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 of cellular physiology. The primary challenge in the use of MFA is that many biological networks are underdetermined systems; it is therefore difficult to narrow down the solution space from the stoichiometric constraints alone. In this tutorial, we present an overview of Flux Balance Analysis (FBA) and (13)C-Metabolic Flux Analysis ((13)C-MFA), both of which are frequently used to solve such underdetermined systems, and we demonstrate FBA and (13)C-MFA using the genome-scale model and the central carbon metabolism model, respectively. Furthermore, because such comprehensive study of intracellular fluxes is inherently complex, we subsequently introduce various pathway mapping and visualization tools to facilitate understanding of these data in the context of the pathways. Specific visualization of MFA results using the BioCyc Omics Viewer and Pathway Projector are shown as illustrative examples.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Toya Y,Kono N,Arakawa K,Tomita Mdoi
10.1021/pr2002885subject
Has Abstractpub_date
2011-08-05 00:00:00pages
3313-23issue
8eissn
1535-3893issn
1535-3907journal_volume
10pub_type
杂志文章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：:Fusarium graminearum (FG) is a serious plant pathogen causing huge losses in global production of wheat and other cereals. Tri5-gene encoded trichodiene synthase is the first key enzyme for biosynthesis of trichothecene mycotoxins in FG. To further our understandings of FG metabolism which is essential for developing ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr101095t
更新日期：2011-05-06 00:00:00
abstract：:Huntington's disease (HD) causes widespread CNS changes and systemic abnormalities including endocrine and immune dysfunction. HD biomarkers are needed to power clinical trials of potential treatments. We used multiplatform proteomic profiling to reveal plasma changes with HD progression. Proteins of interest were eva...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0700753
更新日期：2007-07-01 00:00:00
abstract：:Protein phosphorylation is a reversible post-translational modification that regulates many biological processes in almost all living forms. In the case of the hepatitis C virus (HCV), the nonstructural protein 5A (NS5A) is believed to transit between hypo- and hyper-phosphorylated forms that interact with host protei...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00130
更新日期：2019-07-05 00:00:00
abstract：:Multiple reaction monitoring (MRM)-based mass spectrometric quantification of peptides and their corresponding proteins has been successfully applied for biomarker validation in serum. The option of multiplexing offers the chance to analyze various proteins in parallel, which is especially important in obesity researc...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500722k
更新日期：2014-12-05 00:00:00
abstract：:Arabidopsis MAP kinase 4 (MPK4) has been proposed to be a negative player in plant immunity, and it is also activated by pathogen-associated molecular patterns (PAMPs), such as flg22. The molecular mechanisms by which MPK4 is activated and regulates plant defense remain elusive. In this study, we investigated Arabidop...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00345
更新日期：2019-03-01 00:00:00
abstract：:Hepatocellular carcinoma (HCC) remains as the fifth most common cancer in the world and accounts for more than 700,000 deaths annually. Changes in serum glycosylation have long been associated with this cancer but the source of that material is unknown and direct glycan analysis of HCC tissues has been limited. Our la...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00323
更新日期：2018-10-05 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060508m
更新日期：2007-02-01 00:00:00
abstract：:Ovarian cancer remains a deadly threat to women as the disease is often diagnosed in the late stages when the chance of survival is low. There are no good biomarkers available for early detection and only a few markers have shown clinical utility for prognosis, response to therapy and disease recurrence. We mined cond...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900411g
更新日期：2009-10-01 00:00:00
abstract：:Affinity purification coupled to 1-D gel-free liquid chromatography mass spectrometry (LC-MS) is a well-established and widespread approach for the analyses of noncovalently interacting protein complexes. In this study, two proteins conjugated to a streptavidin-binding peptide and hemagglutinin double tag were express...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4009892
更新日期：2014-02-07 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900365e
更新日期：2009-10-01 00:00:00
abstract：:Complicating proteomic analysis of whole tissues is the obvious problem of cell heterogeneity in tissues, which often results in misleading or confusing molecular findings. Thus, the coupling of tissue microdissection for tumor cell enrichment with capillary isotachophoresis-based selective analyte concentration not o...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300303t
更新日期：2012-08-03 00:00:00
abstract：:Populus tremula L. x P. alba L. (Populus x canescens (Aiton) Smith), clone INRA 717-1-B4, saplings were subjected to 120 ppb ozone exposure for 28 days. Chloroplasts were isolated, and the membrane proteins, solubilized using the detergent 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC), were analyzed in a differen...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr1012009
更新日期：2011-07-01 00:00:00
abstract：:The mechanisms whereby Mycobacterium tuberculosis (Mtb) rewires the host metabolism in vivo are surprisingly unexplored. Here, we used three high-resolution mass spectrometry platforms to track altered lung metabolic changes associated with Mtb infection of mice. The multiplatform data sets were merged using consensus...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00868
更新日期：2020-05-01 00:00:00
