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1.
《Molecular & cellular proteomics : MCP》2018,17(12):2534-2545
Highlights
- •Online PASEF achieves greater than 100 MS/MS per second at full sensitivity.
- •Accurate label-free quantification of over 6000 proteins in 2 h.
- •High throughput demonstrated on 50 ng digests measured in 5 min.
- •High-precision determination of 100,000 peptide collisional cross sections.
2.
《Molecular & cellular proteomics : MCP》2019,18(6):1110-1122
Highlights
- •Comprehensive analysis of inter-individual variation of normal urinary proteome.
- •Significant gender differences were observed.
- •Proteins increased in female urine are enriched in immunological pathways.
- •Estimated reference intervals of proteins as the baseline for biomarker discovery.
3.
《Molecular & cellular proteomics : MCP》2018,17(11):2146-2163
Highlights
- •Construction of threespine stickleback gill assay library using DDA proteomics
- •Population-specific gill proteome signatures of four ecotypes identified by DIA
- •HSP47 and extracellular matrix proteins highly elevated in warm-adapted sticklebacks
- •Inflammasome and proteolytic proteins highly elevated in freshwater sticklebacks
4.
《Molecular & cellular proteomics : MCP》2019,18(3):490-503
Highlights
- •MHC-II-bound peptide repertoires from DO-sufficient and DO-deficient cells.
- •Fewer unique peptides and core epitopes were presented in the absence of DO.
- •Immunopeptidome differences appeared to result from reduced DM editing.
- •DO-dependent self-epitopes elicited CD4 T cell responses in mice.
5.
Spatiotemporal Changes of the Phagosomal Proteome in Dendritic Cells in Response to LPS Stimulation*
《Molecular & cellular proteomics : MCP》2019,18(5):909-922
Highlights
- •Characterization of the phagosomal proteome comparing resting and LPS-treated BMDCs.
- •Label-free quantification determined 2843 phagosomal proteins.
- •Reduced recruitment of hydrolases and V-ATPase to phagosomes of LPS-treated cells.
- •Increased recruitment of antigen cross-presentation molecules to these phagosomes.
6.
《Molecular & cellular proteomics : MCP》2019,18(12):2459-2477
Highlights
- •NNAlign_MA enables full deconvolution of single MHC specificities from MS assays.
- •NNAlign_MA expands MHC allelic coverage, improving identification of T-cell epitopes.
- •NNAlign_MA was benchmarked on MHC classes I and II, outperforming current methods.
- •NNAlign_MA offers a universal solution to analyze and exploit MHC peptidomics data.
7.
《Molecular & cellular proteomics : MCP》2019,18(3):561-570
Highlights
- •Unified identification and quantification error rates for protein quantification.
- •Error propagation using graphical models and Bayesian statistics.
- •Account for uncertainty of missing values instead of overconfident point estimates.
- •Control of differential expression false discovery rate at increased sensitivity.
8.
《Molecular & cellular proteomics : MCP》2019,18(6):1123-1137
Highlights
- •Changes to the proteome of skin fibroblasts subjected to reductive stress have been quantitated.
- •Only a small set of proteins is selectively diminished upon exposure to reductants.
- •Collagens (COL1A2 and COL6A2) emerge as sentinels of reductive stress.
- •Reductive stress triggers receptor-independent Akt phosphorylation at Ser473.
9.
《Molecular & cellular proteomics : MCP》2019,18(12):2433-2446
Highlights
- •The first application of stable isotope-labeled recombinant protein fragments internal standards (SIS PrEST) on clinical samples.
- •Development of a high-precision quantitative SIS PrEST based LC-SRM Tier 2 assay for 13 apolipoproteins.
- •Semi-automated workflow enables precise and robust high-throughput sample processing.
- •The assay quantifies the effects of feNofibrate and omega-3 carboxylic acids on apolipoproteins in human plasma.
10.
《Molecular & cellular proteomics : MCP》2019,18(4):786-795
Highlights
- •Quantitative cross-linking mass spectrometry (QCLMS) was automated by Spectronaut.
