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Quantitative analysis of temporal IP and cell lysate using SWATH-MS (2)

ABSTRACT: We treated wildtype and RIP3 knockout L929 with TNF for 8 time points respectively, and used SWATH-MS to quantify dynamic proteomic change of these two cell lines under a serial TNF treatments.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Cell Culture

SUBMITTER: Chuan-Qi Zhong

LAB HEAD: Chuan-Qi Zhong

PROVIDER: PXD002178 | Pride | 2021-01-11

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	ko_rep1_1timepoint.wiff	Wiff
	ko_rep1_1timepoint.wiff.scan	Wiff
	ko_rep1_2timepoint.wiff	Wiff
	ko_rep1_2timepoint.wiff.scan	Wiff
	ko_rep1_3timepoint.wiff	Wiff

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Publications

Group-DIA: analyzing multiple data-independent acquisition mass spectrometry data files.

Li Yuanyue Y Zhong Chuan-Qi CQ Xu Xiaozheng X Cai Shaowei S Wu Xiurong X Zhang Yingying Y Chen Jinan J Shi Jianghong J Lin Shengcai S Han Jiahuai J

Nature methods 20151201 12

PMID: 26436481

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Quantitative analysis of temporal IP and cell lysate using SWATH-MS (1)

Project description:We treated L929 cells with TNF for six time points and the samples containing TNFR1 complexes were collected by affinity purification and analyzed by SWATH-MS. Accurate and consistent quantification across 18 IP samples showed dynamic profiles of the TNFR1 complex components across six time points.

2021-01-11 | PXD002177 | Pride

BXD Mouse Aging Liver Proteomics

Project description:This is a SWATH proteomic survey of ~330 BXD cohorts, including some biological and technical injection replicates, across an aging time course, with individuals from ~6 to ~24 months of age.

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Project description:This dataset consists of 44 raw MS files, comprising 27 DIA (SWATH) and 15 DDA runs on a TripleTOF 5600 and of two raw mass spectrometry files acquired on a Q Exactive. The composition of the dataset is described in the manuscript by Tsou et al., titled: "DIA-Umpire: comprehensive computational framework for data independent acquisition proteomics", Nature Methods, in press Raw files are deposited here in ProteomeXchange and are associated with the DIA-Umpire processed data. All DIA-Umpire processed results for each sample together with DDA results are deposited in separated folders. Also see the "DataSampleID.xlsx" associated with this Readme file. Internal reference from the Gingras lab ProHits implementation: Project 94, Export version VS2 (Tsou_DIA-Umpire)

2015-01-21 | PXD001587 | Pride

Molecular characterization of triple negative breast cancer formaldehyde-fixed paraffin-embedded samples by DIA proteomics

Project description:Triple negative breast cancer (TNBC) accounts for 15-20% of all breast carcinomas and it is clinically characterized by an aggressive phenotype and bad prognosis. TNBC does not benefit from any targeted therapy, so further characterization is needed to define subgroups with potential therapeutic value. In this work, the proteomes of one hundred twenty-five formalin-fixed paraffin-embedded samples from patients diagnosed with triple negative breast cancer were analyzed by mass spectrometry using data-independent acquisition. Hierarchical clustering, probabilistic graphical models and Significance Analysis of Microarrays were used to characterize molecular groups. Additionally, a predictive signature related with relapse was defined. Two molecular groups with differences in several biological processes as glycolysis, translation and immune response, were defined in this cohort, and a prognostic signature based on the abundance of proteins RBM3 and NIPSNAP1 was defined. This predictor split the population into low-risk and high-risk groups. The differential processes identified between the two molecular groups may serve to design new therapeutic strategies in the future and the prognostic signature could be useful to identify a population at high-risk of relapse that could be directed to clinical trials.

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Comparative proteomic analysis reveals the different hepatotoxic mechanisms of human hepatocytes exposed to silver nanoparticles

Project description:Silver nanoparticles (AgNPs), which have been used extensively in consuming products and eventually released into the natural environment, have aroused concerns recently because of their potentially harmful effects on human beings following various routes of exposure. As the liver is one of the largest accumulation and deposition sites of circulatory AgNPs, it is important to evaluate the hepatotoxicity induced by AgNPs. However, the acting mechanisms of AgNPs-induced hepatotoxicity are still elusive to a great extent. Herein, we investigated the hepatotoxic effects of AgNPs using a comparative proteomics approach. First, we evaluated the cytotoxicity of different-sized AgNPs and found that the cancerous liver cells were generally more sensitive than the normal liver cells. Next, proteomics results suggested that HepG2 and L02 cells showed distinct adaptive responses upon AgNPs exposure. HepG2 cells respond to stresses by adapting energy metabolism, upregulating metallothionein expression and increasing the expression of antioxidants, while L02 cells protect themselves by increasing DNA repair and macro-autophagy. Besides, mitochondrial ROS has been identified as one of the causes of AgNPs-induced hepatotoxicity. Collectively, our results revealed that hepatic cancer cells and normal cells cope with AgNPs in notably different pathways, providing new insights into mechanisms underlying AgNPs-induced hepatotoxicity.

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Comprehensive proteome profiling of nuclear and cytoplasmic fractions of rat Sertoli cells.

Project description:The Sertoli cells (Sc) of 5 days (infant) and 12 days (pubertal) old rat were isolated and cultured in triplicates. Nuclear and cytoplasmic fractionation was done for both the cases. All the four protein fractions (nuclear and cytoplasm of infant and pubertal Sc) were anaysed using Lc-MS/MS.

2017-01-18 | PXD003050 | Pride

Quantitative comparison of manuka and clover honey proteomes with royal jelly

Project description:SWATH-MS was used to compare relative protein quantities of bee origin in manuka and clover honey to royal jelly.

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Comparative analysis of mRNA degradation and protein degradation in prostate tissues indicates high stability of proteins

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