Selective enrichment of Ser-/Thr-phosphorylated peptides in the presence of Ser-/Thr-glycosylated peptides.


:Modification through beta-elimination has proven to be a reliable first step in the approach for enrichment of serine/threonine-phopshorylated (Ser-/Thr) peptides. However, under harsh basic conditions, Ser-/Thr-glycosylated peptides are susceptible to beta-elimination as well. Therefore, we have optimized these conditions to achieve a beta-elimination that is highly selective for phosphorylated peptides. This is the first report of selective beta-elimination and enrichment of phosphorylated peptides in the presence of glycosylated peptides.






Poot AJ,Ruijter E,Nuijens T,Dirksen EH,Heck AJ,Slijper M,Rijkers DT,Liskamp RM




Has Abstract


2006-12-01 00:00:00












  • Quantitative proteomic analysis and functional studies reveal that nucleophosmin is involved in cell death in glioblastoma cell line transfected with siRNA.

    abstract::Previously, we reported that nucleophosmin (NPM) was increased in glioblastoma multiforme (GBM). NPM is a phosphoprotein related to apoptosis, ribosome biogenesis, mitosis, and DNA repair, but details about its function remain unclear. We treated U87MG and A172 cells with small interference RNA (siRNA) and obtained a ...


    pub_type: 杂志文章


    authors: Gimenez M,Marie SK,Oba-Shinjo SM,Uno M,da Silva R,Laure HJ,Izumi C,Otake A,Chammas R,Rosa JC

    更新日期:2012-08-01 00:00:00

  • Proteomic and selected metabolite analysis of grape berry tissues under well-watered and water-deficit stress conditions.

    abstract::In order to investigate the unique contribution of individual wine grape (Vitis vinifera) berry tissues and water-deficit to wine quality traits, a survey of tissue-specific differences in protein and selected metabolites was conducted using pericarp (skin and pulp) and seeds of berries from vines grown under well-wat...


    pub_type: 杂志文章


    authors: Grimplet J,Wheatley MD,Jouira HB,Deluc LG,Cramer GR,Cushman JC

    更新日期:2009-05-01 00:00:00

  • The ROP2 family of Toxoplasma gondii rhoptry proteins: proteomic and genomic characterization and molecular modeling.

    abstract::Four rhoptry proteins (ROP) of Toxoplasma gondii previously identified with mAb have been affinity purified and analyzed by MS; the data obtained allowed the genomic sequences to be assigned to these proteins. As previously suggested for some of them by antibody crossreactivity, these proteins were shown to belong to ...


    pub_type: 杂志文章


    authors: El Hajj H,Demey E,Poncet J,Lebrun M,Wu B,Galéotti N,Fourmaux MN,Mercereau-Puijalon O,Vial H,Labesse G,Dubremetz JF

    更新日期:2006-11-01 00:00:00

  • 2-D DIGE as a quantitative tool for investigating the HUPO Brain Proteome Project mouse series.

    abstract::Brain development and aging is a complex process involving proliferation, differentiation and apoptosis. Elucidating proteome changes in these processes can help to understand the mechanisms of brain development and maintenance as well as neurodegenerative diseases. The research reported here is a contribution to the ...


    pub_type: 杂志文章


    authors: Föcking M,Boersema PJ,O'Donoghue N,Lubec G,Pennington SR,Cotter DR,Dunn MJ

    更新日期:2006-09-01 00:00:00

  • Proteomics Reveals Cell-Surface Urokinase Plasminogen Activator Receptor Expression Impacts Most Hallmarks of Cancer.

    abstract::While metastasis is the primary cause of colorectal cancer (CRC) mortality, the molecular mechanisms underpinning it remains elusive. Metastasis is propagated through driver oncogene/suppressor gene mutations, accompanied by passenger mutations and underlying genomic instability. To understand cancer biology, a unifyi...


    pub_type: 杂志文章


    authors: Ahn SB,Mohamedali A,Pascovici D,Adhikari S,Sharma S,Nice EC,Baker MS

    更新日期:2019-11-01 00:00:00

  • Steady state protein levels in Geobacter metallireducens grown with iron (III) citrate or nitrate as terminal electron acceptor.

