Abstract:
:Biomarkers for colorectal cancer (CRC) early diagnosis are currently lacking. The purpose of this study was to interpret molecular events in the early stage of CRC that may bring about new biomarkers for early diagnosis. Methylation isotope labeling assistant gel-enhanced liquid chromatography-mass spectrometry (GeLC-MS) strategy was developed to improve protein identification in quantitative proteome analysis between pooled early stage CRC and pooled normal counterparts. Expression of candidate biomarkers were in situ verified in a 372-dots tissue array, and their relative concentrations in sera were validated in 84 CRC patients and healthy individuals. Altogether, 501 proteins showing consistent differential expression were discovered. Function analysis highlighted the ubiquitination-proteasome and glycolysis/gluconeogenesis pathways as the most regulated pathways in CRC. Two glycol-proteins, alpha1 antitrypsin (A1AT) and cathepsin D (CTSD), which play central role in proteasome regulation, were further examined due to their possible importance in human cancers. Consistent with proteome data, CRC specimens expressed less A1AT and more CTSD than normal counterparts in both tissue and serum levels. By combining CTSD and A1AT, 96.77% of CRC tissues were distinguished from normal tissues by immunohistochemical analysis on a tissue array (P<0.0001). Combined CTSD and A1AT should be strongly considered for clinical use in early diagnosis of early stage CRC, and the methylation assistant GeLC-MS approach is competent for a global quantitative proteome study.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Xie LQ,Zhao C,Cai SJ,Xu Y,Huang LY,Bian JS,Shen CP,Lu HJ,Yang PYdoi
10.1021/pr100406zsubject
Has Abstractpub_date
2010-09-03 00:00:00pages
4701-9issue
9eissn
1535-3893issn
1535-3907journal_volume
9pub_type
杂志文章abstract::Cyanobacteria developed efficient carbon concentrating mechanisms which significantly improve the photosynthetic performance and survival of cells under limiting CO(2) conditions. Dynamic changes of the Synechocystis proteome to CO(2) limitation were investigated using shotgun LC-MS/MS approach with isobaric tag for r...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr100651w
更新日期:2010-11-05 00:00:00
abstract::Phytopathogenic fungi are one of the most damaging plant parasitic organisms, and can cause serious diseases and important yield losses in crops. The study of the biology of these microorganisms and the interaction with their hosts has experienced great advances in recent years due to the development of moderm, holist...
journal_title:Journal of proteome research
pub_type: 杂志文章,评审
doi:10.1021/pr200873p
更新日期:2012-01-01 00:00:00
abstract::Several high-throughput statistical methods were evaluated for processing data generated by two-dimensional polyacrylamide gel electrophoresis, including how to handle missing data, normalization, and statistical analysis of data obtained from 2-D gels. Quantile normalization combined with a nonparametric permutation ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr049886m
更新日期:2004-11-01 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::Beta-thalassemia results from mutations of the β-hemoglobin (Hbb) gene and reduced functional Hbb synthesis. Excess α-Hb causes globin chain aggregation, oxidation, cytoskeletal damage, and increased red blood cell clearance. These events result in anemia, altered iron homeostasis, and expansion of extramedullary eryt...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr5010778
更新日期:2015-02-06 00:00:00
abstract::A selective method for the enrichment of O-GlcNAcylated peptides using a novel CLICK chemistry reagent is described. Peptides modified by O-GlcNAc were enzymatically labeled with N-azidoacetylgalactosamine. The azide was then reacted with a phospho-alkyne using CLICK chemistry and O-GlcNAcGalNAzPO(4)-containing peptid...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr100565j
更新日期:2011-04-01 00:00:00
abstract::In line with the aims of the Chromosome-based Human Proteome Project and the Biology/Disease-based Human Proteome Project, we have been studying differentially expressed transcripts and proteins in gliomas—the most prevalent primary brain tumors. Here, we present a perspective on important insights from this analysis ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.5b00488
更新日期:2015-09-04 00:00:00
abstract::12-O-Tetradecanoyl-phorbol-13-acetate (TPA) is a plant derivative with multiple function as tumor promoter, differentiation revulsant or leukemia therapy drug. The molecular mechanism of its function is perplexing. Many studies have focused on the mechanism of TPA stimulation in tumor promotion of mouse models or term...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr0497677
更新日期:2005-03-01 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 ability to distinguish between phosphopeptides of high and low stoichiometry is essential to discover the true extent of protein phosphorylation. We here extend the strategy whereby a peptide sample is briefly split in two identical parts and differentially labeled preceding the phosphatase treatment of one part. ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr500889v
更新日期:2015-02-06 00:00:00
abstract::The GalNAc O-glycosylation on Ser/Thr residues of extracellular proteins has not been well characterized from a proteomics perspective. We previously reported a sialic acid capture-and-release protocol to enrich tryptic N- and O-glycopeptides from human cerebrospinal fluid glycoproteins using nano-LC-ESI-MS/MS with co...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr300963h
更新日期:2013-02-01 00:00:00
abstract::As a recently validated reversible post translational modification, lysine malonylation regulates diverse cellular processes from bacteria to mammals, but its existence and function in photosynthetic organisms remain unknown. Cyanobacteria are the most ancient group of photosynthetic prokaryotes and contribute about 5...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.7b00017
