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Human placental tissue LC-MS/MS

ABSTRACT: This project aimed at missing protein identification from human placental tissue, combining sample preparation and mass spectrometry technology development.For sample preparation, low molecular proteins were enriched by C18 solid phase extraction, SDS-PAGE and MWCO filter. For LC-MS/MS analysis, micro-HPLC fractionation was carried out coupled with LUMOS instrument. Proteome Discoverer 2.2 software was used for data analysis to identify missing proteins.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Placenta

SUBMITTER: yuanliang zhang

LAB HEAD: Siqi Liu

PROVIDER: PXD014083 | Pride | 2019-10-10

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	placenta_C18_1_1-30frac.pep.xml	Pepxml
	placenta_C18_1_1-30frac_semi.pep.xml	Pepxml
	placenta_C18_1_F1.raw	Raw
	placenta_C18_1_F10.raw	Raw
	placenta_C18_1_F11.raw	Raw

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1 - 5 of 75

Publications

Alternative Strategy To Explore Missing Proteins with Low Molecular Weight.

Lin Zhilong Z Zhang Yuanliang Y Pan Huozhen H Hao Piliang P Li Siqi S He Yanbin Y Yang Huanming H Liu Siqi S Ren Yan Y

Journal of proteome research 20191108 12

Identifying more missing proteins (MPs) is an important mission of C-HPP. With the number of identified MPs being attenuated year by year (2,949 to 2,129 MPs from 2016 to 2019), we have realized that the difficulty of exploring the remaining MPs is a challenge in technique. Herein, we propose a comprehensive strategy to effectively enrich, separate, and identify proteins with low molecular weights, aiming at the discovery of MPs. Basically, a protein extract from human placenta was passed throug ...[more]

PMID: 31592669

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Human placental tissue LC-MS/MS

Project description:This project aimed at missing protein identification from human placental tissue, combining sample preparation and mass spectrometry technology development.For sample preparation, low molecular proteins were enriched by C18 solid phase extraction, SDS-PAGE and MWCO filter. For LC-MS/MS analysis, micro-HPLC fractionation was carried out coupled with LUMOS instrument. Proteome Discoverer 2.2 software was used for data analysis to identify missing proteins.

2020-10-29 | MSV000086385 | MassIVE

D283 MED, a cell line derived from peritoneal metastatic medulloblastoma — a good choice for missing protein discovery

Project description:Our goal is the identification of more and more missing proteins from cancer cell lines. This project focuses on D283 med and U-118mg cell lines which contribute to 12 missing protein identification.

2020-11-26 | PXD021482 | Pride

Influence of Different Sample Preparation Approaches on Proteoform Identification by Top-Down Proteomics

Project description:Top-down proteomics (TDP) has made significant advances in the past, and a plethora of sample preparation workflows have been developed. Here, we systematically investigated the influence of different sample preparation steps on proteoform and protein identifications, including cell lysis, reduction and alkylation, proteoform enrichment, purification, and fractionation. We found that all steps in sample preparation influence the subset of proteoforms identified, e.g., their number, confidence, physicochemical properties, and artificially generated modifications. The various sample preparations resulted in complementary identifications, significantly increasing the depth of the analysis. Overall, 15,089 proteoforms from 2,780 protein accessions of human Caco-2 cells were identified, providing the most comprehensive dataset of this cell line up to now. The results from our study can serve as a guideline for designing and adapting TDP sample preparation strategies to particular research questions.

2024-08-08 | PXD049969 | Pride

Secretome Processing for Proteomics: A Methods Comparison

Project description:The cancer cell secretome comprises a treasure-trove for biomarkers since it reflects cross-talk between tumor cells and their surrounding environment. In this study, we evaluated six secretome sample processing workflows coupled to single-shot mass spectrometry: 1. Protein concentration by ultrafiltration with a molecular weight cut-off (MWCO) filter and sample preparation through in-gel digestion (IGD); 2. Acetone protein precipitation coupled to IGD; 3. MWCO filter-based protein concentration followed by to in-solution digestion (ISD); 4. Acetone protein precipitation coupled to ISD; 5. Direct ISD; 6. Secretome lyophilization and ISD. To this end, we assessed workflow triplicates in terms of total number of protein identifications, unique identifications, reproducibility of protein identification and quantification and detectability of small proteins with important functions in cancer biology such as cytokines, chemokines and growth factors.

2024-02-12 | PXD043014 | Pride

Gene Expression Profiling of Chronically Inflamed FFPE Placental Tissue

Project description:The aim of this research was to explore gene expression changes in chronically inflammed placental tissue This study compared FFPE tissue with and without chronic placental inflammation, manifested as overlapping chronic chorioamnionitis, chronic villitis of unknown etiology, and chronic deciduitis. RNA expression profiling was conducted on formalin fixed, paraffin embedded placental tissue using Illumina microarrays. To further explore and validate gene expression findings, we conducted immunohistochemical assessment of protein level expression.

