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

ABSTRACT: 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.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Cell Culture

SUBMITTER: Chuan-Qi Zhong

LAB HEAD: Chuan-Qi Zhong

PROVIDER: PXD002177 | Pride | 2021-01-11

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	flag-tnf_rep1_1timepoint_SWATH.wiff	Wiff
	flag-tnf_rep1_1timepoint_SWATH.wiff.scan	Wiff
	flag-tnf_rep1_2timepoint_SWATH.wiff	Wiff
	flag-tnf_rep1_2timepoint_SWATH.wiff.scan	Wiff
	flag-tnf_rep1_3timepoint_SWATH.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 (2)

Project description: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.

2021-01-11 | PXD002178 | Pride

DIA-Umpire: comprehensive computational framework for data independent acquisition proteomics

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

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.

2021-11-03 | PXD009160 | Pride

Mycobacterial strain-specific temporal modulations of newly synthesized macrophage secretome

Project description:THP-1 macrophages were infected with four strains of Mycobacterium tuberculosis to study the temporal dynamics of newly synthesized proteins in the secretome. Temporal snapshots of secretome reflect the macrophage response to pathogenicity which in combination with intracellular events, completes the disease picture. However, such studies are compromised by limitations of quantitative proteomics. Metabolic labeling by SILAC allows a 3-plex experiment while isobaric chemical labeling by iTRAQ/TMT allows up to 8 to 10-plex respectively. This makes studying temporal proteome dynamics an intangible and elusive proposition. We have developed a new variant of hyperplexing method, combining triplex SILAC with 6-plex iTRAQ to achieve 18-plex quantitation in a single MS run. THP-1 macrophages were infected with H37Ra, H37Rv, BND433 and JAL2287 and the newly synthesized secreted host proteins were studied over six temporal frame still 30 hours post infection, at a difference of 4 hours each. For quantitation, the strains were encoded with two sets of triple SILAC- H37Ra & H37Rv in one and BND433 & JAL2287 in another with a control in each. These sets were then iTRAQ labeled to encode for temporal profiles across six time points in 6-plex iTRAQ. Effectively a 36-plex design with 4 replicates of each set, these experiments were completed within few days on the mass spectrometer. Using MaxQuant and in house developed tools and pipelines, we have analysed the data to map the temporal and strain specific dynamics of newly synthesized proteins in host. Hyperplexing enables large scale spatio-temporal systems biology studies where large number of samples can be processed simultaneously and in quantitative manner.

2016-08-10 | PXD004281 | Pride

Windows Scanning Multiomics: Integrated Metabolomics and Proteomics (Proteomics Section)

Project description:To gain comprehensive and accurate system biological information, we developed a multiomics analytical method that integrated metabolomics and proteomics, named Windows Scanning Multiomics (WSM).

2023-12-18 | PXD046554 | Pride

Windows Scanning Multiomics: Integrated Metabolomics and Proteomics (Metabolomics Section)

2023-12-18 | PXD046533 | Pride

Cathepsin B and Cathepsin Z tumor secretome of murine breast cancers

Project description:MS-based proteomics study of the cancer secretome and tumor interstitial fluid of tumor cell/macrophage co-cultures and breast tumors in cells and mice lacking both cathepsin B and cathepsin Z

2021-09-08 | PXD015209 | Pride

Thermal proteome profiling of Arabidopsis thaliana

Project description:Six biological replicates of Arabidopsis thaliana were subjected to protein extraction, ten-temperature gradient precipitation, TMT labeling, off-line alkaline fractionation, and LC-MS/MS. The resulting data was used downstream for untargeted modeling of protein unfolding and melting temperature estimation.

2018-11-23 | PXD011200 | Pride

Recombinant shewasin D and shewasin A specificity preferences profiled by proteomic identification of protease cleavage sites (PICS)

Project description:We determined the specificity preferences of both recombinant shewasin D and shewasin A (pepsin-like aspartic proteases from S. denitrificans and S. amazonensis, respectively) using proteome-derived peptide libraries and observed remarkable similarities between both shewasins and eukaryotic pepsins, in particular with BACE-1 thereby confirming their phylogenetic proximity. We further observed subtle differences in sequence preferences at several positions, suggesting variations in their subsite binding pockets.

2016-04-05 | PXD003078 | Pride

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

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