Detection of hypothetical proteins in human fetal perireticular nucleus.

Abstract:

:There is a legion of hypothetical proteins (HP) in prokaryotic and eukaryotic proteomes and the aim of this study was to describe HP in the perireticular nucleus (PN), a key structure in human brain development. Tissue from four PNs was homogenized and extracted proteins were run on two-dimensional gel electrophoresis followed by in-gel digestion and mass spectrometrical identification of proteins. Several databases were used for obtaining bioinformatic information and searching for functional and structural domains. Five spots represented HP: KIAA0423 protein (Q9Y4F4), hypothetical protein KIAA0153 (Q14166), hypothetical protein DKFZp564A2416 (Q9NTW4), hypothetical protein DKFZp564H1122 (Q9H0W9), and hypothetical protein DKFZp564D1378 (Q9H0R4). These structures were predicted to serve in cell cycle, DNA-condensation, neurogenesis, or apoptosis. The existence of formerly HP proteins in the PN of human fetal brain is shown, thus extending knowledge of the brain proteome and proposing the method used as a suitable analytical tool for searching HP.

journal_name

J Proteome Res

authors

Hepner F,Myung JK,Ulfig N,Pollak A,Lubec G

doi

10.1021/pr050133p

keywords:

subject

Has Abstract

pub_date

2005-11-01 00:00:00

pages

2379-85

issue

6

eissn

1535-3893

issn

1535-3907

journal_volume

4

pub_type

杂志文章
  • Assessment of Quantification Precision of Histone Post-Translational Modifications by Using an Ion Trap and down To 50 000 Cells as Starting Material.

    abstract::Histone post-translational modifications (PTMs) are fundamental players of chromatin regulation, as they contribute to editing histone chemical properties and recruiting proteins for gene transcription and DNA repair. Mass spectrometry (MS)-based proteomics is currently the most widely adopted strategy for high-throug...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.7b00544

    authors: Guo Q,Sidoli S,Garcia BA,Zhao X

    更新日期:2018-01-05 00:00:00

  • On the development of plasma protein biomarkers.

    abstract::The development of plasma biomarkers has proven to be more challenging than initially anticipated. Many studies have reported lists of candidate proteins rather than validated candidate markers with an assigned performance to a specific clinical objective. Biomarker research necessitates a clear rational framework wit...

    journal_title:Journal of proteome research

    pub_type: 杂志文章,评审

    doi:10.1021/pr1008515

    authors: Surinova S,Schiess R,Hüttenhain R,Cerciello F,Wollscheid B,Aebersold R

    更新日期:2011-01-07 00:00:00

  • Processing of data generated by 2-dimensional gel electrophoresis for statistical analysis: missing data, normalization, and statistics.

    abstract::Several high-throughput statistical methods were evaluated for processing data generated by two-dimensional polyacrylamide gel electrophoresis, including how to handle missing data, normalization, and statistical analysis of data obtained from 2-D gels. Quantile normalization combined with a nonparametric permutation ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr049886m

    authors: Chang J,Van Remmen H,Ward WF,Regnier FE,Richardson A,Cornell J

    更新日期:2004-11-01 00:00:00

  • Phosphoproteomic analysis of human mesenchymal stromal cells during osteogenic differentiation.

    abstract::Human mesenchymal stromal cells (hMSCs) are promising candidates for cell therapy and tissue regeneration. Knowledge of the molecular mechanisms governing hMSC commitment into osteoblasts is critical to the development of therapeutic applications for human bone diseases. Because protein phosphorylation plays a critica...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr200868p

    authors: Lo T,Tsai CF,Shih YR,Wang YT,Lu SC,Sung TY,Hsu WL,Chen YJ,Lee OK

    更新日期:2012-02-03 00:00:00

  • Proteomic analysis of leaves and roots of common wheat (Triticum aestivum L.) under copper-stress conditions.

    abstract::Proteomic studies were performed to identify the protein species involved in copper (Cu) stress responses in common wheat. Two-week-old wheat seedlings were exposed to 100 μM CuSO4 treatment for 3 days. Growth of shoots and roots was markedly inhibited and lipid peroxidation was greatly increased. Cu was readily absor...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr4008283

    authors: Li G,Peng X,Xuan H,Wei L,Yang Y,Guo T,Kang G

    更新日期:2013-11-01 00:00:00

  • Gain-Scanning for Protein Microarray Assays.

