当前位置： SCI文献检索 > Journal of Proteomics期刊下所有文献 > Highly reproducible improved label-free quantitative analysis of cellular phosphoproteome by optimization of LC-MS/MS gradient and analytical column construction.

Highly reproducible improved label-free quantitative analysis of cellular phosphoproteome by optimization of LC-MS/MS gradient and analytical column construction.

Abstract：

:Expanding the sequencing depth of the peptides with a statistically significant quantitative change derived from a biological stimulation is critical. Here we demonstrate that optimization of LC gradient and analytical column construction can reveal over 30,000 unique peptides and 23,000 phosphopeptides at high confidence. The quantitative reproducibility of different analytical workflows was evaluated by comparing the phosphoproteome of CD3/4 stimulated and unstimulated T-cells as a model system. A fritless, 50cm-long column packed with 1.9μm particles operated with a standard pressure HPLC significantly improved the sequencing depth 51% and decreased the selected ion chromatogram peak spreading. Most importantly, under the optimal workflow we observed an improvement of over 300% in detection of significantly changed phosphopeptides in the stimulated cells compared with the other workflows. The discovery power of the optimized column configuration was illustrated by identification of significantly altered phosphopeptides harboring novel sites from proteins previously established as important in T cell signaling including A-Raf, B-Raf, c-Myc, CARMA1, Fyn, ITK, LAT, NFAT1/2/3, PKCα, PLCγ1/2, RAF1, and SOS1. Taken together, our results reveal the analytical power of optimized chromatography using sub 2μm particles for the analysis of the T cell phosphoproteome to reveal a vast landscape of significantly altered phosphorylation changes in response to T cell receptor stimulation.

journal_name

J Proteomics

journal_title

Journal of proteomics

authors

Ahsan N,Belmont J,Chen Z,Clifton JG,Salomon AR

doi

10.1016/j.jprot.2017.06.013

subject

Has Abstract

pub_date

2017-08-08 00:00:00

pages

69-74

eissn

1874-3919

issn

1876-7737

pii

S1874-3919(17)30223-3

journal_volume

165

pub_type

杂志文章

相关文献

Journal of Proteomics文献大全
  • Hsp90 inhibition induces both protein-specific and global changes in the ubiquitinome.

    abstract：UNLABELLED:Inhibition of the essential chaperone Hsp90 with drugs causes a global perturbation of protein folding and the depletion of direct substrates of Hsp90, also called clients. Ubiquitination and proteasomal degradation play a key role in cellular stress responses, but the impact of Hsp90 inhibition on the ubiqu...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2015.02.020

    authors： Quadroni M,Potts A,Waridel P

    更新日期：2015-04-29 00:00:00

  • Comparative proteomics and metabolomics of JAZ7-mediated drought tolerance in Arabidopsis.

    abstract：:Jasmonates (JAs) are important phytohormones that regulate a wide range of plant processes, including growth, development and stress responses. Jasmonate ZIM-domain (JAZ) proteins are transcriptional repressors in JA signaling. Overexpression of JAZ7 was found to confer drought tolerance in Arabidopsis thaliana (A. th...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2019.02.001

    authors： Meng L,Zhang T,Geng S,Scott PB,Li H,Chen S

    更新日期：2019-03-30 00:00:00

  • Schistosome infections induce significant changes in the host biliary proteome.

    abstract：UNLABELLED:Schistosomiasis is a disease caused by blood trematodes affecting man and animals that represents an important human health and veterinary problem. Main damages caused by this infection are a consequence of the host inflammatory reaction against the parasite eggs trapped inside the liver. Despite that the he...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2014.11.009

    authors： de la Torre-Escudero E,Pérez-Sánchez R,Manzano-Román R,Oleaga A

    更新日期：2015-01-30 00:00:00

  • iTRAQ-based quantitative proteomic analysis reveals multiple effects of Emodin to Haemophilus parasuis.

