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1.
《Molecular & cellular proteomics : MCP》2020,19(6):1058-1069
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- •Highly parallelizable 4D feature detection in ion mobility enhanced shotgun proteomics.
- •Multidimensional non-linear mass, retention time and ion mobility recalibration.
- •Collision cross section aware matching between runs.
- •Label-free quantification of ion mobility MS data.
2.
Jana Zecha Chien-Yun Lee Florian P. Bayer Chen Meng Vincent Grass Johannes Zerweck Karsten Schnatbaum Thomas Michler Andreas Pichlmair Christina Ludwig Bernhard Kuster 《Molecular & cellular proteomics : MCP》2020,19(9):1503-1522
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- •In-depth proteomes of 4 SARS-CoV-2 cell line models (Vero E6, Calu-3, Caco-2, A549).
- •Proteomic evidence for thousands of Chlorocebus sabaeus proteins.
- •Proteomic response of Vero E6 cells to SARS-CoV-2 infection.
- •Synthetic peptides, spectral libraries, and targeted assays for SARS-CoV-2 proteins.
3.
《Molecular & cellular proteomics : MCP》2020,19(7):1088-1103
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- •Rapid DIA-only library building with gas-phase fractionation.
- •Recommended DIA acquisition strategies with staggered windows and forbidden zones.
- •Optimized DIA instrument settings for several Thermo Orbitrap instruments.
- •Data analysis tutorial using open source DIA software.
4.
《Molecular & cellular proteomics : MCP》2020,19(3):540-553
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- •Repeatable quantification of 200 proteins in dried blood spots.
- •Determined lower limit of quantification, repeatability, parallelism and stability.
- •Protein stability in DBS stored at ambient temperatures for up to 2 months.
- •Concentration ranges for 200 proteins in 20 healthy individuals.
5.
Fengchao Yu Sarah E. Haynes Guo Ci Teo Dmitry M. Avtonomov Daniel A. Polasky Alexey I. Nesvizhskii 《Molecular & cellular proteomics : MCP》2020,19(9):1575-1585
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- •MSFragger now supports raw timsTOF PASEF data.
- •IonQuant performs fast and accurate feature detection and quantification.
- •MSFragger and IonQuant provide excellent performance for timsTOF PASEF data.
- •Flexibility allows for complex analyses, such as semi-enzymatic and open search.
6.
《Molecular & cellular proteomics : MCP》2020,19(11):1767-1776
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- •N-glycan patterns are distinct in pediatric and adult urine.
- •Sex differences of N-glycans are much larger in adults.
- •Pediatric urine has almost no sex differences in N-glycan levels.
- •In adults, the majority of N-glycans were more abundant in males.
7.
《Molecular & cellular proteomics : MCP》2020,19(4):730-743
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- •Detection of low-abundance phosphotyrosine-containing peptides is challenging.
- •Multiplexed TMT allows inclusion of modification(pTyr)-saturated boost channels.
- •Boost channels facilitate selection of pTyr precursor ions for fragmentation.
- •Quantitation depth is increased while maintaining accuracy and precision.
8.
zge Karayel Francesca Tonelli Sebastian Virreira Winter Phillip E. Geyer Ying Fan Esther M. Sammler Dario R. Alessi Martin Steger Matthias Mann 《Molecular & cellular proteomics : MCP》2020,19(9):1546-1560
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- •MS-based clinical assay that accurately determines phospho Rab10 occupancy.
- •Stable isotope labeled phosphopeptide injected as a standard with endogenous tryptic phospho Rab peptide for accurate ratio determination.
- •Determination of pRab levels in neutrophils of Parkinson disease patients.
- •Relevance of pRab levels as marker of PD.
9.
《Molecular & cellular proteomics : MCP》2020,19(6):1047-1057
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- •DEqMS is a method for statistical analysis of quantitative MS-data.
- •Variance estimates based on the actual MS-data structure.
- •Improved statistical power and accuracy in protein differential analysis.
- •DEqMS is available as a user-friendly R package in Bioconductor.
10.
Temporal Quantitative Proteomics of mGluR-induced Protein Translation and Phosphorylation in Neurons
Charlotte A. G. H. van Gelder Renske Penning Tim S. Veth Lisa A. E. Catsburg Casper C. Hoogenraad Harold D. MacGillavry Maarten Altelaar 《Molecular & cellular proteomics : MCP》2020,19(12):1952-1968
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- •Integrated phosphoproteomics and analyses of newly synthesized proteins in neurons.
- •Resource of temporal mGluR-induced signaling pathways upon DHPG stimulation.
