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ProteomicsDeep Learning Powers Protein Identification from Precursor MS Information
We report the DeepMS1, an approach combining deep learning-based retention time, ion mobility, detectability prediction, and linear regression-based scoring for MS1 feature identification.
ORGANISM(S): Homo Sapiens Escherichia Coli 
PXD046171 |
ProteomicsDeep Learning Powers Protein Identification from MS1 Feature Information
We report the DeepMS1, an approach combining deep learning-based retention time, ion mobility, detectability prediction, and linear regression-based scoring for MS1 feature identification.
ORGANISM(S): Homo Sapiens Escherichia Coli 
2024-02-16 | PXD049457 |
ProteomicsDirect data-independent acquisition proteomics with in silico spectral libraries by deep learning
Data-independent acquisition (DIA) proteomics allows systematic and unbiased measurement of protein samples and enables fast quantitative analysis of large cohorts of samples. However, sample-specific spectral libraries are usually required prior to perform DIA experiments. The libraries are built b...
ORGANISM(S): Homo Sapiens 
2019-12-02 | PXD014108 |
ProteomicsMulti-omic Profiling of Multi-Biosamples Reveals the Role of Amino Acid and Nucleotide Metabolism in Endometrial Cancer
This dataset is part of the multi-omic profiling of endometrial cancer. 12 EC and 11 controls were subjected to untargeted proteomic analysis, using a nano-UHPLC-Orbitrap-MS/MS system in the positive ion mode. A total of 9042 proteins were identified and quantified combining the EC and control group...
ORGANISM(S): Homo Sapiens 
2022-03-28 | PXD030222 |
ProteomicsDeepFLR Facilitates False Localization Rate Control in Phosphoproteomics
Site-specific phosphorylation events affect nearly all the cellular processes and correct phosphosite localization plays an important role in biological or medical health studies. However, direct false localization rate (FLR) control remains challenging in phosphoproteomics. Here, we propose DeepFLR...
ORGANISM(S): Homo Sapiens 
2023-04-04 | PXD037580 |
ProteomicsMetaproteomics characterizes human gut microbiota function in colorectal cancer
Alterations in gut microbiota have been implicated in the pathogenesis of Colorectal Cancer (CRC). Here we collected fecal samples from 14 CRC patients and 14 healthy volunteer cohorts, and characterized their microbiota using label-free quantitative metaproteomics method. We have quantified 30,062 ...
ORGANISM(S): Homo Sapiens 
2020-02-23 | PXD013386 |
ProteomicsHigh-Abundance Protein-Guided Hybrid Spectral Library for Data-Independent Acquisition Metaproteomics
Metaproteomics offers a direct avenue to identify microbial proteins in microbiota, enabling compositional and functional characterization of microbiota. Due to the complexity and heterogeneity of microbial communities, in-depth and accurate metaproteomics faces tremendous limitations. One challenge...
ORGANISM(S): Morganella Morganii Clostridium Butyricum Lactobacillus Acidophilus Enterococcus Faecalis Feces Metagenome Enterobacter Asburiae Pseudomonas Aeruginosa 
PXD043890 |
ProteomicsAccurate Taxonomic Annotation from Metagenomic Data for Deep Metaproteomic Coverage of Microbiota
We developed an accurate taxonomic annotation strategy from metagenomic data for deep metaproteomic coverage, and also compared the performance of the state-of-the-art LC-MS/MS techniques using a simulated microbial community with 12 species. In addition, we also achieved deep proteome coverage of h...
ORGANISM(S): Enterococcus Faecalis Escherichia Coli Atcc 25922 Pseudomonas Aeruginosa Klebsiella Pneumoniae Homo Sapiens Enterococcus Casseliflavus Morganella Morganii Lactobacillus Acidophilus Clostridium Butyricum Citrobacter Freundii Complex Enterobacter Asburiae Klebsiella Aerogenes Bacteroides Fragilis 
PXD034815 |
ProteomicsMSRefine: comprehensive evaluation of the data-dependent LC–MS/MS workflow
There are four datasets in this paper, representing different sample types (plasma and tissue), different sample loading amounts, different chromatographic conditions and different mass spectrometers.
ORGANISM(S): Rattus Rattus Homo Sapiens Saccharomyces Cerevisiae 
PXD035468 |
ProteomicsMetaproteomics characterizes the Prepared Daqu microorganism
we collected Prepared Daqu samples from 6 different production cycles of the Kweichow Moutai Liquor and characterized their microbial community and function by label-free quantitative metaproteomic methods.
ORGANISM(S): Enterococcus Faecalis 
2022-08-03 | PXD035791 |
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