Towards data management of the HUPO Human Brain Proteome Project pilot phase.


:The pilot phase of the Human Brain Proteome Project as a part of the Human Proteome Organisation has just been started. In two pilot studies, 18 different laboratories are analyzing mouse brains of three age stages and human brain autopsy versus biopsy material, respectively. The overall aim is to elucidate the portfolio of available techniques as well as to elaborate common standards. As a first step, it was decided to use the common bioinformatics platform ProteinScape that was introduced to the participating groups in a two day course in Bochum, Germany.






Blüggel M,Bailey S,Körting G,Stephan C,Reidegeld KA,Thiele H,Apweiler R,Hamacher M,Meyer HE




Has Abstract


2004-08-01 00:00:00












  • Membrane-Based SDS Depletion Ahead of Peptide and Protein Analysis by Mass Spectrometry.

    abstract::SDS interferes with both bottom-up and top-down MS analysis, requiring removal prior to detection. Filter-aided sample preparation (FASP) is favored for bottom-up proteomics (BUP) while acetone precipitation is popular for top-down proteomics (TDP). We recently demonstrated acetone precipitation in a membrane filter c...


    pub_type: 杂志文章


    authors: Unterlander N,Doucette AA

    更新日期:2018-05-01 00:00:00

  • Proteomic analysis of individual variation in normal livers of human beings using difference gel electrophoresis.

    abstract::Normal Chinese Liver Proteome Expression Profile is one of the major parts of Human Liver Proteome Project. Before starting the studies, it is necessary to examine the interindividual variation of normal liver proteome and evaluate the minimal size of samples for proteomic analysis. In this study, normal liver samples...


    pub_type: 杂志文章


    authors: Zhang X,Guo Y,Song Y,Sun W,Yu C,Zhao X,Wang H,Jiang H,Li Y,Qian X,Jiang Y,He F

    更新日期:2006-10-01 00:00:00

  • Quantitative assessment of the structural bias in protein-protein interaction assays.

    abstract::With recent publications of several large-scale protein-protein interaction (PPI) studies, the realization of the full yeast interaction network is getting closer. Here, we have analysed several yeast protein interaction datasets to understand their strengths and weaknesses. In particular, we investigate the effect of...


    pub_type: 杂志文章


    authors: Björklund AK,Light S,Hedin L,Elofsson A

    更新日期:2008-11-01 00:00:00

  • Determination of the site-specific and isoform-specific glycosylation in human plasma-derived antithrombin by IEF and capillary HPLC-ESI-MS/MS.

    abstract::The glycan structures of the major and more than ten minor populated isoforms of antithrombin (AT) were determined after separation of the isoforms by IEF using IPG strips. The bands excised from the gel were reduced, derivatized by iodoacetamide and submitted to tryptic digestion. The digest was analyzed by RP-HPLC-E...


    pub_type: 杂志文章


    authors: Plematl A,Demelbauer UM,Josic D,Rizzi A

    更新日期:2005-10-01 00:00:00

  • Proteome analysis of human hepatocellular carcinoma tissues by two-dimensional difference gel electrophoresis and mass spectrometry.

    abstract::Proteome analysis of human hepatocellular carcinoma tissues was conducted using two-dimensional difference gel electrophoresis coupled with mass spectrometry. Paired samples from the normal and tumor region of resected human liver were labeled with Cy3 and Cy5, respectively while the pooled standard sample was labeled...


    pub_type: 杂志文章


    authors: Liang CR,Leow CK,Neo JC,Tan GS,Lo SL,Lim JW,Seow TK,Lai PB,Chung MC

    更新日期:2005-05-01 00:00:00

  • A rapid and simple procedure for the depletion of abundant storage proteins from legume seeds to advance proteome analysis: a case study using Glycine max.

    abstract::2-D analysis of plant proteomes containing thousands of proteins has limited dynamic resolution because only abundant proteins can be detected. Proteomic assessment of the non-abundant proteins within seeds is difficult when 60-80% is storage proteins. Resolution can be improved through sample fractionation using sepa...


    pub_type: 杂志文章


    authors: Krishnan HB,Oehrle NW,Natarajan SS

    更新日期:2009-06-01 00:00:00

  • Contribution of proteomics to the molecular analysis of renal cell carcinoma with an emphasis on manganese superoxide dismutase.

    abstract::Renal cell carcinoma (RCC) originates in the renal cortex. It accounts for 2-3 percent of all cancers occurring in adults and it is characterised by lack of early clinical manifestations, unpredictable outcome, and absence of effective treatment modalities except early surgery. RCC comprises a heterogeneous group of t...


