Dataset Information

Human chorionic villus proteome

ABSTRACT: We evaluated the effect of the different solubilization techniques on the reproducibility and width of the chorionic proteome characterized using bottom-up proteomics: SDS-based solubilization coupled with in-gel protein digestion after applying self-named 1DE gel-concentration procedure (SDS-PAGE without fractionating in the resolving gel for SDS removal) and in-solution protein digestion of urea-thiourea extracts. These results indicated that 1DE-concentration procedure coupled with in-gel digestion, LC-MS/MS and combinational usage of different bioinformatics tools provides in-depth analysis of a single protein band, including reliable identification and quantification of low-abundant proteins, e.g. FUCA1, PSG7.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Placenta

SUBMITTER: Olesya Larina

LAB HEAD: Petushkova Natalia

PROVIDER: PXD024759 | Pride | 2022-06-17

REPOSITORIES: Pride

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Publications

Protocol for Increasing the Sensitivity of MS-Based Protein Detection in Human Chorionic Villi.

Shkrigunov Timur T Pogodin Pavel P Zgoda Victor V Larina Olesya O Kisrieva Yulia Y Klimenko Maria M Latyshkevich Oleg O Klimenko Peter P Lisitsa Andrey A Petushkova Natalia N

Current issues in molecular biology 20220509 5

An important step in the proteomic analysis of missing proteins is the use of a wide range of tissues, optimal extraction, and the processing of protein material in order to ensure the highest sensitivity in downstream protein detection. This work describes a purification protocol for identifying low-abundance proteins in human chorionic villi using the proposed "1DE-gel concentration" method. This involves the removal of SDS in a short electrophoresis run in a stacking gel without protein separ ...[more]

PMID: 35678669

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Project description:A rat model of focal cerebral ischemia-reperfusion (I/R) injury was established by 2 hour-middle cerebral artery occlusion (MCAO) followed with 1, 7 and 14 days of reperfusion. Validation of the model was done by the measurement on cerebral blood flow, infarct volume, histological damage and neurological functions. The rat cerebral cortex proteins from the six animal groups (sham and I/R; 1D, 7D and 14D; 4 rats per group) were analyzed with an approach we termed as "1DE-MS profiling", by combining SDS-PAGE, gel slicing, quantitative LC-MS/MS and profile reconstruction. The samples were separated by gradient SDS-PAGE and each lane of the samples was cut into a set of 35 equal-sized (1.1 mm × 1.1 mm) square pieces. All the gel pieces were analyzed with standardized procedures of in-gel digestion and LC-MS/MS. A total of 5943 proteins (37 keratins included) were detected and the MS-detected abundance data were used to reconstruct the gel distributions in the six groups for all the proteins. This dataset includes 1) all the 840 raw files (6 groups x 4 animals x 35 gel squares/sample), named as "*.raw.zip", 2) the 35 peak files, named as "*-peak list.mgf" and 35 search results, named as "*-search result.zip", from the 35 gel squares for the 24 samples, at the levels of peptide fragments, peptides and proteins, respectively, 3) the one gel pattern with the cutting and square numbering, named as "gel pattern and square numbering.pptx", 4) the one Excel file that contains all the protein-level search results and the processed results for 1DE-MS profile making, named as "Protein-level summary and processing for 1DE-MS profile plotting.xlsx", and 5) the gel distributions (termed 1DE-MS profiles) reconstructed for all the detected proteins, named "1DE-MS profiles of 5943 proteins.zip". We think this data set contains a significant amout of information on the brain proteomic changes at different time points with ischemia-reperfusion injury. The 1DE-MS profiles revealed the changes of proteins caused by different physiological or pathological conditions were not just about the total quantity, but of its structural information-rich profile. Examination of the profiles revealed the formation of the detected protein forms, often termed as "proteoforms" in recent years, involved alternative splicing, proteolytic processing, PTMs such as glycosylation, phosphorylation and ubiquitination, and degradation or fragmentation. We think this dataset would provide useful information for rat brain protein analysis and the method of 1DE-MS profiling would provide an option for proteomic analysis, from the view of proteoforms that concerns protein structures.

Project description:Background Segmental duplications (SDs) are not evenly distributed along chromosomes. The reasons for this biased susceptibility to SD insertion are poorly understood. Accumulation of SDs is associated with increased genomic instability, which can lead to structural variants and genomic disorders such as the Williams-Beuren syndrome. Despite these adverse effects, SDs have become fixed in the human genome. Focusing on chromosome 7, which is particularly rich in interstitial SDs, we have investigated the distribution of SDs in the context of evolution and the three dimensional organisation of the chromosome in order to gain insights into the mutual relationship of SDs and chromatin topology. Results Intrachromosomal SDs preferentially accumulate in those segments of chromosome 7 that are homologous to marmoset chromosome 2. Although this formerly compact segment has been re-distributed to three different sites during primate evolution, we can show by means of public data on long distance chromatin interactions that these three intervals, and consequently the paralogous SDs mapping to them, have retained their spatial proximity in the nucleus. Focusing on SD clusters implicated in the aetiology of the Williams-Beuren syndrome locus we demonstrate by cross-species comparison that these SDs have inserted at the borders of a topological domain and that they flank regions with distinct DNA conformation. Conclusions Our study suggests a link of nuclear architecture and the propagation of SDs across chromosome 7, either by promoting regional SD insertion or by contributing to the establishment of higher order chromatin organisation themselves. The latter could compensate for the high risk of structural rearrangements and thus may have contributed to their evolutionary fixation in the human genome. 2 cell lines-5 samples: 2x DNA fragmentation during apoptosis; 3x ChIP (2x H4K8ac, 1x H3) IMR90: 1x DNA fragmentation during apoptosis; 1x H4K8ac ChIP. Both hybridized on a custom designed 4x 180k oligonucleotide microarray

Dataset Information

Human chorionic villus proteome

Publications

Protocol for Increasing the Sensitivity of MS-Based Protein Detection in Human Chorionic Villi.

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