abstract：:Controlled ovarian hyperstimulation is performed to assist with generation of multiple mature oocytes for use in in vitro fertilization (IVF). The goal of our study was to evaluate differences in protein and steroid profiles in ovarian follicular fluid (hFF) samples obtained during oocyte retrieval from women undergoi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300535g
更新日期：2012-10-05 00:00:00
abstract：:There are three quantitative phosphoproteomic strategies most commonly used to study receptor tyrosine kinase (RTK) signaling. These strategies quantify changes in: (1) all three forms of phosphosites (phosphoserine, phosphothreonine and phosphotyrosine) following enrichment of phosphopeptides by titanium dioxide or i...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200697x
更新日期：2011-12-02 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：:To understand bacterial reactions to environmental stress or infection-related processes, it is necessary to identify the involved proteins. In mass spectrometry-based proteomics, the method of choice for spectra-to-peptide-match is database search, but in recent times, spectral libraries have come into focus. Here, w...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00615
更新日期：2020-04-03 00:00:00
abstract：:This paper describes a metabonomic study of prenatal disorders using nuclear magnetic resonance (NMR) spectroscopy of amniotic fluid (AF) collected in the second trimester of pregnancy, to search for metabolite markers of fetal malformations, prediagnostic gestational diabetes (GD), preterm delivery (PTD), early ruptu...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100815q
更新日期：2010-11-05 00:00:00
abstract：:Lipid rafts are dynamic membrane microdomains that orchestrate molecular interactions and are implicated in cancer development. To understand the functions of lipid rafts in cancer, we performed an integrated analysis of quantitative lipid raft proteomics data sets modeling progression in breast cancer, melanoma, and ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b01035
更新日期：2016-10-07 00:00:00
abstract：:In an attempt to identify prostate cancer biomarkers with greater diagnostic and prognostic capabilities, we have developed an integrative proteomic discovery workflow focused on N-linked glycoproteins that refines the target selection process. In this work, hydrazide-based chemistry was used to identify N-linked glyc...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr201200n
更新日期：2012-05-04 00:00:00
abstract：:Large-scale metabolomics studies involving thousands of samples present multiple challenges in data analysis, particularly when an untargeted platform is used. Studies with multiple cohorts and analysis platforms exacerbate existing problems such as peak alignment and normalization. Therefore, there is a need for robu...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00125
更新日期：2016-12-02 00:00:00
abstract：:Most MALDI instrumentation uses UV lasers. We have designed a MALDI-IM-oTOF-MS which employs both a Nd:YAG laser pumped optical parametric oscillator (OPOTEK, lambda = 2.8-3.2 microm at 20 Hz) to perform IR-LDI or IR-MALDI and a Nd:YLF laser (Crystalaser, lambda = 249 nm at 200 Hz) for the UV. Ion mobility (IM) gives ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060055l
更新日期：2006-06-01 00:00:00
abstract：:N-Glycans are an important source of milk oligosaccharides. In addition to free oligosaccharides found in milk, N-glycans can also be utilized by gut microbes. A potential for milk N-glycans to act as gut microbe regulators in suckling animals has attracted considerable attention; however, sow milk N-glycans and their...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00789
更新日期：2019-03-01 00:00:00
abstract：:The low selectivity of Kv1 peptide inhibitors for specific isoforms makes them poor candidates for the development of theraputics. Using combined approaches, we showed that the Kv1 turret is the critical determinant for ADWX-1 peptide inhibitor selectivity of Kv1.3 over Kv1.1. Mutation of Kv1.1 turret residues to matc...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800494a
更新日期：2008-11-01 00:00:00
abstract：:In this work, we developed a general perturbation theory and machine learning method for data mining of proteomes to discover new B-cell epitopes useful for vaccine design. The method predicts the epitope activity εq(cqj) of one query peptide (q-peptide) under a set of experimental query conditions (cqj). The method u...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00477
更新日期：2017-11-03 00:00:00
abstract：:Accurate and sensitive detection of protein-protein and protein-RNA interactions is key to understanding their biological functions. Traditional methods to identify these interactions require cell lysis and biochemical manipulations that exclude cellular compartments that cannot be solubilized under mild conditions. H...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500196b
更新日期：2014-12-05 00:00:00
abstract：:Protein chemical cross-linking combined with mass spectrometry has become an important technique for the analysis of protein structure and protein-protein interactions. A variety of cross-linkers are well developed, but reliable, rapid, and user-friendly tools for large-scale analysis of cross-linked proteins are stil...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00141
更新日期：2018-07-06 00:00:00
abstract：:Tear proteome profiling may generate useful information for the understanding of the interaction between an eye and its contacting objects, such as a contact lens or a lens implant. This is important for designing improved eye-care devices and maintaining the health of an eye. Proteome profiles of tear fluids may also...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0501970
更新日期：2005-11-01 00:00:00
abstract：:Gas chromatography-mass spectrometry (GC-MS) platforms are typically run in electron ionization (EI) mode for mass spectral matching and metabolite annotation. With the advent of high resolution mass spectrometry (HRMS), soft ionization techniques such as chemical ionization (CI) may provide additional coverage for co...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00774
更新日期：2020-07-02 00:00:00
