Quantitative comparative proteomic analysis of ITGB1-knockdown and ITGB1-vector control cells in K562/S
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Cell Suspension Culture
SUBMITTER: 
Neha Agrawal
LAB HEAD: Dr. Rukmini Govekar
PROVIDER: PXD057116 | Pride | 2025-10-30
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ITGB1-KD_set1_IDA-KD1_IDA.mzML | Mzml | |||
| ITGB1-KD_set1_IDA.group | Other | |||
| ITGB1-KD_set1_IDA.mgf | Mgf | |||
| ITGB1-KD_set1_IDA.mzML | Mzml | |||
| ITGB1-KD_set1_IDA.wiff | Wiff |
Items per page: 5 1 - 5 of 122 |
Similar Datasets
Project description:The global phosphoproteome analysis by liquid chromatography-mass spectrometry (LC-MS) has emerged as an important tool to study cell signalling. However, the coverage of phosphoproteome by LC-MS is limited despite various approaches for phosphoprotein enrichment. Studies in literature have exploited the complementary chemistries of affinity materials like metal (immobilized metal ion affinity chromatography- IMAC) and metal oxides (metal oxide affinity chromatography- MOAC) independently and in a sequential elution approach to improve coverage of phosphoproteins. We demonstrate that further improvement in the enrichment of phosphoproteins can be achieved by using these metals and metal oxides independently and pooling the data.
2025-10-30 | PXD057032 | Pride
Project description:The global phosphoproteome analysis by liquid chromatography-mass spectrometry (LC-MS) has emerged as an important tool to study cell signalling. However, the coverage of phosphoproteome by LC-MS is limited despite various approaches for phosphoprotein enrichment. Studies in literature have exploited the complementary chemistries of affinity materials like metal (immobilized metal ion affinity chromatography- IMAC) and metal oxides (metal oxide affinity chromatography- MOAC) independently and in a sequential elution approach to improve coverage of phosphoproteins. We demonstrate that further improvement in the enrichment of phosphoproteins can be achieved by using these metals and metal oxides independently and pooling the data.
2025-05-06 | PXD050933 | Pride
Project description:Immunoprecipitation of ITGB1 and YWHAE was done to understand its interactive partners in K562/S cells. Mass spectrometry was performed to identify interactive molecules. Non-specific proteins (contaminants) such as keratins were excluded from the final analysis based on the results of the negative control IgG
2025-10-30 | PXD056828 | Pride
Project description:In this study, we assessed the effects of lysyl oxidase (LOX/LOXL) inhibition on the composition of extracellular matrix (ECM) produced by in vitro expanded bone marrow derived mesenchymal stromal cells (MSCs) of n=3 patients with myelodysplastic syndromes (MDS) and myeloproliferative neoplasms (MPN).
2023-02-17 | PXD031217 | Pride
Project description:Plant-cyanobacteria symbiosis is considered one of the pivotal events in the history of life. In this symbiosis, the cyanobacterium provides to the plant fixed nitrogen compounds and plant hormones and, in return, the plant provides to the cyanobacterium fixed carbon. Despite the large knowledge in the physiology and ecology of plant-cyanobacteria symbioses, little is known about the molecular mechanisms involved in the crosstalk between partners. It has been shown recently that Nostoc punctiforme is able to stablish an endophytic symbiosis with Oryza sativa. This finding opens a door to explore this symbiotic interaction as a sustainable alternative to nitrogen fertilization of paddy fields. However, molecular mechanisms behind Oryza-Nostoc endosymbiosis are still not clarified. To gain further insights, an LC-MS/MS based label-free quantitative technique was used to evaluate the differential proteomics under N. punctiforme treatment vs. control plants at 1 day and 7 days. Differential expression profiling reveals a significant number of proteins to be down-regulated or missing in both partners, while others were more abundant or only expressed when both partners were in contact. In N. punctiforme, the differential protein expression was primarily connected to primary metabolism, signal transduction and perception, transport of substances and photosynthesis. In O. sativa, the differential protein expression was connected to a wide range of biological functions regulating carbon and nitrogen metabolism and response to biotic and abiotic stresses.
2023-03-10 | PXD022229 | Pride
Project description:Zinc can be limiting in many environments and bacteria have developed acclimation responses to counteract this deficiency. In most bacteria, the acclimation response to zinc limitation is controlled by Zur, a transcriptional regulator of the FUR family. Several proteins that take part in this response are present in the cytoplasm and the cell envelope. However, little is known about the involvement of proteins present in the extracellular space in the response to Zn limitation and whether the protein composition of this space might be also regulated by Zur. Therefore, in order to get an insight into these issues, a comparative analysis of the exoproteomes of the cyanobacterium Anabaena sp. PCC7120 (WT) and its Δzur derivative strain (referred as "MN" in the present dataset) was carried out using SWATH-MS analysis.
2024-02-15 | PXD036795 | Pride
Project description:Mass Spectrometry (MS)-based proteomic measurements are uniquely poised to impact the development of cell and gene therapies. With the adoption of rigorous instrumental performance controls (PQs), large-scale proteomics can move from a research to a manufacturing control tool. Especially suited, data-independent acquisition (DIA) approaches have distinctive qualities to extend multi-attribute method (MAM) principles to characterize the proteome of cell therapies. Here we describe the development of a DIA method for the sensitive identification and quantification of proteins on a Q-TOF instrument. Using the improved acquisition parameters, we defined some control metrics to improve the reproducibility of SWATH acquisition-based proteomic measurements. Finally, we applied the method to analyze the proteome of Jurkat cells that here serves as a model for human T-cells.
