011-05-06 00:00:00
abstract：:We have developed a novel approach to enhance phosphopeptide identification in liquid chromatography/mass spectrometry (LC/MS)-based phosphoproteomics. After enrichment of phosphopeptides with immobilized metal affinity chromatography (IMAC) and titanium dioxide (TiO(2)) microcolumns, samples were coinjected with ethy...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900918h
更新日期：2010-03-05 00:00:00
abstract：:The two key steps for analyzing proteomic data generated by high-resolution MS are database searching and postprocessing. While the two steps are interrelated, studies on their combinatory effects and the optimization of these procedures have not been adequately conducted. Here, we investigated the performance of thre...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00536
更新日期：2015-11-06 00:00:00
abstract：:Multiple reaction monitoring (MRM) is emerging as a promising technique for the detection and quantification of protein biomarkers in complex biological samples. Compared to Western blotting or enzyme assays, its high sensitivity, specificity, accuracy, assay speed, and sample throughput represent a clear advantage fo...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4006712
更新日期：2013-12-06 00:00:00
abstract：:Arctic ground squirrels provide a unique model to investigate metabolic responses to hibernation in mammals. During winter months these rodents are exposed to severe hypothermia, prolonged fasting, and hypoxemia. In the light of their role in oxygen transport/off-loading and owing to the absence of nuclei and organell...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00018
更新日期：2019-04-05 00:00:00
abstract：:Redox regulation plays an important role across a broad spectrum of biology. Accumulating evidence suggests that thioredoxin, a widely distributed redox enzyme, participates in the redox control of numerous target proteins, thus, playing a key role as a signaling intermediate that senses the metabolic state or environ...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/pr8003453
更新日期：2008-08-01 00:00:00
abstract：:In recent years, proteomic data have contributed to genome annotation efforts, most notably in humans and mice, and spawned a field termed "proteogenomics". Yeast, in contrast with higher eukaryotes, has a small genome, which has lent itself to simpler ORF prediction. Despite this, continual advances in mass spectrome...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00734
更新日期：2015-12-04 00:00:00
abstract：:The present study was undertaken to identify proteins interacting with PrP(C) that could provide new insights into its physiological functions and pathological role. Human PrP(C) was expressed in prion protein-deficient murine hippocampus (HpL3-4) neuronal cells. The PrP(C) along with its interacting proteins were aff...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr2001989
更新日期：2011-07-01 00:00:00
abstract：:Nasopharyngeal carcinoma (NPC) is one of the most common malignant tumors in Southeast Asia. Unfortunately, most NPC victims have had metastasis when first diagnosed due to its deep location and vague symptoms. To date, discovery of sensitive and specific biomarkers for improving detection of NPC remains a challenge. ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900454e
更新日期：2009-12-01 00:00:00
abstract：:Rosiglitazone is a thiazolidinedione used to treat insulin resistance in diabetes. Although thiazolidinediones may also exert cardiovascular effects, contrasting results were reported. Favorable effects were shown for pioglitazone, whereas adverse reactions were suspected for rosiglitazone. Therefore, a reassessment o...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900435z
更新日期：2010-01-01 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：:Major depressive disorder (MDD) is a debilitating mental disease with a pronounced impact on the quality of life of many people; however, it is still difficult to diagnose MDD accurately. In this study, a nontargeted metabolomics approach based on ultra-high-performance liquid chromatography equipped with quadrupole t...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00144
更新日期：2015-05-01 00:00:00
abstract：:Extracellular vesicles (EVs) are important mediators of cell-cell communication due to their cargo content of proteins, lipids, and RNAs. We previously reported that small EVs (SEVs) called exosomes promote directed and random cell motility, invasion, and serum-independent growth. In contrast, larger EVs (LEVs) were n...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00647
更新日期：2019-03-01 00:00:00
abstract：:Expansion of human articular chondrocytes (HACs) in serum-free medium (SFM) has been shown to be enhanced by the control of medium osmolality. HACs attained better growth when cultured at osmolalities lower than the average osmolality found in articular cartilage in vivo, although the specific causes for this improved...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100136q
更新日期：2010-05-07 00:00:00