    abstract：:Haemophilus parasuis, a symbiotic bacteria of upper respiratory tract of swine, is the etiological agent of Glässer's disease, which is characterized by fibrinous polyserositis. Emodin, exhibits antibacterial activity against H. parasuis, yet the action mode has not been fully understood. In present study, isobaric ta...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2017.06.020

    authors： Li L,Tian Y,Yu J,Song X,Jia R,Cui Q,Tong W,Zou Y,Li L,Yin L,Liang X,He C,Yue G,Ye G,Zhao L,Shi F,Lv C,Cao S,Yin Z

    更新日期：2017-08-23 00:00:00

  • Proteomic characterization of the mucosal pellicle formed in vitro on a cellular model of oral epithelium.

    abstract：:The oral mucosal pellicle is a thin lubricating layer generated by the binding of saliva proteins on epithelial oral cells. The protein composition of this biological structure has been to date studied by targeted analyses of specific salivary proteins. In order to perform a more exhaustive proteome characterization o...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2020.103797

    authors： Cabiddu G,Maes P,Hyvrier F,Olianas A,Manconi B,Brignot H,Canon F,Cabras T,Morzel M

    更新日期：2020-06-30 00:00:00

  • Effect of the myosin light chain kinase inhibitor ML-7 on the proteome of hearts subjected to ischemia-reperfusion injury.

    abstract：:In the development of ischemia/reperfusion (I/R) injury, the role of the myosin light chain (MLC) phosphorylation has been given increased consideration. ML-7, a MLC kinase inhibitor, has been shown to protect cardiac function from I/R, however the exact mechanism remains unclear. Isolated rat hearts were perfused und...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2012.06.016

    authors： Lin HB,Cadete VJ,Sawicka J,Wozniak M,Sawicki G

    更新日期：2012-09-18 00:00:00

  • Proteomic analysis reveals growth inhibition of soybean roots by manganese toxicity is associated with alteration of cell wall structure and lignification.

    abstract：UNLABELLED:Plant roots, the hidden half of plants, play a vital role in manganese (Mn) toxicity tolerance. However, molecular mechanisms underlying root adaptation to Mn toxicity remain largely unknown. In this study, soybean (Glycine max) was used to investigate alterations of root morphology and protein profiles in r...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2016.03.037

    authors： Chen Z,Yan W,Sun L,Tian J,Liao H

    更新日期：2016-06-30 00:00:00

  • Assessment of BAK1 activity in different plant receptor-like kinase complexes by quantitative profiling of phosphorylation patterns.

    abstract：UNLABELLED:Plant receptor-like kinases (RLKs) constitute a large family of receptors coordinating developmental programs with adaptation to environmental stresses including immune defenses. BRI1-ASSOCIATED KINASE 1 (BAK1), a member of the plant RLK family, forms receptor complexes with multiple RLK proteins including B...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2014.06.009

    authors： Wang Y,Li Z,Liu D,Xu J,Wei X,Yan L,Yang C,Lou Z,Shui W

    更新日期：2014-08-28 00:00:00

  • Earwax: A neglected body secretion or a step ahead in clinical diagnosis? A pilot study.

    abstract：:This work combines the advantages of volatile metabolites profiling as a young growing research field with a non-invasive sampling technique using earwax "a neglected body secretion" for detection and monitoring of biomarkers for diabetes mellitus (types 1 and 2). Earwax samples were collected from 26 diabetic patient...

    journal_title：Journal of proteomics

    pub_type： 临床试验,杂志文章

    doi：10.1016/j.jprot.2017.03.005

    authors： Shokry E,de Oliveira AE,Avelino MAG,de Deus MM,Filho NRA

    更新日期：2017-04-21 00:00:00

  • Immunoproteomic analysis of Schistosoma japonicum schistosomulum proteins recognized by immunoglobulin G in the sera of susceptible and non-susceptible hosts.

    abstract：UNLABELLED:The aim of this study was to search for immunogenic schistosomula proteins in the hope of identifying novel intervention targets. Schistosomula proteins were analyzed by immunoproteomic which the probes were sera derived from BALB/c mice (susceptible hosts) and Microtus fortis (resistant hosts). A total of 1...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2015.04.010

    authors： Hong Y,Zhang M,Yang J,Cao X,Han Q,Han Y,Qiu C,Zhu C,Lu K,Li H,Fu Z,Lin J

    更新日期：2015-06-21 00:00:00

  • Comparative proteomic study in serum of patients with primary open-angle glaucoma and pseudoexfoliation glaucoma.