- •Data-independent acquisition (DIA) was adapted to QCLMS.
- •Accuracy and precision of quantitation improves with DIA over DDA.
- •QCLMS is now ready for use in complex samples.
11.
《Molecular & cellular proteomics : MCP》2019,18(6):1242-1254
Highlights
- •Robust capillary-flow DIA was established at 31 clinical samples per day.
- •1508 samples of dietary intervention study DiOGenes were measured on a single column.
- •Comprehensive biological reactions to weight loss and maintenance were observed.
- •Comparison to independent studies shows high reproducibility of potential biomarkers.
12.
《Molecular & cellular proteomics : MCP》2018,17(12):2448-2461
Highlights
- •Chemical proteomics strategy for quantitative profiling of phosphoprotein phosphatases.
- •Compatible with quantitative multiplexing approaches.
- •Applicable to many samples types including tissues from human to yeast.
13.
《Molecular & cellular proteomics : MCP》2019,18(6):1085-1095
Highlights
- •Rapamycin and zinc induce moderate but significant mitochondrial proteome changes.
- •The mitochondrial proteins processing system is robust under subtoxic conditions.
- •Rapamycin and zinc perturb the mitochondrial proteins processing system.
- •Rapamycin and zinc perturb the mitochondrial proteins homeostasis.
14.
《Molecular & cellular proteomics : MCP》2019,18(1):41-50
Highlights
- •Proteome of mature boar spermatozoa from cauda epididymal and ejaculated sources were analyzed by iTRAQ-based LC-MS/MS.
- •1,723 sperm proteins identified (974 of Sus scrofa taxonomy).
- •1,602 sperm proteins quantified (960 of Sus scrofa taxonomy).
- •32 Sus scrofa sperm proteins were differentially expressed among sperm sources.
- •The proteome of boar spermatozoa is remodelled during ejaculation.
15.
《Molecular & cellular proteomics : MCP》2019,18(8):1683-1699
Highlights
- •High-quality LFQ is valuable technique yet remains extremely challenging.
- •Fluctuating precision, limited robustness, and compromised accuracy are known issues.
- •We proposed a strategy collectively improving LFQ precision, robustness, and accuracy.
- •An online tool incorporating this novel strategy was also developed.
16.
Intact Transition Epitope Mapping – Targeted High-Energy Rupture of Extracted Epitopes (ITEM-THREE),
《Molecular & cellular proteomics : MCP》2019,18(8):1543-1555
Highlights
- •Multiplex epitope mapping/antigenic determinant identification in the gas phase.
- •Intact transition and controlled dissociation of immune complexes by MS.
- •Simultaneous identification and amino acid sequence determination of epitopes.
- •Simplified in-solution sample handling because of ion manipulation and filtering by MS.
17.
《Molecular & cellular proteomics : MCP》2019,18(3):594-605
Highlights
- •A new strategy for simultaneous quantification of protein expression and modification.
- •This top-down LC/MS-based method shows high reproducibility and high throughput.
- •Quantification at the intact protein level with results comparable to Western blot.
- •This top-down proteomics method is applicable to different species and tissues.
18.
19.
《Molecular & cellular proteomics : MCP》2019,18(5):1010-1026
Highlights
- •Comparing proteolytic digestions and precursor fragmentation methods for MS of ADPr
- •Identification of 11,265 unique ADPr-modified peptides
- •Mapping of hundreds of peptides co-modified by phosphorylation and ADPr
- •ADPr modification of specific residue types displays spatial preferences
20.
《Molecular & cellular proteomics : MCP》2019,18(12):2359-2372
Highlights
- •Nonenzymatically Ksu proteins shown different pattern from native cell Ksu proteins.
- •Motif preference of Ksu proteins was associated with different biological processes.
- •Up to 67 developing rice seeds proteins contain PTMs of Kac, Ksu, Kcr, Kmal, and Khib.
- •Some lysine residues of the key pathway enzymes are modified by succinylation.