Abstract:
:Large-scale phosphoproteomic analysis employing liquid chromatography-tandem mass spectrometry (LC-MS/MS) often requires a significant amount of manual manipulation of phosphopeptide datasets in the post-acquisition phase. To assist in this process, we have created software, PhosphoPIC (PhosphoPeptide Identification and Compilation), which can perform a variety of useful functions including automated selection and compilation of phosphopeptide identifications from multiple MS levels, estimation of dataset false discovery rate, and application of appropriate cross-correlation (XCorr) filters. In addition, the output files generated by this program are compatible with downstream phosphorylation site assignment using the Ascore algorithm, as well as phosphopeptide quantification via QUOIL. In this report, we utilized this software to analyze phosphoproteins from short-term vasopressin-treated rat kidney inner medullary collecting duct (IMCD). A total of 925 phosphopeptides representing 173 unique proteins were identified from membrane-enriched fractions of IMCD with a false discovery rate of 1.5%. Of these proteins, 106 were found only in the membrane-enriched fraction of IMCD cells and not in whole IMCD cell lysates. These identifications included a number of well-studied ion and solute transporters including ClC-1, LAT4, MCT2, NBC3, and NHE1, all of which contained novel phosphorylation sites. Using a label-free quantification approach, we identified phosphoproteins that changed in abundance with vasopressin exposure including aquaporin-2 (AQP2), Hnrpa3, IP3 receptor 3, and pur-beta.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Hoffert JD,Wang G,Pisitkun T,Shen RF,Knepper MAdoi
10.1021/pr0701153subject
Has Abstractpub_date
2007-09-01 00:00:00pages
3501-8issue
9eissn
1535-3893issn
1535-3907journal_volume
6pub_type
杂志文章abstract::As a result of the complexity and dynamic range of the cellular proteome, including mutual interactions and interactions with other molecules, focused proteomic approaches are important to study subsets of physiologically important proteins. In one such approach, a small molecule or part of a protein is immobilized on...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr060278b
更新日期:2006-09-01 00:00:00
abstract::Analysis of the cerebrospinal fluid (CSF) proteome has proven valuable to the study of neurodegenerative disorders. To identify new protein/pathway alterations and candidate biomarkers for amyotrophic lateral sclerosis (ALS), we performed comparative proteomic profiling of CSF from sporadic ALS (sALS), healthy control...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.5b00804
更新日期:2015-11-06 00:00:00
abstract::Microorganisms release effector molecules that modulate the host machinery enabling survival, replication, and dissemination of a pathogen. Here we characterized the extracellular proteome of Paracoccidioides brasiliensis at its pathogenic yeast phase. Cell-free culture supernatants from the Pb18 isolate, cultivated i...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr200872s
更新日期:2012-03-02 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::Tomato fruit and seed allergens were detected by IgE-immunoblotting using sera from 18 adult tomato-sensitized patients selected based on a positive history skin prick test (SPT) and specific Immunglobulin (Ig) E-levels. Isolated tomato seed total protein showed high SPT activity comparable or even higher than tomato ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr800186d
更新日期:2009-03-01 00:00:00
abstract::Elevated atmospheric CO2 and nitrogen are major environmental factors affecting shoot growth. The objectives of this study are to determine the interactive effects of elevated CO2 and nitrogen on leaf growth in tall fescue ( Festuca arundinacea) and to identify major proteins and associated metabolic pathways underlyi...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.8b00951
更新日期:2019-06-07 00:00:00
abstract::Due to the increasing prevalence of nosocomial and community-acquired antibiotic resistant Staphylococcus aureus (SA), understanding the determinants of SA nasal carriage has become a major imperative. Previous research has revealed many host and bacterial factors that contribute to SA nasal carriage. To assess bacter...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr200029r
更新日期:2011-04-01 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::To comprehensively study autoantibodies in patients with hepatocellular carcinoma (HCC), we used an approach-based serology and proteomics technologies. Total proteins extracted from HepG2 cells and HepG2.2.15 cells were separated by two-dimensional gel electrophoresis (2DE) and then transferred onto polyvinylidene di...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr070525r
更新日期:2008-02-01 00:00:00
abstract::Almond, as a part of the nut family, is an important source of biological compounds, and specifically, almond skins have been considered an important source of polyphenols, including flavan-3-ols and flavonols. Polyphenol metabolism may produce several classes of metabolites that could often be more biologically activ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr100639v
更新日期:2010-11-05 00:00:00
abstract::In type-1 diabetes mellitus (T1DM) with diabetic nephropathy (DN), accumulation of abnormal proteins in the kidney and other tissues may derive from constitutive alterations of intracellular protein recognition, assembly, and turnover. We characterized the proteins involved in these functions in cultured skin fibrobla...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr060443n
更新日期:2007-03-01 00:00:00
abstract::An individually darkened leaf model was used to study protein changes in the Arabidopsis mutant stay-green1 (sgr1) to partially mimic the process of leaf covering senescence that occurs naturally in the shaded rosettes of Arabidopsis plants. Utilizing this controlled and predictable induced senescence model has allowe...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr300691k
更新日期:2012-11-02 00:00:00