    abstract：UNLABELLED:Alterations in the sera proteins between patients with Primary Open-Angle Glaucoma (POAG), Pseudoexfoliation Glaucoma (PEXG), and healthy controls were identified through a proven approach utilizing equalization of high-abundance serum proteins with ProteoMiner™, two-dimensional fluorescent difference gel el...

    journal_title：Journal of proteomics

    pub_type： 临床试验,杂志文章

    doi：10.1016/j.jprot.2013.12.006

    authors： González-Iglesias H,Álvarez L,García M,Escribano J,Rodríguez-Calvo PP,Fernández-Vega L,Coca-Prados M

    更新日期：2014-02-26 00:00:00

  • Defining the transcriptomic and proteomic profiles of rat ageing skeletal muscle by the use of a cDNA array, 2D- and Blue native-PAGE approach.

    abstract：:We defined the transcriptomic and proteomic profiles of rat ageing skeletal muscle using a combined cDNA array, 2D- and Blue native-PAGE approach. This was allowed to obtain an overview of the interrelated events leading to the transcriptome/proteome/mitoproteome changes likely to underlie the structural/metabolic fea...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2009.02.007

    authors： Lombardi A,Silvestri E,Cioffi F,Senese R,Lanni A,Goglia F,de Lange P,Moreno M

    更新日期：2009-05-02 00:00:00

  • A two-stage spin cartridge for integrated protein precipitation, digestion and SDS removal in a comparative bottom-up proteomics workflow.

    abstract：UNLABELLED:Protein precipitation with organic solvent is an effective means of depleting contaminants such as sodium dodecyl sulfate (SDS), while maintaining high analyte recovery. Here, we report the use of a disposable two-stage spin cartridge to facilitate isolation of the precipitated protein, with subsequent enzym...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2014.09.030

    authors： Crowell AM,MacLellan DL,Doucette AA

    更新日期：2015-04-06 00:00:00

  • S-Nitrosylation in plants: pattern and function.

    abstract：:During the last two decades nitric oxide (NO) has emerged as a new chemical messenger in plant biology, which is involved in many different physiological processes, such as plant defense, transpiration and gas exchange, seed germination, and root development. Protein S-nitrosylation, the post-translational modificatio...

    journal_title：Journal of proteomics

    pub_type： 杂志文章,评审

    doi：10.1016/j.jprot.2009.07.002

    authors： Lindermayr C,Durner J

    更新日期：2009-11-02 00:00:00

  • Proteomic expression profiles of virulent and avirulent strains of Listeria monocytogenes isolated from macrophages.

    abstract：:Listeria monocytogenes is able to survive and proliferate within macrophages. In the current study, the ability of three L. monocytogenes strains (serovar 1/2a strain EGDe, serovar 4b strain F2365, and serovar 4a strain HCC23) to proliferate in the murine macrophage cell line J774.1 was analyzed. We found that the avi...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2011.05.008

    authors： Donaldson JR,Nanduri B,Pittman JR,Givaruangsawat S,Burgess SC,Lawrence ML

    更新日期：2011-09-06 00:00:00

  • Comparative proteomic analysis of four Bacillus clausii strains: proteomic expression signature distinguishes protein profile of the strains.

    abstract：:A comparative proteomic approach, using two dimensional gel electrophoresis and mass spectrometry, has been developed to compare and elucidate the differences among the cellular proteomes of four closely related isogenic O/C, SIN, N/R and T, B. clausii strains during both exponential and stationary phases of growth. I...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2011.06.032

    authors： Lippolis R,Gnoni A,Abbrescia A,Panelli D,Maiorano S,Paternoster MS,Sardanelli AM,Papa S,Gaballo A

    更新日期：2011-11-18 00:00:00

  • Proteomics identifies molecular networks affected by tetradecylthioacetic acid and fish oil supplemented diets.

    abstract：UNLABELLED:Fish oil (FO) and tetradecylthioacetic acid (TTA) - a synthetic modified fatty acid have beneficial effects in regulating lipid metabolism. In order to dissect the mechanisms underlying the molecular action of those two fatty acids we have investigated the changes in mitochondrial protein expression in a lon...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2013.03.027

    authors： Wrzesinski K,R León I,Kulej K,Sprenger RR,Bjørndal B,Christensen BJ,Berge RK,Jensen ON,Rogowska-Wrzesinska A

