scholarly journals Interaction network and mass spectrometry data of Xanthomonas citri subsp. citri surface proteins from differential proteomic analysis of infectious and non-infectious cells

Data in Brief ◽  
2016 ◽  
Vol 8 ◽  
pp. 1400-1411
Author(s):  
Carolina Moretto Carnielli ◽  
Juliana Artier ◽  
Julio Cezar Franco de Oliveira ◽  
Maria Teresa Marques Novo-Mansur
Keyword(s):  
Mass Spectrometry ◽  
Proteomic Analysis ◽  
Interaction Network ◽  
Surface Proteins ◽  
Mass Spectrometry Data ◽  
Xanthomonas Citri

scholarly journals PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data

2016 ◽  
Vol 2016 ◽  
pp. 1-13
Author(s):  
Stefan Kalkhof ◽  
Stefan Schildbach ◽  
Conny Blumert ◽  
Friedemann Horn ◽  
Martin von Bergen ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Isotope Labeling ◽  
Affinity Purification ◽  
Interaction Network ◽  
Mass Spectrometry Data ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
Binding Behavior ◽  
Bona Fide

The functionality of most proteins is regulated by protein-protein interactions. Hence, the comprehensive characterization of the interactome is the next milestone on the path to understand the biochemistry of the cell. A powerful method to detect protein-protein interactions is a combination of coimmunoprecipitation or affinity purification with quantitative mass spectrometry. Nevertheless, both methods tend to precipitate a high number of background proteins due to nonspecific interactions. To address this challenge the software Protein-Protein-Interaction-Optimizer (PIPINO) was developed to perform an automated data analysis, to facilitate the selection of bona fide binding partners, and to compare the dynamic of interaction networks. In this study we investigated the STAT1 interaction network and its activation dependent dynamics. Stable isotope labeling by amino acids in cell culture (SILAC) was applied to analyze the STAT1 interactome after streptavidin pull-down of biotagged STAT1 from human embryonic kidney 293T cells with and without activation. Starting from more than 2,000 captured proteins 30 potential STAT1 interaction partners were extracted. Interestingly, more than 50% of these were already reported or predicted to bind STAT1. Furthermore, 16 proteins were found to affect the binding behavior depending on STAT1 phosphorylation such as STAT3 or the importin subunits alpha 1 and alpha 6.

scholarly journals Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis

2010 ◽  
Vol 28 (1) ◽  
pp. 83-89 ◽  
Author(s):  
Noelle M Griffin ◽  
Jingyi Yu ◽  
Fred Long ◽  
Phil Oh ◽  
Sabrina Shore ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Proteomic Analysis ◽  
Mass Spectrometry Data ◽  
Label Free ◽  
Complex Mass

scholarly journals Mass spectrometry data from proteomic analysis of human skin keratins after exposure to UV radiation

Data in Brief ◽  
2016 ◽  
Vol 7 ◽  
pp. 100-106 ◽  
Author(s):  
Seon Hwa Lee ◽  
Keita Matsushima ◽  
Kohei Miyamoto ◽  
Tomoyuki Oe
Keyword(s):  
Mass Spectrometry ◽  
Human Skin ◽  
Uv Radiation ◽  
Proteomic Analysis ◽  
Mass Spectrometry Data

scholarly journals Targeted Searches for Novel Peptides in Big Mass Spectrometry Data Sets

2017 ◽  
Author(s):  
Yu Gao ◽  
Jiao Ma ◽  
Alan Saghatelian ◽  
John R. Yates
Keyword(s):  
Mass Spectrometry ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Protein Sequences ◽  
Interaction Network ◽  
Database Search ◽  
Mass Spectrometry Data ◽  
Data Sets ◽  
Speed Up ◽  
Guilt By Association

We present Post-Acquisition Targeted Searches (PATS), an easy-to-use tool that allows the identification of novel peptide/protein sequences from existing big mass spectrometry data sets. PATS filters out the unrelated peptidome before the time-consuming database search to significantly speed up the identification. Using interactome data sets, PATS visualizes protein interaction network and helps to assign putative functions to the target protein based on the “guilt by association” concept.

scholarly journals Glutamate receptor δ2 serum antibodies in pediatric opsoclonus myoclonus ataxia syndrome

Neurology ◽  
2018 ◽  
Vol 91 (8) ◽  
pp. e714-e723 ◽  
Author(s):  
Georgina Berridge ◽  
David A. Menassa ◽  
Teresa Moloney ◽  
Patrick J. Waters ◽  
Imogen Welding ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Glutamate Receptor ◽  
Membrane Surface ◽  
Surface Proteins ◽  
Mass Spectrometry Data ◽  
Antigen Discovery ◽  
Rat Pups ◽  
Specific Immunoglobulin ◽  
Cerebellar Tissue ◽  
Ataxia Syndrome

ObjectiveTo identify neuronal surface antibodies in opsoclonus myoclonus ataxia syndrome (OMAS) using contemporary antigen discovery methodology.MethodsOMAS patient serum immunoglobulin G immunohistochemistry using age-equivalent rat cerebellar tissue was followed by immunoprecipitation, gel electrophoresis, and mass spectrometry. Data are available via ProteomeXchange (identifier PXD009578). This generated a list of potential neuronal surface cerebellar autoantigens. Live cell-based assays were used to confirm membrane-surface antigens and adsorb antigen-specific immunoglobulin Gs. The serologic results were compared to the clinical data.ResultsFour of the 6 OMAS sera tested bound rat cerebellar sections. Two of these sera with similar immunoreactivities were used in immunoprecipitation experiments using cerebellum from postnatal rat pups (P18). Mass spectrometry identified 12 cell-surface proteins, of which glutamate receptor δ2 (GluD2), a predominately cerebellar-expressed protein, was found at a 3-fold-higher concentration than the other 11 proteins. Antibodies to GluD2 were identified in 14/16 (87%) OMAS samples, compared with 5/139 (5%) pediatric and 1/38 (2.6%) adult serum controls (p < 0.0001), and in 2/4 sera from patients with neuroblastoma without neurologic features. Adsorption of positive OMAS sera against GluD2-transfected cells substantially reduced but did not eliminate reactivity toward cerebellar sections.ConclusionAutoantibodies to GluD2 are common in patients with OMAS, bind to surface determinants, and are potentially pathogenic.

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