abstract::The presence of the fungal pathogen, Botrytis cinerea, in the vineyard causes reductions in both quality and quantity of grapes and wine. Because proteins are involved in the foam stabilization of sparkling wines, we have undertaken, for the first time, a thorough proteomic analysis of two champagne base wines prepare...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr070419p
更新日期:2008-03-01 00:00:00
abstract::Campylobacter jejuni, an important foodborne microorganism, poses severe and emergent threats to human health as antibiotic resistance becomes increasingly prevalent. The mechanisms of drug resistance are hard to decipher, and little is known at the metabolic level. Here we apply metabolomic profiling to discover meta...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr501061d
更新日期:2015-02-06 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::The proteome of any system is a dynamic entity, such that the intracellular concentration of a protein is dictated by the relative rates of synthesis and degradation. In this work, we have analyzed time-dependent changes in the incorporation of a stable amino acid resolved precursor, a protocol we refer to as "dynamic...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr800641v
更新日期:2009-01-01 00:00:00
abstract::Difference gel electrophoresis (DiGE) allows the reliable comparison of proteome differences between two or three samples within a single gel, by way of a CyDye fluorescent labeling system. This facilitates identification of protein differences avoiding the difficulties associated with gel-to-gel variation. A drawback...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr0606878
更新日期:2007-09-01 00:00:00
abstract::N-glycosylation of proteins is well known to occur at asparagine residues that fall within the canonical consensus sequence N-X-S/T but has also been identified at a small number of asparagine residues within N-X-C motifs, including the N491 residue of human serotransferrin. Here we report novel glycosylation sites wi...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.5b00733
更新日期:2016-07-01 00:00:00
abstract::Schwann cells (SCs) are the principal glial cells of the peripheral nervous system (PNS). As a result of tissue heterogeneity and difficulties in the isolation and culture of primary SCs, a considerable understanding of SC biology is obtained from SC lines. However, the differences between the primary SCs and SC lines...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr201221u
更新日期:2012-06-01 00:00:00
abstract::Cystinuria is a purely renal, rare genetic disease caused by mutations in cystine transporter genes and characterized by defective cystine reabsorption leading to kidney stones. In 14% of cases, patients undergo nephrectomy, but given the difficulty to predict the evolution of the disease, the identification of marker...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr501003q
更新日期:2015-01-02 00:00:00
abstract::The network of the fibrillar collagens I, III, and V, extracted from fetal calf skin and cleaved with cyanogen bromide, was studied by means of ultraviolet matrix-assisted laser desorption ionization time-of-flight mass spectrometry (UV-MALDI MS). Nearly all of the expected cyanogen bromide peptides of the different a...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr070318r
更新日期:2007-11-01 00:00:00
abstract::Proteomics of human milk has been used to identify the comprehensive cargo of proteins involved in immune and cellular function. Very little is known about the effects of gestational diabetes mellitus (GDM) on lactation and breast milk components. The objective of the current study was to examine the effect of GDM on ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr500818d
更新日期:2015-01-02 00:00:00
abstract::Malignant processes such as metastasis, invasion, or angiogenesis are tightly dependent on the composition of the extracellular medium, which is itself affected by the release of proteins by the tumor cells. p53, a major tumor suppressor protein very frequently mutated and/or inactivated in cancer cells, is known to m...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr900383g
更新日期:2009-10-01 00:00:00
abstract::Carcinoma, the most common type of cancer, arises from epithelial cells. The transition from adenoma to carcinoma is associated with the loss of E-cadherin and, in consequence, the disruption of cell-cell contacts. E-cadherin is a tumor suppressor, and it is down-regulated during epithelial-to-mesenchymal transition (...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.7b00046
更新日期:2017-08-04 00:00:00
abstract::To estimate the potential of the state-of-the-art proteomics technologies on full coverage of the encoding gene products, the Chinese Human Chromosome Proteome Consortium (CCPC) applied a multiomics strategy to systematically analyze the transciptome, translatome, and proteome of the same cultured hepatoma cells with ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr4009018
更新日期:2014-01-03 00:00:00
abstract::In this study, we aim to identify the potential biomarkers in hTG pathogenesis in schisandrin B-induced hTG mouse model. To investigate whether these identified biomarkers are only specific to schisandrin B-induced hTG mouse model, we also measured these biomarkers in a high fat diet (HFD)-induced hTG mouse model. We ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr3010327
更新日期:2013-03-01 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::The application of metabolic phenotyping to epidemiological studies involving thousands of biofluid samples presents a challenge for the selection of analytical platforms that meet the requirements of high-throughput precision analysis and cost-effectiveness. Here direct infusion-nanoelectrospray (DI-nESI) was compare...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.8b00413
更新日期:2018-10-05 00:00:00
abstract::Patients with triple-negative breast cancer (TNBC) are unresponsive to endocrine and anti-HER2 pharmacotherapy, limiting their therapeutic options to chemotherapy. TNBC is frequently associated with abnormalities in the PI3K/AKT/mTOR signaling pathway; drugs targeting this pathway are currently being evaluated in thes...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.6b00918
更新日期:2017-05-05 00:00:00
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
更新日期:2016-06-03 00:00:00