更新日期:2017-05-05 00:00:00
abstract::Metabonomics methods have been successfully applied to the drug discovery, toxicology, phytochemistry, and clinical fields. Here, we report a self-developed metabonomics platform which is based on high performance liquid chromatography-mass spectrometry (HPLC-MS) technique and applied to the investigation of acute det...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr050364w
更新日期:2006-03-01 00:00:00
abstract::We have investigated the transcriptome and proteome of the venom of a cryptic Australian elapid snake Drysdalia coronoides. To probe into the transcriptome, we constructed a partial cDNA library from the venom gland of D. coronoides. The proteome of the venom of D. coronoides was explored by tryptic digestion of the c...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr1008916
更新日期:2011-02-04 00:00:00
abstract::Skeletal muscle has emerged as an important secretory organ that produces so-called myokines, regulating energy metabolism via autocrine, paracrine, and endocrine actions; however, the nature and extent of the muscle secretome has not been fully elucidated. Mass spectrometry (MS)-based proteomics, in principle, allows...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.5b00720
更新日期:2015-11-06 00:00:00
abstract::In the framework of the C-HPP, our Franco-Swiss consortium has adopted chromosomes 2 and 14, coding for a total of 382 missing proteins (proteins for which evidence is lacking at protein level). Over the last 4 years, the French proteomics infrastructure has collected high-quality data sets from 40 human samples, incl...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr5010345
更新日期:2015-09-04 00:00:00
abstract::A role for Src Family Kinases (SFKs) in the dynamics of endocytic and secretory pathways has previously been reported. Identification of low-abundance compartmentalized complexes still remains challenging, highlighting the need for novel tools. Here we describe analysis of SFK-signaling complexes of hepatic Golgi/endo...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr900481b
更新日期:2010-02-05 00:00:00
abstract::Mass spectrometry is the main analytical technique currently used to address the challenges of glycomics as it offers unrivalled levels of sensitivity and the ability to handle complex mixtures of different glycan variations. Determination of glycan structures from analysis of MS data is a major bottleneck in high-thr...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr7008252
更新日期:2008-04-01 00:00:00
abstract::Reference materials are vital to benchmarking the reproducibility of clinical tests and essential for monitoring laboratory performance for clinical proteomics. The reference material utilized for mass spectrometric analysis of the human proteome would ideally contain enough proteins to be suitably representative of t...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.8b00165
更新日期:2018-06-01 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::Various mammalian cells including tumor cells secrete extracellular vesicles (EVs), otherwise known as exosomes and microvesicles. EVs are nanosized bilayered proteolipids and play multiple roles in intercellular communication. Although many vesicular proteins have been identified, their functional interrelationships ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr200842h
更新日期:2012-02-03 00:00:00
abstract::Quantitative analysis of protein biomarkers in plasma is typically done by ELISA, but this method is limited by the availability of high-quality antibodies. An alternative approach is protein immunoprecipitation combined with multiple reaction monitoring mass spectrometry (IP-MRM). We compared IP-MRM to ELISA for the ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr400877e
更新日期:2013-12-06 00:00:00
abstract::Pathogenic events in Alzheimer's disease are believed to involve an imbalance between the production and clearance of the neurotoxic 42 amino acid form of the beta-amyloid peptide (Abeta1-42). Although much is known about the production of Abeta1-42, many questions remain about its degradation. Here, we describe an op...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr0703627
更新日期:2007-11-01 00:00:00
abstract::In this report, we use a proteomic strategy to identify glycoproteins on the surface of exosomes derived from myeloid-derived suppressor cells (MDSCs), and then test if selected glycoproteins contribute to exosome-mediated chemotaxis and migration of MDSCs. We report successful modification of a surface chemistry meth...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.6b00811
更新日期:2017-01-06 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::We successfully modified an existing method to investigate protein-protein interactions in the pathogenic bacterium Salmonella enterica serovar Typhimurium (Salmonella Typhimurium). This method includes (i) addition of a histidine-biotin-histidine tag to the bait proteins via recombinant DNA techniques, (ii) in vivo c...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr800865d
更新日期:2009-03-01 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::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::Enzyme-mediated 18O/16O differential labeling of proteome samples often suffers from incomplete exchange of the carboxy-terminus oxygen atoms, resulting in ambiguity in the measurable abundance differences. In this study, an 18O/16O labeling strategy was optimized for and applied to the solution-based comparative anal...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr049790s
更新日期:2005-03-01 00:00:00
abstract::Peroxiredoxin V, an atypical thioredoxin peroxidase, is widely expressed in mammalian tissues. In addition, Prdx V is localized in mitochondria, peroxisome, cytosol, and the nucleus. Prdx V has been reported to protect a wide range of cellular environments as an antioxidant enzyme, and its dysfunctions may be implicat...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr100190b
更新日期:2010-08-06 00:00:00