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ProteomicsUSP7 represses lineage differentiation genes in mouse embryonic stem cells by both catalytic and non-catalytic activity
USP7, a ubiquitin-specific peptidase (USP), plays an important role in many cellular processes through its catalytic deubiquitination of various substrates. However, its nuclear function to shape the transcriptional network in mouse embryonic stem cells (mESCs) remains poorly understood. Here, we re...
ORGANISM(S): Mus musculus (Mouse) 
2023-07-20 | PXD039633 | Pride
Pluripotent stem cells  usp7  polycomb  epigenetic regulation 
ProteomicsFilter-aided expansion proteomics
Hydrogel-based tissue expansion combined with mass spectrometry (MS) offers an emerging spatial proteomics approach. Here, we present a filter-aided expansion proteomics (FAXP) strategy for spatial proteomics analysis of archived formalin-fixed paraffin-embedded (FFPE) specimens. Compared to our pre...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2024-10-01 | PXD041412 | Pride
Mass spectrometry Tissue expansion Ffpe Spatial proteomics Data-independent acquisition Colorectal cancer 
ProteomicsMassNet: billion-scale AI-ready mass spectral corpus empowering scalable deep learning in proteomics
Breakthroughs in artificial intelligence (AI) for natural language processing and computer vision have been largely driven by high-quality, large-scale datasets such as OpenWebText and ImageNet. Inspired by this, we present MassNet, a foundational resource for proteomics designed to accelerate deep ...
ORGANISM(S): Danio rerio (Zebrafish) (Brachydanio rerio) Toxoplasma gondii Glycine max Mus musculus (Mouse) Capsicum annuum Acinetobacter baumannii Sus scrofa domesticus (domestic pig) Rhodopseudomonas palustris Homo sapiens (Human) Zea mays (Maize) Streptomyces coelicolor Callithrix jacchus Rattus norvegicus (Rat) Bacillus subtilis Legionella pneumophila Arabidopsis thaliana (Mouse-ear cress) Trypanosoma brucei Staphylococcus epidermidis Gallus gallus (Chicken) Drosophila melanogaster (Fruit fly) Oryza sativa (Rice) Caenorhabditis elegans Bacillus cereus Chlamydomonas reinhardtii Bos taurus (Bovine) Moorella thermoacetica Zymomonas mobilis Oryctolagus cuniculus (Rabbit) Pseudomonas aeruginosa Coffea arabica (Arabian coffee) Canis familiaris (Dog) (Canis lupus familiaris) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) Staphylococcus aureus Equus caballus (Horse) 
2026-10-20 | PXD071590 | Pride
ProteomicsiDIA-QC: AI-empowered Data-Independent Acquisition Mass Spectrometry-based Quality Control
Quality control (QC) in mass spectrometry (MS)-based proteomics is mainly based on data-dependent acquisition (DDA) analysis of standard samples. Here, we collected 2638 files acquired by data independent acquisition (DIA) and paired DDA files from mouse liver digests using 21 mass spectrometers acr...
ORGANISM(S): Mus musculus (Mouse) 
2025-05-06 | PXD051878 | Pride
Quality control  data independent acquisition  machine learning 
ProteomicsHuman thyroid cell line complex CF-DIA-MS
This project aims to explore the protein interaction network of thyroid cancer cell lines through a robotics platform combined with proteomic techniques. The primary method involves using CF-DIA-MS (Co-fractionation Data-Independent Acquisition Mass Spectrometry) to acquire data from three different...
ORGANISM(S): Homo sapiens (Human) 
2025-12-20 | PXD059608 | Pride
Human Thyroid Cell line Cf-dia-ms 
ProteomicsProteomics-derived biomarker panel facilitates distinguishing primary lung adenocarcinomas with intestinal or mucinous differentiation (PAIM) from lung metastatic colorectal cancer (lmCRC)
The diagnosis of primary lung adenocarcinomas with intestinal or mucinous differentiation (PAIM) remains challenging due to the overlapping histomorphological, immunohistochemical and genetic characteristics with lung metastatic colorectal cancer (lmCRC). This study aimed to explore the protein biom...
ORGANISM(S): Homo sapiens (Human) 
2024-06-23 | PXD050416 | Pride
Primary lung adenocarcinomas  intestinal or mucinous differentiation  lung metastatic colorectal cancer  proteomics 
ProteomicsA comprehensive mass spectral library for human thyroid tissues
Thyroid nodules occur in about 60% of the population. Current diagnostic strategies, however, often fail at distinguishing malignant nodules before surgery, thus leading to unnecessary, invasive treatments. As proteins are involved in all physio/pathological processes, a proteome investigation of bi...
ORGANISM(S): Homo sapiens (Human) 
2022-05-20 | PXD026395 | Pride
Dia Spectral library Human thyroid 
ProteomicsA targeted proteomics assay for the preoperative diagnosis of thyroid nodules
The multi-omics model shows high performance in diagnosing thyroid nodules. Especially for indeterminate nodules, while maintaining high specificity, the sensitivity has increased by 10% compared to BRAF V600E mutation.
ORGANISM(S): Homo sapiens (Human) 
2026-01-21 | PXD046014 | Pride
ProteomicsPCP39: prostate cancer proteome for 39 patients by PCT-SWATH
here we processed 105 biopsy-level tissues from 39 prostate cancer patients using pressure cycling technology (PCT) and SWATH-MS
ORGANISM(S): Homo sapiens (Human) 
2018-10-17 | PXD004589 | Pride
Prostate cancer  pct  swath 
Proteomics45 serum samples after CAR-T treatment analysis by proteomic and validate by PRM
45 serum samples from eight B-ALL patients at six time points from pre-, post-CD19-specific CAR-T cell treatment to recovery and profiled by proteomic
ORGANISM(S): Homo Sapiens 
2024-04-07 | PXD051253 |
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