2015-09-01 | E-GEOD-68474 | biostudies-arrayexpress

Regulatory role of multinucleated giant cells derived from placental CD14+ macrophages: Pathophysiological implications

Project description:The role of placental macrophages is largely ignored in the success of pregnancy. We found that CD14+ macrophages purified from at-term placentas spontaneously matured into multinucleated giant cells (MGCs). MGCs lost the expression of CD14 and co-inhibitory molecules, such as Programmed cell Death-Ligands 1 and 2. Although MGCs kept phagocytosis and property to produce ROS, their inflammatory potential measured by TNF/IL-10 imbalance and activation of p38 MAPK and NF-M-NM-:B was blunted without being associated with M2 phenotype. The investigation of gene expression revealed the enrichment with categories related to inflammation, apoptosis and canonical functions of macrophages in MGCs. Whereas most of the genes associated with inflammation and immune responses were down-modulated, those such as VEGFC or associated with matrix remodeling were specifically up-regulated in MGCs. Importantly, we found that patients with preeclampsia or chorioamnionitis, two inflammatory and infectious pathologies, respectively, that affect placentas, were unable to generate MGCs. Taken together, these results suggest that MGCs represent a new way to regulate the inflammatory and cytocidal activity of placental macrophages in a context that imposes contradictory constraints, such as semi-allograft acceptance and defense against aggression. The dysregulation of MGC formation may be associated with placental inflammatory and infectious pathologies. Placental macrophages CD14+ were cultured for 9 days to form multinucleated giant cells (MGC). The transcriptome of MGCs was compared to the transcriptome of placental macrophages (CD14+)

2014-01-07 | E-GEOD-38747 | biostudies-arrayexpress

E12.5 CD9+ Mouse Placental Trophoblast Microarray, Wild-type vs c-Met KO

Project description:The placenta serves as the structural interface for nutrient and waste exchange for proper fetal development. Although defects in placental function result in various placental disorders, molecular mechanisms orchestrating placental development and function are poorly understood. Gene targeting studies have shown that Hgf or c-Met KO embryos exhibit growth retardation and markedly smaller size of the placenta, and die by E14.5. Stem/progenitor cells in various tissues express c-Met and they participate in morphogenesis and tissue repair. Thus, we hypothesized that the HGF/c-Met signaling pathway is essential for the emergence, proliferation, and/or differentiation of putative stem/precursor cells of labyrinth trophoblasts at the midgestation stage. To examine the downstream mechanisms of HGF/c-Met signaling pathway that regulate placental labyrinth development, we performed microarray analysis and compared the transcriptional profiles of wild-type and c-Met g-KO placentas. The highly enriched gene ontology categories among the transcripts that were down-regulated in the mutant placentas were related to cell cycle, transcription, and placenta development. Surprisingly, the most highly enriched GO category among the up-regulated genes was immune response. Furthermore, genes classified as “unsaturated fatty acid metabolic process” were also significantly enriched among the up-regulated genes. This expression data suggested that HGF/c-Met signaling pathway positively regulates progression of cell cycle and transcription of placenta specific genes, and negatively regulates inflammatory reaction and fatty acids synthesis in the trophoblasts, thereby coordinating many critical cellular processes in the placenta. Freshly harvested mouse placental trophoblast was enriched for CD9 from wild -type and c-Met KO placenta with 2 independent biological replicates

2013-12-31 | E-GEOD-38342 | biostudies-arrayexpress

Maternal pre-pregnancy obesity is associated with altered placental transcriptome

Project description:Maternal obesity is becoming a major health consideration for successful pregnancy outcomes. There is growing proof that maternal obesity has a negative influence on placental development and function, thereby adversely influencing offspring programming and health outcomes. However, the molecular mechanisms underlying these processes are so far poorly understood. We set out to analyse term placenta whole transcriptome in obese (n=5) and normoweight women (n=5), using Affymetrix microarray platform compromising of 50,000 probe sets. Our analysis shows that the placental transcriptome differs between normoweight and obese women. Different processes and pathways among placenta from obese women were dysregulated, including inflammation and immune responses, lipid metabolism, cell death and survival and cancer pathways, vasculogenesis and angiogenesis, and glucocorticoid receptor signaling pathway. Together, this global gene expression profiling approach demonstrates and confirms that maternal obesity creates a unique in utero environment that impairs placental transcriptome.

2017-01-07 | E-MTAB-4541 | biostudies-arrayexpress

Placental mRNA Expression data from pregnant smokers and non-smokers

Project description:We used microarrays to determine the transcriptional profiles of placental tissue obtained from women who smoked during pregnancy and from women who did not smoke during pregnancy. Fetal growth restriction is a frequent complication in mothers who smoke cigarettes during pregnancy. To evaluate novel pathways that regulate fetal growth affected by mothers who smoke, we isolated placental mRNA from smoking mothers with severe fetal growth restriction and compared them by microarray analysis to non-smoking mothers with appropriately grown fetuses. Bioinformatics analysis revealed distinct transcriptional patterns in the placentas of smoking mothers when compared to placentas from control non-smoking women. Analyses of the top upregulated and downregulated genes revealed several gene products such as secreted frizzled related protein 1 that was markedly upregulated in the placentas from women who smoked cigarettes during pregnancy. Total RNA was isolated from placental specimens obtained at time of delivery. RNA was hybridized to Affymetrix arrays, and analyzed.

2016-08-08 | E-GEOD-71931 | biostudies-arrayexpress

Optimization of label-free nano LC-MS/MS analysis of the placental proteome

Project description:We optimized a protocol to analyze the placental proteome by means of label-free nano-LC-MS/MS mass spectrometry with regard to sample treatment, protein extraction, and protein digestion, in order to obtain a high protein concentration for identification of a specific protein signature according to the conditions studied.

2020-10-13 | PXD020438 | Pride

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