Browse
Submit Data
Databases
API
Help

Dataset Information

293 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Phosphorylation of OSBL8 protein in interphase vs mitotic human cells

ABSTRACT: Phosphorylation of OSBL8 human protein was compared in interphase vs mitotic Hela cells with a new software developed in-house, Msviz, a graphical software tool developed for in-depth manual validation and quantitation of post-translational modifications.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

SUBMITTER: Patrice Waridel

LAB HEAD: Manfredo Quadroni

PROVIDER: PXD006254 | Pride | 2017-07-03

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

MsViz: A Graphical Software Tool for In-Depth Manual Validation and Quantitation of Post-translational Modifications.

Martín-Campos Trinidad T Mylonas Roman R Masselot Alexandre A Waridel Patrice P Petricevic Tanja T Xenarios Ioannis I Quadroni Manfredo M

Journal of proteome research 20170706 8

Mass spectrometry (MS) has become the tool of choice for the large scale identification and quantitation of proteins and their post-translational modifications (PTMs). This development has been enabled by powerful software packages for the automated analysis of MS data. While data on PTMs of thousands of proteins can nowadays be readily obtained, fully deciphering the complexity and combinatorics of modification patterns even on a single protein often remains challenging. Moreover, functional in ...[more]

PMID: 28636386

Similar Datasets

MStern Blot vs. FASP - Different sample types

Project description:Three different sample types (HeLa lysate, human CSF and human Urine) that were prepared with MStern Blot and FASP. For each sample type there are four replicates.

2015-07-30 | PXD002572 | Pride

Data in support of Identification of potential autoantigens in anti-CCP-positive and anti-CCP-negative rheumatoid arthritis

Project description:The presence or absence of autoantibodies against citrullinated proteins (ACPAs) distinguishes two main groups of rheumatoid arthritis (RA) patients with different etiology, prognosis, disease severity, and, presumably, disease pathogenesis. The heterogeneous responses of RA patients to various biologics, even among ACPA-positive patients, emphasize the need for further stratification of the patients. We use high-density protein array technology to evaluate ACPA reactivity. Identification of the proteome recognized by ACPAs may be a step to stratify RA patients according to immune reactivity. Methods: Pooled plasma samples from 10 anti-CCP negative and 15 anti-CCP positive RA patients were assessed for ACPA-content using a modified protein microarray containing 1,631 different natively folded proteins citrullinated in situ by protein arginine deiminases (PAD) 2 and PAD4. Results: IgG antibodies from anti-CCP positive RA plasma showed high-intensity binding to 87 proteins citrullinated by PAD2 and 99 proteins citrullinated by PAD4 without binding significantly to the corresponding native proteins. Curiously, the binding of IgG antibodies in anti-CCP-negative plasma was also enhanced by PAD2- and PAD4-mediated citrullination for 29 and 26 proteins, respectively. For only 4 proteins, significantly more ACPA-binding occurred after citrullination with PAD2 compared to citrullination with PAD4, while the opposite was true for 1 protein.

2022-01-05 | PXD024955 | Pride

Spectral Library Search for Improved TMTpro Labelled Peptide Assignment in Human Plasma Proteomics

Project description:Clinical biomarker discovery is often based on the analysis of human plasma samples. However, the high dynamic range and complexity of plasma pose significant challenges to mass spectrometry-based proteomics. Current methods for improving protein identifications require laborious pre-analytical sample preparation. In this study, we developed and evaluated a TMTpro-specific spectral library for improved protein identification in human plasma proteomics. The library was constructed by LC-MS/MS analysis of highly fractionated TMTpro-tagged human plasma, human cell lysates, and relevant arterial tissues. The library was curated using several quality filters to ensure reliable peptide identifications. Our results show that spectral library searching using the TMTpro spectral library improves the identification of proteins in plasma samples compared to conventional sequence database searching.

2023-10-24 | PXD042546 | Pride

Proteogenomics reanalysis of human testis data

Project description:Reanalysis of the human testis tissue dataset acquired for the Chromosome-centric Human Proteome Project (C-HPP; PRIDE project PXD002179), with a focus on identifying novel peptides for genome annotation.

2016-11-28 | PXD004785 | Pride

Proteogenomics of Venturia pirina

Project description:This dataset relates to a proteogenomic analysis for Venturia pirina, a fungus that causes scab disease on European pear (Pyrus communis). V. pirina is host specific and infection is thought to be mediated by small, secreted effector proteins. To focus on these effectors we analysed extracts from V. pirina grown in vitro, on cellophane sheets, that mimics the growth habit in infected leaves. LC-MS/MS data was queried against a protein database generated by combining in-silico predicted transcripts with six-frame translations of a whole genome sequence for V. pirina.

2014-07-02 | PXD000710 | Pride

Large collection of HeLa LFQ quality control and maintenance runs

Project description:Collection of HeLa maintenance and quality control runs for several years. The dataset was acquired to be used for exploration of deep learning models, initially in the scope of imputation. The repository for this archiv contains hints on how to use the three curated datasets and the single runs as filtered data. It provides links to the files on PRIDE.https://github.com/RasmussenLab/hela_qc_mnt_data The current pre-print of the data descriptor can be found here:https://doi.org/10.21203/rs.3.rs-3083547/v2

2023-12-12 | PXD042233 | Pride

Exposure of cells to glyphosate and formulations including glyphosate

Project description:MUTZ-3-derived cells were exposed to different substances for 24h and sampled for proteome analysis.

2020-03-10 | PXD016859 | Pride

Secretome of Solanum tuberosum grown in the presence of proalexin

Project description:Secretome of Desiree potato grown in the presence of phosphite (proalexin).

2014-11-20 | PXD001031 | Pride

Ave1 Homologs in Venturia pirina and Venturia inequalis

Project description:This dataset relates to a proteomic analysis of Ave1 homologs in the fungal pathogens Venturia pirina and Venturia inequalis. These species are the cause of scab disease on European pear (Pyrus communis) and apple (Malus pumila). Sample preparation for both V. pirina and V. inequalis was designed to focus on effectors and eliminate host proteins. To do this the fungi were grown in vitro, on cellophane sheets mimicing the growth habit in infected leaves and proteins were extracted using a gentle washing procedure designed to avoid cell wall breakage. LC-MS/MS data was queried against a protein database generated from gene predictions obtained from whole genome sequences of V. pirina and V. inequalis.

2022-03-02 | PXD005614 | Pride

IDENTIFICATION OF THE CANIDAE IRON REGULATORY HORMONE HEPCIDIN

Project description:Quantification and characterisation of canine hepcidin by LC-MS

2020-05-26 | PXD015661 | Pride