    pub_type: 杂志文章


    authors: Sarto C,Déon C,Doro G,Hochstrasser DF,Mocarelli P,Sanchez JC

    更新日期:2001-10-01 00:00:00

  • Comparative investigation of seed coats of brown- versus yellow-colored soybean seeds using an integrated proteomics and metabolomics approach.

    abstract::Seed coat color is an important attribute determining consumption of soybean seeds. Soybean cultivar Mallikong (M) has yellow seed coat while its naturally mutated cultivar Mallikong mutant (MM), has brown colored seed coat. We used integrated proteomics and metabolomics approach to investigate the differences between...


    pub_type: 杂志文章


    authors: Gupta R,Min CW,Kim SW,Wang Y,Agrawal GK,Rakwal R,Kim SG,Lee BW,Ko JM,Baek IY,Bae DW,Kim ST

    更新日期:2015-05-01 00:00:00

  • N-Terminal methylation of proteasome subunit Rpt1 in yeast.

    abstract::The 26S proteasome is a multicatalytic protease complex that degrades ubiquitinated proteins in eukaryotic cells. It consists of a proteolytic core (the 20S proteasome) as well as regulatory particles, which contain six ATPase (Rpt) subunits involved in unfolding and translocation of substrates to the catalytic chambe...


    pub_type: 杂志文章


    authors: Kimura Y,Kurata Y,Ishikawa A,Okayama A,Kamita M,Hirano H

    更新日期:2013-11-01 00:00:00

  • Proteomics of ischemia and reperfusion injuries in rabbit myocardium with and without intervention by an oxygen-free radical scavenger.

    abstract::A brief period of ischemia followed by timely reperfusion may lead to prolonged, yet reversible, contractile dysfunction (myocardial stunning). Damage to the myocardium occurs not only during ischemia, but also during reperfusion, where a massive release of oxygen-free radicals (OFR) occurs. We have previously utilize...


    pub_type: 杂志文章


    authors: White MY,Tchen AS,McCarron HC,Hambly BD,Jeremy RW,Cordwell SJ

    更新日期:2006-12-01 00:00:00

  • IQuant: an automated pipeline for quantitative proteomics based upon isobaric tags.

    abstract::Quantitative proteomics technology based on isobaric tags is playing an important role in proteomic investigation. In this paper, we present an automated software, named IQuant, which integrates a postprocessing tool of protein identification and advanced statistical algorithms to process the MS/MS signals generated f...


    pub_type: 杂志文章


    authors: Wen B,Zhou R,Feng Q,Wang Q,Wang J,Liu S

    更新日期:2014-10-01 00:00:00

  • A two-dimensional liquid-phase separation method coupled with mass spectrometry for proteomic studies of breast cancer and biomarker identification.

    abstract::A two-dimensional liquid-phase separation scheme coupled with mass spectrometry (MS) is presented for proteomic analysis of cell lysates from normal and malignant breast epithelial cell lines. Liquid-phase separations consist of isoelectric focusing as the first dimension and nonporous silica reverse-phase high-perfor...


    pub_type: 杂志文章


    authors: Hamler RL,Zhu K,Buchanan NS,Kreunin P,Kachman MT,Miller FR,Lubman DM

    更新日期:2004-03-01 00:00:00

  • Proteomic analysis of acute myeloid leukemia: Identification of potential early biomarkers and therapeutic targets.

    abstract::The main goal of this study was to analyze, using proteomic techniques, changes in protein expression of acute myeloid leukemia (AML) cells that could give insights into a better early prognosis for tumor pathophysiology. Proteomic analysis of different subtypes of AML cells was carried out using 2-DE and MALDI-TOF PM...


    pub_type: 杂志文章


    authors: López-Pedrera C,Villalba JM,Siendones E,Barbarroja N,Gómez-Díaz C,Rodríguez-Ariza A,Buendía P,Torres A,Velasco F

    更新日期:2006-04-01 00:00:00

  • A glycoproteomic approach to identify novel glycomarkers for cancer stem cells.

    abstract::Most cancers consist of heterogeneous populations of cells with substantial differences in tumorigenicity. Cells that possess self-renewal and tumor-initiating properties are often called cancer stem cells (CSCs). Since CSCs underlie tumor recurrence and metastasis and are resistant to current anti-cancer therapies, n...


    pub_type: 杂志文章,评审


    authors: Sawanobori A,Moriwaki K,Takamatsu S,Kamada Y,Miyoshi E

    更新日期:2016-12-01 00:00:00

  • Label-free analysis of human cerebrospinal fluid addressing various normalization strategies and revealing protein groups affected by multiple sclerosis.