2022-04-11 | PXD029780 | Pride
Project description:The use of data-independent acquisition methods such as SWATH for mass spectrometry based proteomics is usually performed using peptide MS/MS reference ion assay libraries which enable identification and quantitation of peptide peak areas. Reference assay libraries can be generated locally through information dependent acquisition, or obtained from shared data repositories for commonly studied organisms. However, there have been no studies performed to systematically evaluate how locally-generated or repository-based assay libraries affect SWATH performance for proteomic studies. To undertake this analysis we developed a software workflow, SwathXtend, which generates extended peptide assay libraries using a local seed library and delivers statistical analysis of SWATH-based sample comparisons. We designed test samples using peptides from a yeast extract spiked into peptides from human K562 cell lysates at different ratios to simulate common protein abundance change comparisons. SWATH-MS data with 2, 5 and 10% of yeast peptides spiked into the human cell lysate were assessed using several local and repository-based assay libraries of different complexities and proteome compositions. We evaluated detection specificity and accuracy to detect differentially abundant proteins and reporting thresholds for statistical analyses. We demonstrate that extended assay libraries integrated with local seed libraries achieve better performance than local limited assay libraries alone from the aspects of the number of peptides and proteins identified and the specificity to detect differentially abundant proteins; the performance of extended assay libraries heavily depend on the similarity of the seed and add-on libraries; statistical analysis with multiple testing correction can improve the statistical rigor needed when using large, extended assay libraries.
2016-05-12 | PXD002836 | Pride
Project description:Several proteomics studies have been performed in the past in order to define the mammalian peroxisomal proteome. During the last decade, it has as well become evident, that a significant number of proteins is shared between several subcellular compartments and that specialized proteins subsets are constituents of membrane contact zones, which bridge two adjacent organelle to allow metabolite exchange. In this respect, a number of proteins, which have been considered as mere contaminants in previous studies, might be indeed proteins, which are to a minor extent indeed truly associated with peroxisomes. Ongoing technical improvements in mass spectrometry (MS) allow to identify and to quantify the enrichment of such less abundant proteins in individual fractions. Accordingly, this study reassessed the proteome of mouse liver peroxisomes by parallel isolation of peroxisomes from a mitochondria- and a microsome-enriched pre-fraction combining density gradient centrifugation with a SWATH-MS quantitative proteomics approach to unveil novel peroxisomal or peroxisome-associated proteins. In total, 1071 proteins from the MS-samples were identified in amounts, which allowed their quantification in order to assess their enrichment in either high density peroxisomal or low-density gradient fractions, containing the bulk of organelle material. Combining the data from isolations from the mitochondria- and microsome-enriched prefractions allowed to identify specific protein clusters characteristic for mitochondria, the ER and peroxisomes. Among the proteins, which were significantly enriched in the peroxisomal cluster, were several proteins, which were not previously associated with the organelles implying that they are novel peroxisomal candidates. In order to validate the organelle proteomics strategy, five of the candidates were selected for further colocalization studies. The peroxismal import of two candidates, HTATIP2 and PAFAH2, which contain potential peroxisome targeting sequences 1, could be confirmed by overexpression in HepG2 cells. Two other candidates, SAR1B and PDCD6, which are known from ER exit sites, did not directly colocalize with peroxisomes but were found to reside at ER sites which often surrounded peroxisomes. Hence, both proteins might concentrate at peroxisome-ER membrane contact sites, which might be co-purified with peroxisomes. Intriguingly, the last candidate, OCIA domain-containing protein 1, was previously described to decrease mitochondrial branching and network formation. In this work, we not only validate its secondary peroxisomal localization but also observed a reduction in peroxisome numbers in response OCIAD1 expression. Hence, OCIAD1 appears to be a novel protein, which has an impact on both mitochondrial and peroxisomal maintenance.
2024-06-22 | PXD047931 | Pride
Project description:In blood banks, platelets are stored until 7 days after a pathogen reduction technology (PRT) treatment, Mirasol® (vitamin B2 plus UVB light) in the present case. The storage time under these conditions may have an impact on platelets and their releasate leading to potential adverse reactions following transfusion to patients. The aim of this study was to analyze the proteome of extracellular vesicles generated by platelets at different storage days (2 and 7) to gain deeper information on the platelet concentrates state at those moments. EVs were isolated by a centrifugation-based approach and characterized by dynamic light scattering and transmission electron microscopy. Proteomic analysis was by LC-MS/MS and quantification by SWATH. In this way, 151 proteins were found up-regulated at day 7 of storage. This group includes CCL5 and Platelet factor 4, chemokines with power to attract neutrophils and monocytes, which could generate transfusion adverse reactions. In addition, other glycoproteins and platelet activation markers were also found elevated at day 7. Proteins related to glycolysis and lactate production were found altered with high fold changes, showing a deregulation of platelet metabolism at day 7. The obtained results provide novel information about possible effects of platelet-derived EVs on transfusion adverse reactions.
2022-09-30 | PXD014694 | Pride