当前位置： SCI文献检索 > JOURNAL OF PROTEOME RESEARCH期刊下所有文献 > Large-scale identification of Caenorhabditis elegans proteins by multidimensional liquid chromatography-tandem mass spectrometry.

Large-scale identification of Caenorhabditis elegans proteins by multidimensional liquid chromatography-tandem mass spectrometry.

Abstract：

:A proteome of a model organism, Caenorhabditis elegans, was analyzed by an integrated liquid chromatography (LC)-based protein identification system, which was constructed by microscale two-dimensional liquid chromatography (2DLC) coupled with electrospray ionization (ESI) tandem mass spectrometry (MS/MS) on a high-resolution hybrid mass spectrometer with an automated data analysis system. Soluble and insoluble protein fractions were prepared from a mixed growth phase culture of the worm C. elegans, digested with trypsin, and fractionated separately on the 2DLC system. The separated peptides were directly analyzed by on-line ESI-MS/MS in a data-dependent mode, and the resultant spectral data were automatically processed to search a genome sequence database, wormpep 66, for protein identification. The total number of proteins of the composite proteome identified in this method was 1,616, including 110 secreted/targeted proteins and 242 transmembrane proteins. The codon adaptation indices of the identified proteins suggested that the system could identify proteins of relatively low abundance, which are difficult to identify by conventional 2D-gel electrophoresis (GE) followed by an offline mass spectrometric analysis such as peptide mass fingerprinting. Among the approximately 5,400 peptides assigned in this study, many peptides with post-translational modifications, such as N-terminal acetylation and phosphorylation, were detected. This expression profile of C. elegans, containing 571 hypothetical gene products, will serve as the basic data of a major proteome set expressed in the worm.

journal_name

J Proteome Res

journal_title

Journal of proteome research

authors

Mawuenyega KG,Kaji H,Yamuchi Y,Shinkawa T,Saito H,Taoka M,Takahashi N,Isobe T

doi

10.1021/pr025551y

keywords:

subject

Has Abstract

pub_date

2003-01-01 00:00:00

pages

23-35

issue

1

eissn

1535-3893

issn

1535-3907

journal_volume

2

pub_type

杂志文章

相关文献

JOURNAL OF PROTEOME RESEARCH文献大全
  • Plasma metabonomics as a novel diagnostic approach for major depressive disorder.

    abstract：:Major depressive disorder (MDD) is a socially detrimental psychiatric disorder, contributing to increased healthcare expenditures and suicide rates. However, no empirical laboratory-based tests are available to support the diagnosis of MDD. In this study, a NMR-based plasma metabonomic method for the diagnosis of MDD ...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/pr2010082

    authors： Zheng P,Gao HC,Li Q,Shao WH,Zhang ML,Cheng K,Yang DY,Fan SH,Chen L,Fang L,Xie P

    更新日期：2012-03-02 00:00:00

  • Transgenomic metabolic interactions in a mouse disease model: interactions of Trichinella spiralis infection with dietary Lactobacillus paracasei supplementation.

    abstract：:Irritable Bowel Syndrome (IBS) is a common multifactorial intestinal disorder for which the aetiology remains largely undefined. Here, we have used a Trichinella spiralis (T. spiralis)-induced model of post-infective IBS, and the effects of probiotic bacteria on gut dysfunction have been investigated using a metabonom...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/pr060157b

    authors： Martin FP,Verdu EF,Wang Y,Dumas ME,Yap IK,Cloarec O,Bergonzelli GE,Corthesy-Theulaz I,Kochhar S,Holmes E,Lindon JC,Collins SM,Nicholson JK

    更新日期：2006-09-01 00:00:00

  • Special Enrichment Strategies Greatly Increase the Efficiency of Missing Proteins Identification from Regular Proteome Samples.

    abstract：:As part of the Chromosome-Centric Human Proteome Project (C-HPP) mission, laboratories all over the world have tried to map the entire missing proteins (MPs) since 2012. On the basis of the first and second Chinese Chromosome Proteome Database (CCPD 1.0 and 2.0) studies, we developed systematic enrichment strategies t...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/acs.jproteome.5b00481

    authors： Su N,Zhang C,Zhang Y,Wang Z,Fan F,Zhao M,Wu F,Gao Y,Li Y,Chen L,Tian M,Zhang T,Wen B,Sensang N,Xiong Z,Wu S,Liu S,Yang P,Zhen B,Zhu Y,He F,Xu P

    更新日期：2015-09-04 00:00:00

  • Process and Workflow for Preparation of Disparate Mouse Tissues for Proteomic Analysis.

    abstract：:We investigated the effect of homogenization strategy and protein precipitation on downstream protein quantitation using multiple reaction monitoring mass spectrometry (MRM-MS). Our objective was to develop a workflow capable of processing disparate tissue types with high throughput, minimal variability, and maximum p...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/acs.jproteome.0c00399

    authors： Michaud SA,Pětrošová H,Jackson AM,McGuire JC,Sinclair NJ,Ganguly M,Flenniken AM,Nutter LMJ,McKerlie C,Schibli D,Smith D,Borchers CH

    更新日期：2021-01-01 00:00:00

  • Interactive feature finding in liquid chromatography mass spectrometry data.