    abstract::The aims of the study were to: (i) identify differentially regulated proteins in cerebrospinal fluid (CSF) between multiple sclerosis (MS) patients and non-MS controls; (ii) examine the effect of matching the CSF samples on either total protein amount or volume, and compare four protein normalization strategies for CS...


    pub_type: 杂志文章


    authors: Opsahl JA,Vaudel M,Guldbrandsen A,Aasebø E,Van Pesch V,Franciotta D,Myhr KM,Barsnes H,Berle M,Torkildsen Ø,Kroksveen AC,Berven FS

    更新日期:2016-04-01 00:00:00

  • Proteomic characterization of the major arthropod associates of the carnivorous pitcher plant Sarracenia purpurea.

    abstract::The array of biomolecules generated by a functioning ecosystem represents both a potential resource for sustainable harvest and a potential indicator of ecosystem health and function. The cupped leaves of the carnivorous pitcher plant, Sarracenia purpurea, harbor a dynamic food web of aquatic invertebrates in a fully ...


    pub_type: 杂志文章


    authors: Gotelli NJ,Smith AM,Ellison AM,Ballif BA

    更新日期:2011-06-01 00:00:00

  • Determination of protein markers in human serum: Analysis of protein expression in toxic oil syndrome studies.

    abstract::Toxic oil syndrome (TOS) is a disease that appeared in Spain in 1981. It affected more than 20 000 people and produced over 300 deaths in the first 2 years. In this paper, a prospective study on the differences in gene expression in sera between a control versus a TOS-affected population, both originally exposed to th...


    pub_type: 杂志文章


    authors: Quero C,Colomé N,Prieto MR,Carrascal M,Posada M,Gelpí E,Abian J

    更新日期:2004-02-01 00:00:00

  • Quantitative iTRAQ proteome and comparative transcriptome analysis of elicitor-induced Norway spruce (Picea abies) cells reveals elements of calcium signaling in the early conifer defense response.

    abstract::Long-lived conifer trees depend on both constitutive and induced defenses for resistance against a myriad of potential pathogens and herbivores. In species of spruce (Picea spp.), several of the late events of pathogen-, insect-, or elicitor-induced defense responses have previously been characterized at the anatomica...


    pub_type: 杂志文章


    authors: Lippert DN,Ralph SG,Phillips M,White R,Smith D,Hardie D,Gershenzon J,Ritland K,Borchers CH,Bohlmann J

    更新日期:2009-01-01 00:00:00

  • A detergent- and cyanogen bromide-free method for integral membrane proteomics: application to Halobacterium purple membranes and the human epidermal membrane proteome.

    abstract::A simple and rapid method for characterizing hydrophobic integral membrane proteins and its utility for membrane proteomics using microcapillary liquid chromatography coupled on-line with tandem mass spectrometry (microLC-MS/MS) is described. The present technique does not rely on the use of detergents, strong organic...


    pub_type: 杂志文章


    authors: Blonder J,Conrads TP,Yu LR,Terunuma A,Janini GM,Issaq HJ,Vogel JC,Veenstra TD

    更新日期:2004-01-01 00:00:00

  • 6th HUPO Annual World Congress - Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea.

    abstract::The plenary session of the Proteomics Standards Initiative of the Human Proteome Organisation at the 6th annual HUPO world congress updated the delegates on the current status of the ongoing work of this group. The new MS interchange format, mzML, had been entered into the HUPO document process immediately prior to th...




    authors: Orchard S,Martens L,Tasman J,Binz PA,Albar JP,Hermjakob H

    更新日期:2008-04-01 00:00:00

  • Thiol-based redox proteomics in cancer research.

    abstract::Cancer cells maintain their intracellular ROS concentrations at required levels for their survival. Changes in ROS concentrations can regulate biochemical signaling mechanisms that control cell function. It has been demonstrated that ROS regulate the cellular events through redox regulation of redox-sensitive proteins...


    pub_type: 杂志文章,评审


    authors: Yuan K,Liu Y,Chen HN,Zhang L,Lan J,Gao W,Dou Q,Nice EC,Huang C

    更新日期:2015-01-01 00:00:00

  • The stoichiometry of protein phosphorylation in adipocyte lipid droplets: analysis by N-terminal isotope tagging and enzymatic dephosphorylation.

    abstract::Most phosphoproteomic studies to date have been limited to the identification of phosphoproteins and their phosphorylation sites, and have not assessed the stoichiometry of protein phosphorylation, a critical parameter reflecting the dynamic equilibrium between phosphorylated and non-phosphorylated pools of proteins. ...


    pub_type: 杂志文章


    authors: Kanshin E,Wang S,Ashmarina L,Fedjaev M,Nifant'ev I,Mitchell GA,Pshezhetsky AV