    abstract::Geobacter species predominate in aquatic sediments and submerged soils where organic carbon sources are oxidized with the reduction of Fe(III). The natural occurrence of Geobacter in some waste sites suggests this microorganism could be useful for bioremediation if growth and metabolic activity can be regulated. 2-DE ...


    pub_type: 杂志文章


    authors: Ahrendt AJ,Tollaksen SL,Lindberg C,Zhu W,Yates JR 3rd,Nevin KP,Babnigg G,Lovley DR,Giometti CS

    更新日期:2007-11-01 00:00:00

  • Global profiling of proteolytically modified proteins in human metastatic hepatocellular carcinoma cell lines reveals CAPN2 centered network.

    abstract::Proteolysis affects every protein at some point in its life cycle. Many biomarkers of disease or cancer are stable proteolytic fragments in biological fluids. There is great interest and a challenge in proteolytically modified protein study to identify physiologic protease-substrate relationships and find potential bi...


    pub_type: 杂志文章


    authors: Shen C,Yu Y,Li H,Yan G,Liu M,Shen H,Yang P

    更新日期:2012-06-01 00:00:00

  • A proteomic approach to evaluate the butyrophilin gene family expression in human milk fat globule membrane.

    abstract::Human butyrophilin (BTN) expression in milk fat globule (MFGM) was evaluated using two dimensional electrophoresis (2-DE) as the separation technique, and peptide mass mapping by matrix-assisted laser desorption/ionisation-mass spectrometry (MALDI-MS) as the identification tool. Since milk composition changes througho...


    pub_type: 杂志文章


    authors: Cavaletto M,Giuffrida MG,Fortunato D,Gardano L,Dellavalle G,Napolitano L,Giunta C,Bertino E,Fabris C,Conti A

    更新日期:2002-07-01 00:00:00

  • Double chip protein arrays using recombinant single-chain Fv antibody fragments.

    abstract::Protein arrays permit the parallel analysis of many different markers in a small sample volume. However, the problem of cross-reactivity limits the degree of multiplexing in parallel sandwich immunoassays (using monoclonal antibodies (mAbs)), meaning antibodies must be prescreened in order to reduce false positives. I...


    pub_type: 杂志文章


    authors: Gilbert I,Schiffmann S,Rubenwolf S,Jensen K,Mai T,Albrecht C,Lankenau A,Beste G,Blank K,Gaub HE,Clausen-Schaumann H

    更新日期:2004-05-01 00:00:00

  • In Silico Prediction and Validation of Novel RNA Binding Proteins and Residues in the Human Proteome.

    abstract::Deciphering a complete landscape of protein-RNA interactions in the human proteome remains an elusive challenge. We computationally elucidate RNA binding proteins (RBPs) using an approach that complements previous efforts. We employ two modern complementary sequence-based methods that provide accurate predictions from...


    pub_type: 杂志文章


    authors: Chowdhury S,Zhang J,Kurgan L

    更新日期:2018-11-01 00:00:00

  • Human galectin-3 interacts with two anticancer drugs.

    abstract::Human galectin-3 (hGal-3) is a mammalian lectin involved in regulation of RNA splicing, apoptosis, cell differentiation, and proliferation. Multimerized extracellular hGal-3 is thought to crosslink cells by binding to glycoproteins and glycosylated cancer antigens on the cell surface or extracellular matrix. Fluoresce...


    pub_type: 杂志文章


    authors: Bogoeva VP,Varriale A,John CM,D'Auria S

    更新日期:2010-05-01 00:00:00

  • Proteomic and phosphoproteomic analyses of chromatin-associated proteins from Arabidopsis thaliana.

    abstract::The nucleus is the organelle where basically all DNA-related processes take place in eukaryotes, such as replication, transcription, and splicing as well as epigenetic regulation. The identification and description of the nuclear proteins is one of the requisites toward a comprehensive understanding of the biological ...


    pub_type: 杂志文章


    authors: Bigeard J,Rayapuram N,Bonhomme L,Hirt H,Pflieger D

    更新日期:2014-10-01 00:00:00

  • Apoptosis induced by staurosporine alters chaperone and endoplasmic reticulum proteins: Identification by quantitative proteomics.

    abstract::Apoptosis contributes to cell death after cerebral ischaemia. A quantitative proteomics approach has been employed to define alterations in protein levels in apoptosis induced with staurosporine (STS). Human neuroblastoma derived SH-SY5Y cells were treated with STS (500 nM for 6 h) to induce apoptosis. Quantitative 2-...