    更新日期：2013-06-12 00:00:00

  • Proteomic alterations induced by ionic liquids in Aspergillus nidulans and Neurospora crassa.

    abstract：UNLABELLED:This study constitutes the first attempt to understand at the proteomic level the fungal response to ionic liquid stress. Ascomycota are able to grow in media supplemented with high concentrations of an ionic liquid, which, in turn, lead to major alterations in the fungal metabolic footprint. Herein, we anal...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2013.09.015

    authors： Martins I,Hartmann DO,Alves PC,Planchon S,Renaut J,Leitão MC,Rebelo LP,Silva Pereira C

    更新日期：2013-12-06 00:00:00

  • Label-free proteomic analysis of PBMCs reveals gender differences in response to long-term antiretroviral therapy of HIV.

    abstract：:The association of gender with the treatment outcome during long-term antiretroviral therapy (ART) in human immunodeficiency virus (HIV)-infected patients has been controversial. Here, we performed a comparative proteomic analysis of peripheral blood mononuclear cells (PBMC) by using a label-free shotgun method with n...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2015.05.033

    authors： Zhang L,Wang Z,Chen Y,Zhang C,Xie S,Cui Y,Wang Z

    更新日期：2015-08-03 00:00:00

  • Proteome and phosphoproteome analysis of commensally induced dendritic cell maturation states.

    abstract：:Dendritic cells (DCs) can shape the immune system towards an inflammatory or tolerant state depending on the bacterial antigens and the environment they encounter. In this study we provide a proteomic catalogue of differentially expressed proteins between distinct DC maturation states, brought about by bacteria that d...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2017.11.008

    authors： Korkmaz AG,Popov T,Peisl L,Codrea MC,Nahnsen S,Steimle A,Velic A,Macek B,von Bergen M,Bernhardt J,Frick JS

    更新日期：2018-05-30 00:00:00

  • A Fusarium graminearum strain-comparative proteomic approach identifies regulatory changes triggered by agmatine.

    abstract：UNLABELLED:Plant pathogens face different environmental clues depending on the stage of the infection cycle they are in. Fusarium graminearum infects small grain cereals producing trichothecenes type B (TB) that act as virulence factor in the interaction with the plant and have important food safety implications. This ...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2015.11.010

    authors： Pasquali M,Serchi T,Cocco E,Leclercq CC,Planchon S,Guignard C,Renaut J,Hoffmann L

    更新日期：2016-03-30 00:00:00

  • iTRAQ-based quantitative proteomic analysis provides insights into strong broodiness in Muscovy duck (Cairina moschata) combined with metabolomics analysis.

    abstract：:Much attention has been paid to the broodiness of the Muscovy duck, but the molecular mechanism of broodiness remains largely unknown. In this study, the ovary tissues of Muscovy ducks during the broody and laying periods were used to investigate differentially expressed proteins (DEPs) by the iTRAQ-based proteomics a...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2019.103401

    authors： Wu X,Pan X,Cao S,Xu F,Lan L,Zhang Y,Lian S,Yan M,Li A

    更新日期：2019-07-30 00:00:00

  • Vitamin D-binding protein as a biomarker of active disease in acute intermittent porphyria.

    abstract：UNLABELLED:Acute intermittent porphyria (AIP) is an autosomal dominant metabolic disorder caused by a deficiency of hepatic porphobilinogen deaminase (PBGD). The disease is characterized by life threatening acute neurovisceral attacks. The aim of this study was to identify metabolites secreted by the hepatocytes that r...

    journal_title：Journal of proteomics

    pub_type： 临床试验,杂志文章

    doi：10.1016/j.jprot.2015.05.004

    authors： Serrano-Mendioroz I,Sampedro A,Mora MI,Mauleón I,Segura V,Enríquez de Salamanca R,Harper P,Sardh E,Corrales FJ,Fontanellas A