    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

    authors： Clifford D,Buckley M,Fung KY,Cosgrove L

    更新日期：2006-11-01 00:00:00

  • High-throughput middle-down analysis using an orbitrap.

    abstract：:This report demonstrates the application of a capillary LC-LTQ-orbitrap system to provide automated middle-down analysis of proteolytic peptides in the mass range 3000 to 10,000 Da. The novel workflow combines an underutilized method in the orbitrap-high resolution, mass-accurate product ion measurements-with software...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/pr1000994

    authors： Cannon J,Lohnes K,Wynne C,Wang Y,Edwards N,Fenselau C

    更新日期：2010-08-06 00:00:00

  • Subcellular proteomics reveals a role for nucleo-cytoplasmic trafficking at the DNA replication origin activation checkpoint.

    abstract：:Depletion of DNA replication initiation factors such as CDC7 kinase triggers the origin activation checkpoint in healthy cells and leads to a protective cell cycle arrest at the G1 phase of the mitotic cell division cycle. This protective mechanism is thought to be defective in cancer cells. To investigate how this ch...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/pr3010919

    authors： Mulvey CM,Tudzarova S,Crawford M,Williams GH,Stoeber K,Godovac-Zimmermann J

    更新日期：2013-03-01 00:00:00

  • Metabolic Mechanism for l-Leucine-Induced Metabolome To Eliminate Streptococcus iniae.

    abstract：:Crucial metabolites that modulate hosts' metabolome to eliminate bacterial pathogens have been documented, but the metabolic mechanisms are largely unknown. The present study explores the metabolic mechanism for l-leucine-induced metabolome to eliminate Streptococcus iniae in tilapia. GC-MS-based metabolomics was used...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/acs.jproteome.6b00944

    authors： Du CC,Yang MJ,Li MY,Yang J,Peng B,Li H,Peng XX

    更新日期：2017-05-05 00:00:00

  • Proteomic evidence for roles for nucleolin and poly[ADP-ribosyl] transferase in drug resistance.

    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

    authors： Fu Z,Fenselau C

    更新日期：2005-09-01 00:00:00

  • Expression profiling of herpesvirus and vaccinia virus proteins using a high-throughput baculovirus screening system.

    abstract：:We have developed a high-throughput system for generating baculoviruses and testing the expression, solubility, and affinity column purification of encoded proteins. We have used this system to generate baculoviruses for and analyze the expression of 337 proteins from three different herpesviruses (HSV-1, EBV, and CMV...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/pr050137u

    authors： Gao M,Brufatto N,Chen T,Murley LL,Thalakada R,Domagala M,Beattie B,Mamelak D,Athanasopoulos V,Johnson D,McFadden G,Burks C,Frappier L

    更新日期：2005-11-01 00:00:00

  • Chromatin Proteomics Reveals Variable Histone Modifications during the Life Cycle of Trypanosoma cruzi.

    abstract：:Histones are well-conserved proteins that form the basic structure of chromatin in eukaryotes and undergo several post-translational modifications, which are important for the control of transcription, replication, DNA damage repair, and chromosome condensation. In early branched organisms, histones are less conserved...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/acs.jproteome.6b00208

    authors： de Jesus TC,Nunes VS,Lopes Mde C,Martil DE,Iwai LK,Moretti NS,Machado FC,de Lima-Stein ML,Thiemann OH,Elias MC,Janzen C,Schenkman S,da Cunha JP

    更新日期：2016-06-03 00:00:00

  • Pancreatic cancer serum detection using a lectin/glyco-antibody array method.

    abstract：:Pancreatic cancer is a formidable disease and early detection biomarkers are needed to make inroads into improving the outcomes in these patients. In this work, lectin antibody microarrays were utilized to detect unique glycosylation patterns of proteins from serum. Antibodies to four potential glycoprotein markers th...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/pr8007013

    authors： Li C,Simeone DM,Brenner DE,Anderson MA,Shedden KA,Ruffin MT,Lubman DM

    更新日期：2009-02-01 00:00:00

  • Incorporating In-Source Fragment Information Improves Metabolite Identification Accuracy in Untargeted LC-MS Data Sets.

