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1.
《Molecular & cellular proteomics : MCP》2020,19(2):224-232
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- •Lectins and glycan-binding antibodies are valuable as probe of glycans.
- •Advanced bioinformatics tools enable the mining of glycan-array data.
- •New insights into protein-glycan interactions have value in biological research.
2.
《Molecular & cellular proteomics : MCP》2020,19(1):11-30
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- •A broad-based interlaboratory study of the glycosylation of a reference antibody: NISTmAb.
- •103 reports were received from 76 diverse laboratories worldwide.
- •Analysis involved two samples, the NISTmAb and an enzymatically modified sample, enabling within-lab separation of random and systematic errors using the “Youden two-sample” method.
- •Consensus values were derived and similar performance across all experimental methods was noted.
3.
Deborah Chang William E. Hackett Lei Zhong Xiu-Feng Wan Joseph Zaia 《Molecular & cellular proteomics : MCP》2020,19(9):1533-1545
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- •Changes in N-linked glycosylation in influenza A virus affect antigenicity of the virus.
- •Glycosylation similarity can be quantified, even in heterogeneously glycosylated proteins.
- •Glycosylation is measurably and site-specifically distinct in influenza from related strains.
4.
《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.
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.
Eugen Netz Tjeerd M. H. Dijkstra Timo Sachsenberg Lukas Zimmermann Mathias Walzer Thomas Monecke Ralf Ficner Olexandr Dybkov Henning Urlaub Oliver Kohlbacher 《Molecular & cellular proteomics : MCP》2020,19(12):2157-2168
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- •OpenPepXL is a new XL-MS identification tool with a high sensitivity.
- •It is available for all common operating systems and remote computing environments.
- •OpenPepXL is open source and supports open OpenPepXL is available as part of OpenMS data formats like mzML and mzIdentML.
- •at https://www.openms.de/openpepxl.
7.
《Molecular & cellular proteomics : MCP》2020,19(1):1-10
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- •Co-elution stands out as a global interactome mapping method.
- •Benefits include all-to-all protein analysis and measurement of interactome perturbations.
- •Different separation, quantification and bioinformatic strategies are available.
- •Design considerations depend largely on system under study.
8.
《Molecular & cellular proteomics : MCP》2020,19(7):1120-1131
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- •Quantitative proteomics of isolated lysosomes, autophagosomes and proteasomes.
- •Pharmacological inhibition of proteasomes leads to their accumulation within lysosomes.
- •Inhibition of classical autophagy pathways cannot completely block this process.
- •Known autophagy adaptor proteins are not involved.
9.
《Molecular & cellular proteomics : MCP》2020,19(7):1193-1208
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- •cGAS acetylations and phosphorylations under basal and immune-stimulated states.
- •K384 and K414 acetylations and S305 phosphorylation inhibit cGAS-mediated apoptosis.
- •Acetylation at K198 stimulates cGAS-dependent interferon signaling.
- •K198 acetylation is decreased upon herpesvirus infection.
10.
《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.
11.
《Molecular & cellular proteomics : MCP》2020,19(2):421-430
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- •Modern DIA methods contain high quality MS1 and MS2.
- •We developed a statistical procedure incorporating MS1 and MS2.
- •Benchmarking, the combined method outperformed the individual use of MS1 or MS2.
12.
Prashali Bansal Johannes Madlung Kristina Schaaf Boris Macek Fulvia Bono 《Molecular & cellular proteomics : MCP》2020,19(9):1485-1502
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- •Label-free and dimethyl labeling MS analysis of 6 RBPs from Drosophila ovaries.
- •Functionally related RBPs show overlapping proteomes.
- •Selective co-purification of splicing factors and translational regulators.
- •Validation of 26 novel interactions by co-immunoprecipitation.
13.
《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.
14.
《Molecular & cellular proteomics : MCP》2020,19(4):690-700
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- •Two molecular groups in anal squamous carcinoma according proteomic profile.
- •Differences in possible targeted processes such as metabolism or immune response.
- •Different percentage of tumor lymphocyte infiltration.
- •Difference in the frequency of ATM variants, related to PPAR inhibitors.
15.
《Molecular & cellular proteomics : MCP》2020,19(4):655-671
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- •Acute inhibition of growth-regulatory AGC-kinases Sch9, PKA and Ypk1.
- •Phospho-proteomic profiling of 6373 phsopho-sites.
- •Ypk1 regulates phospho-sites in RRxS/T-context and functionally overlaps with PKA.
- •Ypk1 and PKA activate trehalase activity of Nth1.
16.
《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.
17.
《Molecular & cellular proteomics : MCP》2020,19(1):128-141
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- •Laser microdissection of highly vulnerable hippocampal region.
- •Proteomic analysis of postmortem human brain tissue of AD and control cases.
- •Decreased levels of presynaptic proteins, but not postsynaptic proteins, in AD.
- •Immunohistochemistry verifies decreased levels of selected presynaptic proteins.
18.
《Molecular & cellular proteomics : MCP》2020,19(6):916-927
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- •Summarize the development of functional protein microarray.
- •Application of functional proteome microarray in basic research.
- •Application of functional proteome microarray in translational research.
- •Fabrication of functional membrane protein array using virion display method.
19.
《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.
20.
《Molecular & cellular proteomics : MCP》2020,19(6):928-943
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- •EGFR-TKI molecular response profiling covering 10138 proteins and 13486 mRNAs.
- •EGFR-TKI combination therapy screen using a library of 528 compounds.
- •Several new candidate EGFR-TKI escape mechanisms and combination therapy targets.
- •Combined targeting of the oncogene BCL6 and EGFR results in synergy in NSCLC cells.