    abstract::Protein microarrays consist of known proteins spotted onto solid substrates and are used to perform highly multivariate assessments of protein-binding interactions. Human protein arrays are routinely applied to pathogen detection, immune response biomarker profiling, and antibody specificity profiling. Here, we descri...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00892

    authors: Feng F,Ataca ST,Ran M,Wang Y,Breen M,Kepler TB

    更新日期:2020-07-02 00:00:00

  • Temporal quantitative proteomics by iTRAQ 2D-LC-MS/MS and corresponding mRNA expression analysis identify post-transcriptional modulation of actin-cytoskeleton regulators during TGF-beta-Induced epithelial-mesenchymal transition.

    abstract::To gain insights into how TGF-beta regulates epithelial-mesenchymal transition (EMT), we assessed the time course of proteins and mRNAs during EMT by multiplex iTRAQ labeling and 2D-LC-MS/MS, and by hybridization, respectively. Temporal iTRAQ analysis identified 66 proteins as differentially expressed during EMT, incl...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr8006478

    authors: Keshamouni VG,Jagtap P,Michailidis G,Strahler JR,Kuick R,Reka AK,Papoulias P,Krishnapuram R,Srirangam A,Standiford TJ,Andrews PC,Omenn GS

    更新日期:2009-01-01 00:00:00

  • Exploration of the Fecal Microbiota and Biomarker Discovery in Equine Grass Sickness.

    abstract::Equine grass sickness (EGS) is a frequently fatal disease of horses, responsible for the death of 1 to 2% of the U.K. horse population annually. The etiology of this disease is currently uncharacterized, although there is evidence it is associated with Clostridium botulinum neurotoxin in the gut. Prevention is current...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.7b00784

    authors: Leng J,Proudman C,Darby A,Blow F,Townsend N,Miller A,Swann J

    更新日期:2018-03-02 00:00:00

  • Metabolic Response in Rabbit Urine to Occurrence and Relief of Unilateral Ureteral Obstruction.

    abstract::Ureteral obstruction will lead clinically to hydronephrosis, which may further develop into partial or complete loss of kidney function and even cause permanent histological damage. However, there is little knowledge of metabolic responses during the obstructed process and its recoverability. In this study, a complete...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.8b00304

    authors: Wang Z,Xu R,Shen G,Feng J

    更新日期:2018-09-07 00:00:00

  • Impact of Amidination on Peptide Fragmentation and Identification in Shotgun Proteomics.

    abstract::Peptide amidination labeling using S-methyl thioacetimidate (SMTA) is investigated in an attempt to increase the number and types of peptides that can be detected in a bottom-up proteomics experiment. This derivatization method affects the basicity of lysine residues and is shown here to significantly impact the idios...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.6b00468

    authors: Li S,Dabir A,Misal SA,Tang H,Radivojac P,Reilly JP

    更新日期:2016-10-07 00:00:00

  • The Muscle Metabolome Differs between Healthy and Frail Older Adults.

    abstract::Populations around the world are aging rapidly. Age-related loss of physiological functions negatively affects quality of life. A major contributor to the frailty syndrome of aging is loss of skeletal muscle. In this study we assessed the skeletal muscle biopsy metabolome of healthy young, healthy older and frail olde...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00840

    authors: Fazelzadeh P,Hangelbroek RW,Tieland M,de Groot LC,Verdijk LB,van Loon LJ,Smilde AK,Alves RD,Vervoort J,Müller M,van Duynhoven JP,Boekschoten MV

    更新日期:2016-02-05 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

  • Compartment proteomics analysis of white perch (Morone americana) ovary using support vector machines.

    abstract::Compartment proteomics enable broad characterization of target tissues. We employed a simple fractionation method and filter-aided sample preparation (FASP) to characterize the cytosolic and membrane fractions of white perch ovary tissues by semiquantitative tandem mass spectrometry using label-free quantitation based...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr401067g

    authors: Schilling J,Nepomuceno A,Schaff JE,Muddiman DC,Daniels HV,Reading BJ

    更新日期:2014-03-07 00:00:00

  • abFASP-MS: affinity-based filter-aided sample preparation mass spectrometry for quantitative analysis of chemically labeled protein complexes.