    abstract：:In-source fragmentation occurs as a byproduct of electrospray ionization. We find that ions produced as a result of in-source fragmentation often match fragment ions produced during MS/MS fragmentation, and we take advantage of this phenomenon in a novel algorithm to analyze LC-MS metabolomics data sets. Our approach ...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/acs.jproteome.8b00601

    authors： Seitzer PM,Searle BC

    更新日期：2019-02-01 00:00:00

  • Relative and Quantitative Phosphoproteome Analysis of Macrophages in Response to Infection by Virulent and Avirulent Mycobacteria Reveals a Distinct Role of the Cytosolic RNA Sensor RIG-I in Mycobacterium tuberculosis Pathogenesis.

    abstract：:Comparative phosphoproteomics of Mycobacterium tuberculosis (Mtb)- and Mycobacterium bovis BCG (BCG)-infected macrophages could be instrumental in understanding the characteristic post-translational modifications of host proteins and their subsequent involvement in determining Mtb pathogenesis. To identify proteins ac...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/acs.jproteome.9b00895

    authors： Choudhary E,Bullen CK,Goel R,Singh AK,Praharaj M,Thakur P,Dhiman R,Bishai WR,Agarwal N

    更新日期：2020-06-05 00:00:00

  • Proteomic analysis of multiprotein complexes in the thylakoid membrane upon cadmium treatment.

    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

    authors： Fagioni M,D'Amici GM,Timperio AM,Zolla L

    更新日期：2009-01-01 00:00:00

  • Identification of the amyloid β-protein precursor and cystatin C as novel epidermal growth factor receptor regulated secretory proteins in nasopharyngeal carcinoma by proteomics.

    abstract：:The epidermal growth factor receptor (EGFR) is usually overexpressed in nasopharyngeal carcinoma (NPC) and is associated with pathogenesis of NPC. However, while EGFR-modulated intracellular proteins have been extensively studied, little is known concerning their extracellular counterparts. To identify EGFR-regulated ...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/pr100663p

    authors： Tang CE,Guan YJ,Yi B,Li XH,Liang K,Zou HY,Yi H,Li MY,Zhang PF,Li C,Peng F,Chen ZC,Yao KT,Xiao ZQ

    更新日期：2010-12-03 00:00:00

  • SearchGUI: A Highly Adaptable Common Interface for Proteomics Search and de Novo Engines.

    abstract：:Mass-spectrometry-based proteomics has become the standard approach for identifying and quantifying proteins. A vital step consists of analyzing experimentally generated mass spectra to identify the underlying peptide sequences for later mapping to the originating proteins. We here present the latest developments in S...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/acs.jproteome.8b00175

    authors： Barsnes H,Vaudel M

    更新日期：2018-07-06 00:00:00

  • Selenite-induced toxicity in cancer cells is mediated by metabolic generation of endogenous selenium nanoparticles.

    abstract：:Selenite has been a touted cancer chemopreventative agent but generates conflicting outcomes. Multiple mechanisms of selenite cytotoxicity in cancer cells are thought to be induced by metabolites of selenite. We observed that intracellular metabolism of selenite generates endogenous selenium nanoparticles (SeNPs) in c...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/pr501086e

    authors： Bao P,Chen Z,Tai RZ,Shen HM,Martin FL,Zhu YG

    更新日期：2015-02-06 00:00:00

  • Discovery of Metabolite Biomarkers for Acute Ischemic Stroke Progression.

    abstract：:Stroke remains a major public health problem worldwide; it causes severe disability and is associated with high mortality rates. However, early diagnosis of stroke is difficult, and no reliable biomarkers are currently established. In this study, mass-spectrometry-based metabolomics was utilized to characterize the me...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/acs.jproteome.6b00779

    authors： Liu P,Li R,Antonov AA,Wang L,Li W,Hua Y,Guo H,Wang L,Liu P,Chen L,Tian Y,Xu F,Zhang Z,Zhu Y,Huang Y

    更新日期：2017-02-03 00:00:00

  • Identification of trans-golgi network proteins in Arabidopsis thaliana root tissue.

    abstract：:Knowledge of protein subcellular localization assists in the elucidation of protein function and understanding of different biological mechanisms that occur at discrete subcellular niches. Organelle-centric proteomics enables localization of thousands of proteins simultaneously. Although such techniques have successfu...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/pr4008464

    authors： Groen AJ,Sancho-Andrés G,Breckels LM,Gatto L,Aniento F,Lilley KS

    更新日期：2014-02-07 00:00:00

  • B. subtilis ribosomal proteins: structural homology and post-translational modifications.

    abstract：:Ribosomal proteins of the model gram-positive bacterium B. subtilis 168 were extensively characterized in a proteomic study. Mass spectra of the 52 proteins expected to be constitutive components of the 70S ribosome were recorded. Peptide MS/MS analysis with an average sequence coverage of 85% supported the identifica...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/pr801114k

    authors： Lauber MA,Running WE,Reilly JP

    更新日期：2009-09-01 00:00:00

  • Quantitative Phosphoproteomics Revealed Glucose-Stimulated Responses of Islet Associated with Insulin Secretion.