    pub_type: 杂志文章


    authors: Short DM,Heron ID,Birse-Archbold JL,Kerr LE,Sharkey J,McCulloch J

    更新日期:2007-09-01 00:00:00

  • Simplified validation of borderline hits of database searches.

    abstract::Along with unequivocal hits produced by matching multiple MS/MS spectra to database sequences, LC-MS/MS analysis often yields a large number of hits of borderline statistical confidence. To simplify their validation, we propose to use rapid de novo interpretation of all acquired MS/MS spectra and, with the help of a s...


    pub_type: 杂志文章


    authors: Thomas H,Shevchenko A

    更新日期:2008-10-01 00:00:00

  • In vitro oxidative footprinting provides insight into apolipoprotein B-100 structure in low-density lipoprotein.

    abstract::Low-density lipoprotein (LDL) is a major cholesterol carrier in human blood. Oxidations of apolipoprotein B-100 (apo B-100, LDL protein) could be proatherogenic and play critical roles in early stages of plaque formation in the arterial wall. The structure of apo B-100 is still poorly understood, partially due to its ...


    pub_type: 杂志文章


    authors: Chakraborty S,Cai Y,Tarr MA

    更新日期:2014-11-01 00:00:00

  • Comparative proteomics of bacterial pathogens.

    abstract::The monitoring of gene expression via the technologies encompassed under the term 'proteomics' allows proteins of significance to be related to phenotypes associated with strain variability, environmental influences and the effects of genetic manipulation. The characterizations of these molecules are routinely perform...


    pub_type: 杂志文章,评审


    authors: Cordwell SJ,Nouwens AS,Walsh BJ

    更新日期:2001-04-01 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

  • Comparative proteomic analysis in children with idiopathic short stature (ISS) before and after short-term recombinant human growth hormone (rhGH) therapy.

    abstract::This study was undertaken to identify growth hormone (GH) responsive proteins and protein expression patterns by short-term recombinant human growth hormone (rhGH) therapy in patients with idiopathic short stature (ISS) using proteomic analysis. Seventeen children (14 males and three females) with ISS were included. T...


    pub_type: 临床试验,杂志文章


    authors: Heo SH,Choi JH,Kim YM,Jung CW,Lee J,Jin HY,Kim GH,Lee BH,Shin CH,Yoo HW

    更新日期:2013-04-01 00:00:00

  • Cobalt Phthalocyanine Tetracarboxylic Acid Functionalized Polymer Monolith for Selective Enrichment of Glycopeptides and Glycans.

    abstract::In this study, poly(glycidyl methacrylate-ethyleneglycol dimethacrylate) monolith functionalized with cobalt phthalocyanine tetracarboxylic acid is prepared. The polymer monolithic material is used for glycopeptides enrichment coupled with MALDI-TOF MS. By taking advantage of cobalt phthalocyanine including hydrogen b...


    pub_type: 杂志文章


    authors: Zhang W,Song N,Zheng H,Feng W,Jia Q

    更新日期:2018-10-01 00:00:00

  • Sensitive, quantitative, and fast modifications for Coomassie Blue staining of polyacrylamide gels.

    abstract::In spite of the high sensitivity of silver staining and the wide dynamic range of various fluorescent detection methods, Coomassie Brilliant Blue staining is still the most widely used protein detection technique for proteins separated by polyacrylamide gel electrophoresis. There are several reasons: Low price, Visibl...


    pub_type: 杂志文章


    authors: Westermeier R

    更新日期:2006-09-01 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

  • Proteome analysis of a human uveal melanoma primary cell culture by 2-DE and MS.

    abstract::We present here the first proteomics analysis of uveal melanoma (UM) cells. These cells represent a good model for the identification of polypeptide markers, which could be developed as diagnostic tools. UM is the most common primary intraocular tumour in adults. In contrast to other cancers, the survival rate of pati...


    pub_type: 杂志文章


    authors: Pardo M,García A,Thomas B,Piñeiro A,Akoulitchev A,Dwek RA,Zitzmann N

    更新日期:2005-12-01 00:00:00

  • Mass spectrometric characterization of the Campylobacter jejuni adherence factor CadF reveals post-translational processing that removes immunogenicity while retaining fibronectin binding.