    更新日期：2015-09-08 00:00:00

  • Comparative proteomic analysis of sex-biased proteins in ovary and testis at different stages of Spodoptera litura.

    abstract：:Sex-biased protein is thought to be able to drive the phenotypic differences in males and females in insects. In this study, 1385 and 1727 proteins were identified as differentially accumulated proteins (DAPs) by comparing the protein abundances at pupae stage with those at adult stage in ovary and testis of S.litura,...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2019.103439

    authors： Sun R,Sun Z,Chen Y,Zhu F,Li Y,Zhong G,Yi X

    更新日期：2019-08-30 00:00:00

  • Proteome analysis of aerobically and anaerobically grown Saccharomyces cerevisiae cells.

    abstract：:The yeast Saccharomyces cerevisiae is able to grow under aerobic as well as anaerobic conditions. We and others previously found that transcription levels of approximately 500 genes differed more than two-fold when cells from anaerobic and aerobic conditions were compared. Here, we addressed the effect of anaerobic gr...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2008.11.012

    authors： Bruckmann A,Hensbergen PJ,Balog CI,Deelder AM,Brandt R,Snoek IS,Steensma HY,van Heusden GP

    更新日期：2009-01-30 00:00:00

  • Proteome response of dental pulp cells to exogenous FGF8.

    abstract：:FGF8 specifies early tooth development by directing the migration of the early tooth founder cells to the site of tooth emergence. To date the effect of the FGF8 in adult dental pulp has not been studied. We have assessed the regenerative potential of FGF8 by evaluating changes in the proteome landscape of dental pulp...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2018.05.004

    authors： Tsikandelova R,Mladenov P,Planchon S,Kalenderova S,Praskova M,Mihaylova Z,Stanimirov P,Mitev V,Renaut J,Ishkitiev N

    更新日期：2018-07-15 00:00:00

  • Applicability of 2-DE to assess differences in the protein profile between cold storage and not cold storage in nectarine fruits.

    abstract：:Cold storage is being used to increase nectarine fruits' postharvest life. However, low temperatures lead to chilling injury and limit their commercial quality and value. In this study a proteomic approach was used to compare the protein profile between control and cold storage nectarine fruits. Protein extracted from...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2012.08.005

    authors： Giraldo E,Díaz A,Corral JM,García A

    更新日期：2012-10-22 00:00:00

  • Oncolytic adenovirus Delta-24-RGD induces a widespread glioma proteotype remodeling during autophagy.

    abstract：:Adenovirus Delta-24-RGD has shown a remarkable efficacy in a phase I clinical trial for glioblastoma. Delta-24-RGD induces autophagy in glioma cells, however, the molecular derangements associated with Delta-24-RGD infection remains poorly understood. Here, proteomics was applied to characterize the glioma metabolic d...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2018.11.020

    authors： González-Morales A,Zabaleta A,García-Moure M,Alonso MM,Fernández-Irigoyen J,Santamaría E

    更新日期：2019-03-01 00:00:00

  • Shotgun proteomic analysis of the unicellular alga Ostreococcus tauri.

    abstract：:Ostreococcus tauri is a unicellular green alga and amongst the smallest and simplest free-living eukaryotes. The O. tauri genome sequence was determined in 2006. Molecular, physiological and taxonomic data that has been generated since then highlight its potential as a simple model species for algae and plants. Howeve...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2011.05.028

    authors： Le Bihan T,Martin SF,Chirnside ES,van Ooijen G,Barrios-Llerena ME,O'Neill JS,Shliaha PV,Kerr LE,Millar AJ

    更新日期：2011-09-06 00:00:00

  • The HLA-DP peptide repertoire from human respiratory syncytial virus is focused on major structural proteins with the exception of the viral polymerase.

    abstract：:The recognition by specific T helper cells of viral antigenic peptides complexed with HLA class II molecules exposed on the surface of antigen presenting cells is the first step of the complex cascade of immunological events that generates the protective cellular and humoral immune responses. The HLA class II-restrict...

    journal_title：Journal of proteomics

    pub_type： 杂志文章

    doi：10.1016/j.jprot.2020.103759

    authors： Lorente E,Barnea E,Mir C,Admon A,López D

    更新日期：2020-06-15 00:00:00