    abstract：:As central tissue of glucose homeostasis, islet has been an important focus of diabetes research. Phosphorylation plays pivotal roles in islet function, especially in islet glucose-stimulated insulin secretion. A systematic view on how phosphorylation networks were coordinately regulated in this process remains lackin...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/acs.jproteome.5b00507

    authors： Li J,Li Q,Tang J,Xia F,Wu J,Zeng R

    更新日期：2015-11-06 00:00:00

  • Proteome changes after metabolic engineering to enhance aerobic mineralization of cis-1,2-dichloroethylene.

    abstract：:Metabolically engineered Escherichia coli has previously been used to degrade cis-1,2-dichloroethylene (cis-DCE). The strains express the six genes of an evolved toluene ortho-monooxygenase from Burkholderia cepacia G4 (TOM-Green, which formed a reactive epoxide) with either (1) gamma-glutamylcysteine synthetase (GSHI...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/pr060008t

    authors： Lee J,Cao L,Ow SY,Barrios-Llerena ME,Chen W,Wood TK,Wright PC

    更新日期：2006-06-01 00:00:00

  • Compositional Proteomics: Effects of Spatial Constraints on Protein Quantification Utilizing Isobaric Tags.

    abstract：:Mass spectrometry (MS) has become an accessible tool for whole proteome quantitation with the ability to characterize protein expression across thousands of proteins within a single experiment. A subset of MS quantification methods (e.g., SILAC and label-free) monitor the relative intensity of intact peptides, where t...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/acs.jproteome.7b00699

    authors： O'Brien JJ,O'Connell JD,Paulo JA,Thakurta S,Rose CM,Weekes MP,Huttlin EL,Gygi SP

    更新日期：2018-01-05 00:00:00

  • Metabolic flux analysis and visualization.

    abstract：:One of the ultimate goals of systems biology research is to obtain a comprehensive understanding of the control mechanisms of complex cellular metabolisms. Metabolic Flux Analysis (MFA) is a important method for the quantitative estimation of intracellular metabolic flows through metabolic pathways and the elucidation...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/pr2002885

    authors： Toya Y,Kono N,Arakawa K,Tomita M

    更新日期：2011-08-05 00:00:00

  • Proteomic analysis of left ventricular remodeling in an experimental model of heart failure.

    abstract：:The development of chronic heart failure (CHF) following myocardial infarction is characterized by progressive alterations of left ventricle (LV) structure and function called left ventricular remodeling (LVR), but the mechanism of LVR remains still unclear. Moreover, information concerning the global alteration prote...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/pr800409u

    authors： Cieniewski-Bernard C,Mulder P,Henry JP,Drobecq H,Dubois E,Pottiez G,Thuillez C,Amouyel P,Richard V,Pinet F

    更新日期：2008-11-01 00:00:00

  • Probing Protein Interaction Networks by Combining MS-Based Proteomics and Structural Data Integration.

    abstract：:Protein-protein interactions play a major role in the molecular machinery of life, and various techniques such as AP-MS are dedicated to their identification. However, those techniques return lists of proteins devoid of organizational structure, not detailing which proteins interact with which others. Proposing a hier...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/acs.jproteome.0c00066

    authors： Postic G,Marcoux J,Reys V,Andreani J,Vandenbrouck Y,Bousquet MP,Mouton-Barbosa E,Cianférani S,Burlet-Schiltz O,Guerois R,Labesse G,Tufféry P

    更新日期：2020-07-02 00:00:00

  • Model for Quality Control of Allergen Products with Mass Spectrometry.

    abstract：:Birch pollen allergy is diagnosed and treated with aqueous extracts from birch pollen, which contain a mixture of allergens and nonallergenic proteins, including large numbers of closely related sequence variants, so-called iso-allergens of the major allergen, Bet v 1. The quality of therapeutic and diagnostic allerge...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/acs.jproteome.7b00490

    authors： Spiric J,Schulenborg T,Schwaben L,Engin AM,Karas M,Reuter A

    更新日期：2017-10-06 00:00:00

  • Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.

    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

    authors： Li X,Gerber SA,Rudner AD,Beausoleil SA,Haas W,Villén J,Elias JE,Gygi SP

    更新日期：2007-03-01 00:00:00

  • Implementation of an algorithm for modeling disulfide bond patterns using mass spectrometry.

    abstract：:The paper describes the implementation of a software system based on the Fenyö disulfide bond assignment algorithm. The system allows an investigator to enter data derived from mass spectrum peak assignments, a target protein sequence and other experimental conditions. The output of the system is the set of disulfide ...

    journal_title：Journal of proteome research

    pub_type： 杂志文章

    doi：10.1021/pr034016a

    authors： Craig R,Krokhin O,Wilkins J,Beavis RC

    更新日期：2003-11-01 00:00:00