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1.
《Molecular & cellular proteomics : MCP》2020,19(1):114-127
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- •Quantitative proteomics and machine learning to study plasma biomarkers in HCM.
- •Six peptides are increased in plasma of LVH+ HCM compared to controls.
- •Peptide biomarkers correlate with imaging markers of phenotype severity.
- •Peptide biomarkers correlate with the estimated sudden cardiac death risk.
2.
《Molecular & cellular proteomics : MCP》2020,19(2):233-244
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- •Mapping kinase-substrate relationships is vital in discovering new tuberculosis drug targets.
- •LC-MS/MS-based phosphoproteomics expand mycobacterial STPK substrate catalogues.
- •We review and integrate MS-generated datasets on novel candidate substrates.
- •Validation studies are necessary to confirm true physiological substrates of STPKs.
3.
Jack William Houghton Guy Carpenter Joachim Hans Manuel Pesaro Steven Lynham Gordon Proctor 《Molecular & cellular proteomics : MCP》2020,19(10):1664-1676
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- •Salivary secretion was increased by mouth rinsing with TRP channel agonists.
- •The salivary proteome varied over time and was changed by TRP channel stimulation.
- •Immunoreactive Cystatin S was increased in saliva after TRPV1 stimulation.
4.
《Molecular & cellular proteomics : MCP》2020,19(6):994-1004
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- •HLA-B*27:05 and ERAP2 are risk factors for ankylosing spondylitis.
- •The effects of ERAP2 on the B*27:05 ligandome are defined.
- •P1, P2, P3, P7, and PΩ peptide positions are influenced by ERAP2.
- •These effects provide a basis for the association of ERAP2 with the autoimmune disease.
5.
《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.
6.
《Molecular & cellular proteomics : MCP》2020,19(5):871-883
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- •A novel HLA-ABC-triple knockout cell model to study the HLA-B*51 peptidome.
- •Enrichment of the unconventional non-Pro/Ala2 HLA-B*51 peptides following ERAP1 silencing.
- •Knockdown of ERAP1 increases the length of non-Pro/Ala2 and Ala2 peptides, not that of Pro2.
- •ERAP1 regulation of HLA-B*51 cell surface expression is cell type dependent.
7.
Lok Man Ashleigh L. Dale William P. Klare Joel A. Cain Zeynep Sumer-Bayraktar Paula Niewold Nestor Solis Stuart J. Cordwell 《Molecular & cellular proteomics : MCP》2020,19(8):1263-1280
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- •Growth in the bile salt deoxycholate (DOC) induces virulence proteins in C. jejuni.
- •A putative symporter Cj0025c is associated with DOC growth and cystine transport.
- •Deletion of cj0025c results in loss of cystine transport and a sulfur starved proteotype.
- •Cj0025c is required for wild-type virulence phenotypes including human cell invasion.
8.
《Molecular & cellular proteomics : MCP》2020,19(6):1005-1016
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- •Brain membrane protein extraction.
- •Protein prenylation.
- •Prenyl peptide capture and characterization by LC-MS/MS.
- •HCD and EThcD peptide fragmentation.
9.
10.
《Molecular & cellular proteomics : MCP》2020,19(3):456-466
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- •Urinary proteomes of patients with recurrent UTI, renal scarring, and VUR.
- •80 proteins differentially expressed, compared to healthy controls.
- •62 proteins may be indicative of susceptibility for UTI.
- •Altered acute phase response, extracellular matrix and carbohydrate metabolism.
11.
《Molecular & cellular proteomics : MCP》2020,19(5):828-838
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- •Higher AGC significantly improves quantitation quality in single-cell analysis.
- •The boosting-to-sample ratio should be carefully evaluated and optimized.
- •iBASIL allows for precise quantitation of 1,500 proteins from 104 AML single cells.
- •iBASIL recapitulates major biological differences in different AML single cells.
12.
《Molecular & cellular proteomics : MCP》2020,19(1):181-197
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- •Provision of data generated on the basis of a gold standard spike-in sample set.
- •Choice of spectral library has great impact on identification and quantification.
- •DIA is superior to DDA in quantification reproducibility, specificity and accuracy.
- •DIA outperforms DDA in the quantification of low protein amounts.
- •Quantification on peptide level is generally preferable.
13.
Barbara Steigenberger Henk W.P. van den Toorn Emiel Bijl Jean-Franois Greisch Oliver Rther Markus Lubeck Roland J. Pieters Albert J.R. Heck Richard A. Scheltema 《Molecular & cellular proteomics : MCP》2020,19(10):1677-1687
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- •Cross-linked peptides are physically separated from mono-linked peptides in the gas-phase by TIMS ion mobility.
- •Development of a novel data acquisition routine that a-priori distinguishes cross-linked from mono-linked peptides called caps-PASEF.
- •First application of PhoX-driven cross-linking mass spectrometry on the timsTOF Pro.
- •Application of cross-linking mass spectrometry to medium to high complexity samples.
14.
《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.
15.
Nataly Mancette Rijensky Netta R. Blondheim Shraga Eilon Barnea Nir Peled Eli Rosenbaum Aron Popovtzer Solomon M. Stemmer Alejandro Livoff Mark Shlapobersky Neta Moskovits Dafna Perry Eitan Rubin Itzhak Haviv Arie Admon 《Molecular & cellular proteomics : MCP》2020,19(8):1360-1374
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- •Sufficient tumor tissues are often unavailable large HLA peptidome discovery.
- •Using patient derived xenograft (PDX) tumors can overcome this limitation.
- •The large PDX HLA peptidomes expand significantly those of the original biopsies.
- •The HLA peptidomes of the PDX tumors included many tumor antigens.
16.
《Molecular & cellular proteomics : MCP》2020,19(2):390-404
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- •Curation of 2066 phosphorylated HLA class I peptides from immunopeptidomics data.
- •Determination of 22 HLA class I binding motifs for phosphorylated peptides.
- •Observation of a higher frequency of phosphorylated ligands binding HLA-C molecules.
- •Development of a predictor of phosphorylated peptide interactions with HLA class I.
17.
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.
18.
《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.
19.
《Molecular & cellular proteomics : MCP》2020,19(3):432-443
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- •Validation of an omic method for antigen identification using LC-MS/MS.
- •Validation of accuracy, precision, specificity, limit of detection and robustness.
- •Validation according to the current FDA and EMA guidelines.
20.
《Molecular & cellular proteomics : MCP》2020,19(5):793-807
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- •Proteome of airway secretions derived from mock- and hRSV-infected WD-PBEC cultures.
- •A polarised secretome in uninfected WD-PBECs, skewed in hRSV-infected cultures.
- •CXCL6, CXCL16, CECACAM1 and CSF3 induced only upon hRSV-infection.
- •Detection of CXCL6, CXCL16 and CSF3 in NPAs from hRSV-positive children.