    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

    authors: Huber ML,Sacco R,Parapatics K,Skucha A,Khamina K,Müller AC,Rudashevskaya EL,Bennett KL

    更新日期:2014-02-07 00:00:00

  • Characterization of cancer associated mucin type O-glycans using the exchange sialylation properties of mammalian sialyltransferase ST3Gal-II.

    abstract::Our previous studies suggest that the α2,3sialylated T-antigen (NeuAcα2,3Galβ1,3GalNac-) and associated glycan structures are likely to be elevated during cancer. An easy and reliable strategy to label mucinous glycans that contain such carbohydrates can enable the identification of novel glycoproteins that are cancer...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr201108q

    authors: Chandrasekaran EV,Xue J,Xia J,Locke RD,Patil SA,Neelamegham S,Matta KL

    更新日期:2012-04-06 00:00:00

  • A comparative proteomic analysis of human and rat embryonic cerebrospinal fluid.

    abstract::During vertebrate central nervous system development, the apical neuroepithelium is bathed with embryonic Cerebrospinal Fluid (e-CSF) which plays regulatory roles in cortical cell proliferation and maintenance. Here, we report the first proteomic analysis of human e-CSF and compare it to an extensive proteomic analysi...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr070247w

    authors: Zappaterra MD,Lisgo SN,Lindsay S,Gygi SP,Walsh CA,Ballif BA

    更新日期:2007-09-01 00:00:00

  • The protein interaction network of extracellular vesicles derived from human colorectal cancer cells.

    abstract::Various mammalian cells including tumor cells secrete extracellular vesicles (EVs), otherwise known as exosomes and microvesicles. EVs are nanosized bilayered proteolipids and play multiple roles in intercellular communication. Although many vesicular proteins have been identified, their functional interrelationships ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr200842h

    authors: Choi DS,Yang JS,Choi EJ,Jang SC,Park S,Kim OY,Hwang D,Kim KP,Kim YK,Kim S,Gho YS

    更新日期:2012-02-03 00:00:00

  • System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects.

    abstract::Advances in mass spectrometry have made the quantitative measurement of proteins across multiple samples a reality, allowing for the study of complex biological systems such as the metabolic syndrome. Although the deregulation of lipid metabolism and increased hepatic storage of triacylglycerides are known to play a p...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.6b00815

    authors: Terfve C,Sabidó E,Wu Y,Gonçalves E,Choi M,Vaga S,Vitek O,Saez-Rodriguez J,Aebersold R

    更新日期:2017-02-03 00:00:00

  • Quantitative Proteomics Reveals Differences in the Response of Neutrophils Isolated from Healthy or Diabetic Subjects to Infection with Capsule-Variant Burkholderia thailandensis.

    abstract::In Thailand, diabetes mellitus is the most significant risk factor for melioidosis, a severe disease caused by Burkholderia pseudomallei. In this study, neutrophils isolated from healthy or diabetic subjects were infected with B. thailandensis E555, a variant strain with a B. pseudomallei-like capsular polysaccharide ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00166

    authors: Withatanung P,Kurian D,Tangjittipokin W,Plengvidhya N,Titball RW,Korbsrisate S,Stevens JM

    更新日期:2019-07-05 00:00:00

  • Porphyromonas gingivalis Gingipains Display Transpeptidation Activity.

    abstract::Porphyromonas gingivalis is a keystone periodontal pathogen that has been associated with autoimmune disorders. The cell surface proteases Lys-gingipain (Kgp) and Arg-gingipains (RgpA and RgpB) are major virulence factors, and their proteolytic activity is enhanced by small peptides such as glycylglycine (GlyGly). The...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.8b00286

    authors: Zhang L,Veith PD,Huq NL,Chen YY,Seers CA,Cross KJ,Gorasia DG,Reynolds EC

    更新日期:2018-08-03 00:00:00

  • Enhanced Validation of Antibodies Enables the Discovery of Missing Proteins.

    abstract::The localization of proteins at a tissue- or cell-type-specific level is tightly linked to the protein function. To better understand each protein's role in cellular systems, spatial information constitutes an important complement to quantitative data. The standard methods for determining the spatial distribution of p...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.0c00486

    authors: Sivertsson Å,Lindström E,Oksvold P,Katona B,Hikmet F,Vuu J,Gustavsson J,Sjöstedt E,von Feilitzen K,Kampf C,Schwenk JM,Uhlén M,Lindskog C

    更新日期:2020-12-04 00:00:00

  • Altered chaperone and protein turnover regulators expression in cultured skin fibroblasts from type 1 diabetes mellitus with nephropathy.