    abstract::Campylobacter jejuni is a major gastrointestinal pathogen that colonizes host mucosa via interactions with extracellular matrix proteins, such as fibronectin (Fn). Fn-binding is mediated by a 37 kDa outer membrane protein termed Campylobacter adherence Factor (CadF). The outer membrane protein profile of a recent gast...


    pub_type: 杂志文章


    authors: Scott NE,Marzook NB,Deutscher A,Falconer L,Crossett B,Djordjevic SP,Cordwell SJ

    更新日期:2010-01-01 00:00:00

  • Advances in high-resolution accurate mass spectrometry application to targeted proteomics.

    abstract::Targeted quantitative proteomic analyses aim at systematically measuring the abundance of proteins in large sets of samples, without biases or missing values. One typical implementation is the verification of biomarker candidates in bodily fluids, which measures extended lists of validated transitions using triple qua...


    pub_type: 杂志文章,评审


    authors: Lesur A,Domon B

    更新日期:2015-03-01 00:00:00

  • Proteomic analysis of the phytopathogenic fungus Botrytis cinerea during cellulose degradation.

    abstract::The ascomycete Botrytis cinerea is a phytopathogenic fungus infecting and causing significant yield losses in a number of crops. Moreover, in the last few years, B. cinerea has been adopted as an important model system in molecular phytopathology. In spite of these contributions, the molecular basis of the infection c...


    pub_type: 杂志文章


    authors: Fernández-Acero FJ,Colby T,Harzen A,Cantoral JM,Schmidt J

    更新日期:2009-05-01 00:00:00

  • Analysis of earthworm Eisenia fetida proteomes during cadmium exposure: An ecotoxicoproteomics approach.

    abstract::Identification of differential proteomic responses to cadmium (Cd) would provide a means for better understanding the survival mechanisms of the earthworm, Eisenia fetida, living in a Cd-polluted environment, and the stress responses can be assessed by ecotoxiptoromics approaches. Extracts of whole earthworm collected...


    pub_type: 杂志文章


    authors: Wang X,Chang L,Sun Z,Zhang Y,Yao L

    更新日期:2010-12-01 00:00:00

  • Comparative analyses of three legume species reveals conserved and unique root extracellular proteins.

    abstract::Increasing evidence suggests that root extracellular proteins are involved in interactions between roots and their soil environment. In the present study, exudates released by 6-day-old roots of the three legume species white lupin (Lupinus albus), soybean (Glycine max), and cowpea (Vigna sinensis) were collected unde...


    pub_type: 杂志文章


    authors: Liao C,Hochholdinger F,Li C

    更新日期:2012-11-01 00:00:00

  • Prediction of biological protein-protein interactions using atom-type and amino acid properties.

    abstract::Identification and analysis of types of biological protein-protein interactions and their interfaces to predict obligate and non-obligate complexes is a problem that has drawn the attention of the research community in the past few years. In this paper, we propose a prediction approach to predict these two types of co...


    pub_type: 杂志文章


    authors: Aziz MM,Maleki M,Rueda L,Raza M,Banerjee S

    更新日期:2011-10-01 00:00:00

  • Proteomic Biomarkers to Guide Stratification for Covid-19 Treatment: Exemplifying a Path Forward Toward Implementation?

    abstract::Proteins and peptides serve as biomarkers in the context of multiple pathologies. The hypothesis that protein or peptide biomarkers may also be of value in the context of the Covid-19 pandemic appears self-evident. Proteome based biomarkers are not expected to display significant added value in the detection of viral ...


    pub_type: 杂志文章


    authors: Jankowski J

    更新日期:2020-12-01 00:00:00

  • Improved mass spectrometric identification of gel-separated hydrophobic membrane proteins after sodium dodecyl sulfate removal by ion-pair extraction.

    abstract::Separation and identification of hydrophobic membrane proteins is a major challenge in proteomics. Identification of such sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE)-separated proteins by peptide mass fingerprinting (PMF) via matrix-assisted laser desorption/ionization-time of flight (MALDI-TO...


    pub_type: 杂志文章


    authors: Zischka H,Gloeckner CJ,Klein C,Willmann S,Swiatek-de Lange M,Ueffing M

    更新日期:2004-12-01 00:00:00