    更新日期:2009-11-01 00:00:00

  • Partial hepatectomy induced liver proteome changes in mice.

    abstract::Acceleration of liver regeneration could be of great clinical benefit in various liver-associated diseases. However, at present little is known about therapeutic interventions to enhance this regenerative process. Our limited understanding and the complexity of the mechanisms involved have prevented the identification...


    pub_type: 杂志文章


    authors: Strey CW,Winters MS,Markiewski MM,Lambris JD

    更新日期:2005-01-01 00:00:00

  • NanoLC-FT-ICR MS improves proteome coverage attainable for approximately 3000 laser-microdissected breast carcinoma cells.

    abstract::Proteomics assays hold great promise for unraveling molecular events that underlie human diseases. Effective analysis of clinical samples is essential, but this task is considerably complicated by tissue heterogeneity. Laser capture microdissection (LCM) can be used to selectively isolate target cells from their nativ...


    pub_type: 杂志文章


    authors: Umar A,Luider TM,Foekens JA,Pasa-Tolić L

    更新日期:2007-01-01 00:00:00

  • Mucin-induced apoptosis of monocyte-derived dendritic cells during maturation.

    abstract::Many tumors arising from epithelial tissues produce mucins, which readily come into contact with infiltrating cells in cancer tissues. MUC2 mucins were purified from the conditioned medium of a colorectal cancer cell line, LS180 cells. It is known that in cancer patients, the number of dendritic cells (DCs) is reduced...


    pub_type: 杂志文章


    authors: Ishida A,Ohta M,Toda M,Murata T,Usui T,Akita K,Inoue M,Nakada H

    更新日期:2008-08-01 00:00:00

  • Proteomic profiling of PrP27-30-enriched preparations extracted from the brain of hamsters with experimental scrapie.

    abstract::Transmissible spongiform encephalopathies (TSEs) are neurodegenerative disorders characterized by the accumulation in the CNS of a pathological conformer (PrP(TSE)) of the host-encoded cellular prion protein (PrP(C)). PrP(TSE) has a central role in the pathogenesis of the disease but other factors are likely involved ...


    pub_type: 杂志文章


    authors: Giorgi A,Di Francesco L,Principe S,Mignogna G,Sennels L,Mancone C,Alonzi T,Sbriccoli M,De Pascalis A,Rappsilber J,Cardone F,Pocchiari M,Maras B,Schininà ME

    更新日期:2009-08-01 00:00:00

  • A nascent proteome study combining click chemistry with 2DE.

    abstract::To investigate the dynamic cellular response to a condition change, selective labeling of the nascent proteome is necessary. Here, we report a method combining click chemistry protein labeling with 2D DIGE. To test the relevance of the method, we compared nascent proteomes of actively growing bacterial cells with that...


    pub_type: 杂志文章


    authors: Osterman IA,Ustinov AV,Evdokimov DV,Korshun VA,Sergiev PV,Serebryakova MV,Demina IA,Galyamina MA,Govorun VM,Dontsova OA

    更新日期:2013-01-01 00:00:00

  • Analysis of PNGase F-Resistant N-Glycopeptides Using SugarQb for Proteome Discoverer 2.1 Reveals Cryptic Substrate Specificities.

    abstract::SugarQb ( is a freely available collection of computational tools for the automated identification of intact glycopeptides from high-resolution HCD MS/MS datasets in the Proteome Discoverer environment. We report the migration of SugarQb to the latest and free version of Proteome Discoverer...


    pub_type: 杂志文章


    authors: Stadlmann J,Hoi DM,Taubenschmid J,Mechtler K,Penninger JM

    更新日期:2018-07-01 00:00:00

  • Defining Cell Identity with Single-Cell Omics.

    abstract::Cells are a fundamental unit of life, and the ability to study the phenotypes and behaviors of individual cells is crucial to understanding the workings of complex biological systems. Cell phenotypes (epigenomic, transcriptomic, proteomic, and metabolomic) exhibit dramatic heterogeneity between and within the differen...


    pub_type: 杂志文章,评审


    authors: Mincarelli L,Lister A,Lipscombe J,Macaulay IC

    更新日期:2018-09-01 00:00:00

  • Identification of human nasal mucous proteins using proteomics.

    abstract::The determination of possible biomarkers in nasal secretion of healthy subjects can have a role in early diagnosis of diseases such as rhinosinusitis. For this purpose, nasal lavage fluids (NLFs) from ten volunteers, collected before and after they had been submitted to nasal provocations, were investigated. Separatio...


    pub_type: 杂志文章


    authors: Casado B,Pannell LK,Iadarola P,Baraniuk JN

    更新日期:2005-07-01 00:00:00