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ProteomicsAn optimized SP3 sample processing workflow for in-depth phos-phoproteomics and improved identification of multiply phosphory-lated peptides
Protein phosphorylation is a critical and ubiquitous post-translational modification (PTM) found across the kingdoms of life. Advances in high-throughput mass spectrometry have transformed our ability to interrogate the phosphoproteome. However, sample prepara-tion methodologies optimized for phosp...
ORGANISM(S): Homo sapiens (Human) 
2025-08-25 | PXD061013 | Pride
Phosphorylation  multiply phosphorylated  mass spectrometry  ptm  sp3  tio2  c18. 
UnknownAn Optimized SP3 Sample Processing Workflow for In-Depth and Reproducible Phosphoproteomics.
Not available
S-EPMC12322947 | biostudies-literature
TranscriptomicsExpression data from CD4 single positive thymocyte subsets from C57BL/6 mice of 6-8 wks of age
After positive selection in the thymus, the newly generated single positive (SP) thymocytes are phenotypically and functionally immature and undergo apoptosis upon antigen stimulation. In the thymic medullary microenvironment, SP cells progressively acquire immunocompetence. Negative selection to r...
ORGANISM(S): Mus musculus 
2012-02-13 | E-GEOD-30083 | biostudies-arrayexpress
ProteomicsDifferences in Protein Capture by SP3 and SP4 Demonstrate Mechanistic Insights of Proteomics Clean-up Techniques.
The goal of proteomics experiments is to identify proteins to observe changes in cellular processes and diseases. One challenge in proteomics is the removal of contaminants following protein extraction, which can limit protein identifications. Single-pot, solid-phase-enhanced sample preparation (SP3...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2024-02-20 | MSV000094130 | MassIVE
ProteomicsNanomaterials trigger functional responses in primary human immune cells
Targeting the immune system with nanoparticles (NPs) to deliver immunomodulatory molecules emerged as a solution to address intra-tumoral immunosuppression and enhance therapeutic response. While the potential of nanoimmunotherapies in reactivating immune cells has been evaluated in several preclini...
ORGANISM(S): Homo sapiens (Human) 
2025-10-27 | PXD056695 | Pride
Nanomaterials  human lymphocytes  nlc-ms/ms  sp3-spe  differential analysis 
ProteomicsProteomics Data of "Integrated Clinical Trial and Molecular Profiling Reveals Immune Drivers of Chronic Hand Eczema" Study
Background: Chronic hand eczema (CHE) is a debilitating skin condition characterized by pain, itch, and chronic inflammation, with a complex multifactorial origin. Its diverse presentations, including overlapping traits of atopic dermatitis, contact dermatitis, and psoriasis, make diagnosis and trea...
ORGANISM(S): Homo sapiens (Human) 
2026-02-26 | PXD059218 | Pride
ProteomicsFlash proteotyping of microbial isolates by tandem mass spectrometry
Flash proteotyping is a methodology for ultra-fast identification of microorganisns by tandem mass spectrometry. Here, we obtained results on five reference strains and ten new bacterial isolates. The methodology is based on direct sample infusion into the mass spectromete and an original, highly se...
ORGANISM(S): Kocuria rhizophila Microvirga ossetica Staphylococcus warneri Staphylococcus equorum Pseudomonas putida KT2440 Klebsiella aerogenes KCTC 2190 Pseudomonas psychrotolerans Roseomonas mucosa Ruegeria pomeroyi DSS-3 Deinococcus proteolyticus MRP Micrococcus luteus (Micrococcus lysodeikticus) Paenibacillus catalpae Pseudomonas zeshuii 
2023-12-21 | PXD045510 | Pride
Taxonomy Proteomics Isolates Proteotyping Bacteria Identification 
ProteomicsA de novo mutation in /ITPR3/ causes combined immunodeficiency
This study reports two unrelated patients with a combined immunodeficiency. Whole-exome sequencing of both patients, their healthy parents and siblings identified in both families a /de novo/ missense variant in /ITPR3/ (NM_002224.3:c.7570C>T, p.Arg2524Cys). While the mRNA level in patients remained...
ORGANISM(S): Homo sapiens (Human) 
2024-06-18 | PXD038284 | Pride
Shotgun proteomics Rnaseq Itpr3 mutation Immunophenotying 
ProteomicsMultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes
Background: The multiome is an integrated assembly of distinct classes of molecules and molecular properties, or “omes,” measured in the same biospecimen. Freezing and formalin-fixed paraffin-embedding (FFPE) are two common ways to store tissues, and these practices have generated vast biospecimen r...
ORGANISM(S): Mus musculus (Mouse) 
2025-02-14 | PXD041462 | Pride
Matrix-chip Matrix-merip Matrix-rt Multiomicstracks96 Pixul Matrix-medip Segway Cryogrid Lc-ms/ms 
ProteomicsAdrenergic Signaling and Proteomic Responses in Breast Cancer Spheroids: Implications for Tumor Microenvironment and Therapeutic Strategies
Breast cancer, a global health challenge, exhibits molecular heterogeneity and complex interactions with the tumor microenvironment. We investigated adrenergic modulation in breast cancer spheroids, differentiating between basal-like (MDA-MB-231 and BT549) and luminal-like (T47D and MCF-7) subtypes....
ORGANISM(S): Homo sapiens (Human) 
2025-10-13 | PXD046841 | Pride
Breast cancer Proteomics Propranolol Noradrenalin Cancer Adrenergic signaling 
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