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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 
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 
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
ProteomicsProteomic and Metabolomic Characterization of COVID-19 Patient Sera MRMHR
Targeted mass spectrometric assays for the 22 proteins in a second test cohort containing 19 COVID-19 patients
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2020-05-30 | MSV000085515 | MassIVE
MetabolomicsGNPS - Proteomic and Metabolomic Characterization of COVID-19 Patient Sera MRMHR
Targeted mass spectrometric assays for the 22 proteins in a second test cohort containing 19 COVID-19 patients
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2020-05-30 | MSV000085515 | GNPS
MetabolomicsGNPS - Proteomic and Metabolomic Characterization of COVID-19 Patient Sera
Early detection and effective treatment of severe COVID-19 patients remain major challenges. Here, we performed proteomic and metabolomic profiling of sera from 46 COVID-19 and 53 control individuals. We then trained a machine learning model using proteomic and metabolomic measurements from a traini...
ORGANISM(S): Severe Acute Respiratory Syndrome Coronavirus 2 (ncbitaxon:2697049) Homo Sapiens (ncbitaxon:9606) 
2020-05-29 | MSV000085507 | GNPS
ProteomicsProteomic and Metabolomic Characterization of COVID-19 Patient Sera
Early detection and effective treatment of severe COVID-19 patients remain major challenges. Here, we performed proteomic and metabolomic profiling of sera from 46 COVID-19 and 53 control individuals. We then trained a machine learning model using proteomic and metabolomic measurements from a traini...
ORGANISM(S): Severe Acute Respiratory Syndrome Coronavirus 2 (ncbitaxon:2697049) Homo Sapiens (ncbitaxon:9606) 
2020-05-29 | MSV000085507 | MassIVE
ProteomicsProtein restriction reprograms the multi-organ proteomic landscape of mouse aging
We conducted an extensive study involving the collection of 41 mouse organs at eight distinct time points spanning the mouse lifespan and implemented a dietary intervention with varying protein intake for different age and sex groups. We also obtained plasma samples from both mice and humans to inve...
ORGANISM(S): Mus musculus (Mouse) 
2026-07-13 | PXD080876 | Pride
Dda files for library generation 
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) 
2025-05-07 | PXD055173 | Pride
Machine learning Dia Quality control Swath Mouse liver Diapasef 
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