    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

    authors: Tessari P,Puricelli L,Iori E,Arrigoni G,Vedovato M,James P,Coracina A,Millioni R

    更新日期:2007-03-01 00:00:00

  • Quantitative mass spectrometric immunoassay of insulin like growth factor 1.

    abstract::Reported in this work are the development of mass spectrometric immunoassay (MSIA) devices and methods for the qualitative analysis of IGF-1 and -2, and the rigorous quantification of IGF-1 from human plasma. A method involving addition of SDS in moderate concentration to unfractionated plasma for disrupting IGF/IGFBP...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr0499388

    authors: Nelson RW,Nedelkov D,Tubbs KA,Kiernan UA

    更新日期:2004-07-01 00:00:00

  • Suppression of peptide sample losses in autosampler vials.

    abstract::Protein or peptide sample losses could accompany all steps of the proteomic analysis workflow. We focused on suppression of sample adsorptive losses during sample storage in autosampler vials. We examined suppression capabilities of six different sample injection solutions and seven types of autosampler vial surfaces ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr400183v

    authors: Stejskal K,Potěšil D,Zdráhal Z

    更新日期:2013-06-07 00:00:00

  • Snake venomics of Bothriechis nigroviridis reveals extreme variability among palm pitviper venoms: different evolutionary solutions for the same trophic purpose.

    abstract::We report the proteomic characterization and biological activities of the venom of the black-speckled palm pitviper, Bothriechis nigroviridis, a neotropical arboreal pitviper from Costa Rica. In marked contrast to other Bothriechis species investigated, the venom of B. nigroviridis does not possess detectable Zn(2+)-d...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr100545d

    authors: Fernández J,Lomonte B,Sanz L,Angulo Y,Gutiérrez JM,Calvete JJ

    更新日期:2010-08-06 00:00:00

  • Proteomic and Biochemical Analyses Reveal a Novel Mechanism for Promoting Protein Ubiquitination and Degradation by UFBP1, a Key Component of Ufmylation.

    abstract::Protein post-translational modification by ubiquitin-fold modifier 1, UFM1, regulates many biological processes such as response to endoplasmic reticulum stress and regulation of tumor progression. A recent study has indicated that the UFM1-binding and PCI domain-containing protein 1 (UFBP1) is required for the conjug...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.7b00843

    authors: Zhu Y,Lei Q,Li D,Zhang Y,Jiang X,Hu Z,Xu G

    更新日期:2018-04-06 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

  • A two-dimensional array for simultaneous sequencing of N- and o-glycans and their glycoforms on specific glycosylation sites.

    abstract::Glycans play major roles in living organisms. Thus, essential information is required on diverse glycans, their location, and moieties in proteins, as well as for technology in a high-throughput manner, for improving functional glycomics. In the present study, we describe a new approach involving a 2-D array, which ha...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr070392+

    authors: Tzur Y,Markovich A,Lichtenstein RG

    更新日期:2008-03-01 00:00:00

  • Comparison of ERLIC-TiO2, HILIC-TiO2, and SCX-TiO2 for global phosphoproteomics approaches.

    abstract::Reversible phosphorylations play a critical role in most biological pathways. Hence, in signaling studies great effort has been put into identification of a maximum number of phosphosites per experiment. Mass spectrometry (MS)-based phosphoproteomics approaches have been proven to be an ideal analytical method for map...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr200092z

    authors: Zarei M,Sprenger A,Metzger F,Gretzmeier C,Dengjel J

    更新日期:2011-08-05 00:00:00

  • Interaction of Drug Candidates with Various SARS-CoV-2 Receptors: An in Silico Study to Combat COVID-19.

    abstract::The world is currently facing the COVID-19 pandemic caused by the SARS-CoV-2 virus. The pandemic is causing the death of people around the world, and public and social health measures to slow or prevent the spread of COVID-19 are being implemented with the involvement of all members of society. Research institutions a...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.0c00327

    authors: Barros RO,Junior FLCC,Pereira WS,Oliveira NMN,Ramos RM

    更新日期:2020-11-06 00:00:00