- •Validation of PKC, MAPK1, CAMKIIa, and CDK2 in mGluR-activation and signaling.
- •Validation of Intersectin-1 in DHPG-induced AMPAR internalization.
11.
《Molecular & cellular proteomics : MCP》2020,19(4):589-607
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- •P. aeruginosa grown with exosiderophores and analyzed by proteomic and RT-qPCR.
- •Catechol-type exosiderophores strongly induce the expression of their transporters.
- •Repression of the endogenous iron uptake pathways.
- •Complex phenotypic plasticity in the expression of the various iron-uptake pathways.
12.
《Molecular & cellular proteomics : MCP》2020,19(7):1209-1219
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- •In depth performance assessment of leading tools for differential protein abundance.
- •Novel fast modular framework MSqRobSum for robust protein summarization and inference.
- •MsqRobSum outperforms leading protein summarization-based tools.
- •MSqRobSum is on par with top-performing peptide based tool MSqRob.
13.
Xufeng Zhang Han Hu Bin Han Qiaohong Wei Lifeng Meng Fan Wu Yu Fang Mao Feng Chuan Ma Olav Rueppell Jianke Li 《Molecular & cellular proteomics : MCP》2020,19(10):1632-1648
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- •The RJB syndrome is mainly due to a shift in nurse bee alloparental care behavior.
- •The RJB nurses spontaneously respond more often to larval odors compared to ITB nurses but their subsequent learning ability are similar.
- •The RJBs evolve neurophysiological adaptations that increase the nurse bees' alloparental care behavior.
- •Major royal jelly proteins and hexamerins play crucial neurobiological roles for the nervous system.
14.
《Molecular & cellular proteomics : MCP》2020,19(5):839-851
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- •A detailed investigation of the protein extraction step from FFPE tissue is shown.
- •Acidification during peptide wash increased peptide recovery of the SP3 method.
- •LCM of substantia nigra enriched neuron-specific proteins including TH.
- •>5,600 proteins were quantified using 3000 cells per sample from substantia nigra.
15.
Felicia Grasso Stefania Mochi Federica Fratini Anna Olivieri Chiara Curr Inga Siden Kiamos Elena Deligianni Cecilia Birago Leonardo Picci Elisabetta Pizzi Tomasino Pace Marta Ponzi 《Molecular & cellular proteomics : MCP》2020,19(12):1986-1997
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- •Quantitative analysis of Plasmodium sexual stage egress secretome.
- •Activated gametocytes release gender-related proteins.
- •Gametocyte egress process involves different types of vesicles.
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17.
Fei Fang Qun Zhao Huiying Chu Mingwei Liu Baofeng Zhao Zhen Liang Lihua Zhang Guohui Li Liming Wang Jun Qin Yukui Zhang 《Molecular & cellular proteomics : MCP》2020,19(10):1724-1737
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- •Mechanistic insights into ionic liquids and proteins at molecular level.
- •Extractants prescreen for proteome analysis with MD simulation system.
- •A loss-less sample preparation method developed for in-depth proteome profiling.
- •Over 3,300 proteins were confidently identified from 1,000 HeLa cells in a 1 h run.
- •Label-free quantitative proteome analysis of human liver cancer tissues.
18.
《Molecular & cellular proteomics : MCP》2020,19(7):1179-1192
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- •Proteomics uncovers the flow-induced remodeling of the endothelial basement membrane.
- •Flow alters the composition and localization of the laminin-integrin network.
- •Flow induces proteolytic processing of LAMA4, resulting in shedding of LG4–5 region.
- •TNFα- and flow-exposure induce a distinct proteomic signature with limited interplay.
19.
Matthias Schittmayer Nemanja Vujic Barbara Darnhofer Melanie Korbelius Sophie Honeder Dagmar Kratky Ruth Birner-Gruenberger 《Molecular & cellular proteomics : MCP》2020,19(12):2104-2115
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- •Activity based serine hydrolase profiles in 11 fractions along the murine small intestine.
- •AADAC and Ces2e activity profiles correlate with chylomicron secretion.
- •Ces2e shows the highest activity based enrichment in the entire small intestine.
20.
Ting Huang Meena Choi Manuel Tzouros Sabrina Golling Nikhil Janak Pandya Balazs Banfai Tom Dunkley Olga Vitek 《Molecular & cellular proteomics : MCP》2020,19(10):1706-1723
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- •Statistical approach for differential abundance analysis for proteomic experiments with TMT labeling.
- •Applicable to large-scale experiments with complex or unbalanced design.
- •An open-source R/Bioconductor package compatible with popular data processing tools.