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ProteomicsOpen-pFind Enhances the Identification of Missing Proteins from Human Testis Tissue
In recent years, high-throughput technologies have contributed to development a more precise picture of the human proteome. However, 2,129 proteins remain listed as missing proteins (MPs) in the newest neXtProt release (2019-02). The main reasons for MPs are a low abundance, low-molecular-weight (LM...
ORGANISM(S): Homo sapiens (Human) 
2019-11-04 | PXD015759 | Pride
Testis Open-pfind，efficiency Chromosome-centric human proteome project Missing proteins 
ProteomicsOpen-pFind enables precise, comprehensive and rapid peptide identification in shotgun proteomics, part 1
Shotgun proteomics has grown rapidly in recent decades, but a large fraction of tandem mass spectrometry (MS/MS) data in shotgun proteomics are not successfully identified. We have developed a novel database search algorithm, Open-pFind, to efficiently identify peptides even in an ultra-large search...
ORGANISM(S): Escherichia coli 
2018-07-11 | PXD008782 | Pride
Open-pfind Metabolically label E. coli Yeast 
ProteomicsOpen-pFind enables precise, comprehensive and rapid peptide identification in shotgun proteomics, part 2
Shotgun proteomics has grown rapidly in recent decades, but a large fraction of tandem mass spectrometry (MS/MS) data in shotgun proteomics are not successfully identified. We have developed a novel database search algorithm, Open-pFind, to efficiently identify peptides even in an ultra-large search...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2018-07-11 | PXD008783 | Pride
Open-pfind Yeast Q exactive hf Metabolically label 
ProteomicsA proteomics data analysis protocol using Open-pFind
High-throughput proteomics based on mass spectrometry (MS) analysis has permeated biomedical science and propelled numerous research projects. pFind 3 is a database search engine for high-speed and in-depth proteomics data analysis (Chi et al. 2018). pFind 3 features a swift open search workflow tha...
ORGANISM(S): Homo Sapiens Caenorhabditis Elegans 
2021-01-31 | PXD023901 |
ProteomicsIdentification of missing proteins in the proteome atlas of multiple healthy human tissues
We re-analyzed the deep proteome atlas of 29 paired healthy human from the published paper (Wang, Dongxue, et al. Molecular systems biology 15.2 (2019)) to identify missing proteins.
ORGANISM(S): Homo sapiens (Human) 
2020-11-17 | PXD021391 | Pride
Chpp Open-pfind Missing proteins Mutiple tissues 
UnknownA protocol of using PTMiner for quality control and localization of protein modifications identified by open or closed search of tandem mass spectra.
Not available
S-EPMC10166509 | biostudies-literature
ProteomicsDiscovery and visualization of uncharacterized drug-protein adducts using mass spectrometry
Drugs are often metabolized to reactive intermediates that form protein adducts. Adducts can inhibit protein activity, elicit immune responses, and cause life threatening adverse drug reactions. The masses of reactive metabolites are frequently unknown, rendering traditional mass spectrometry-based ...
ORGANISM(S): Homo sapiens (Human) Rattus norvegicus (Rat) 
2022-02-24 | PXD025019 | Pride
Magnum Raloxifene Dicloxacillin Adduct Plasma Cyp3a4 Open search Metamorpheus Comet Human serum albumin Msfragger Penicillin Moda Hsa Xenobiotic Reactive metabolite P450-reductase Flucloxacillin Open-pfind Comet-ptm Limelight 
ProteomicsReliability of Serum-Derived Connectome Indicators in Identifying Cirrhosis
Patients with cirrhosis are at a relatively high risk of developing complications, such as hepatic decompensation and hepatocellular carcinoma. Identifying cirrhosis in patients is essential in clinical practice because of the need to control disease progression and select different treatment strateg...
ORGANISM(S): Homo sapiens (Human) 
2025-07-23 | PXD055743 | Pride
Connectome strategy  proteomics  open search  post-translational modifications  peptide spectral matches 
UnknownMany kinds of oxidized proteins are present more in the urine of the elderly.
Not available
S-EPMC9214981 | biostudies-literature
ProteomicsLysine acylations of humangut microbiome
In this study we developed an analytical workflow by integrating a serial immunoaffinity enrichment with high resolution mass spectrometry and unrestricted metaproteomic database search strategy, which enables efficient and comprehensive identification and quantification of lysine acetylation, propi...
ORGANISM(S): gut metagenome 
2021-08-26 | PXD022875 | Pride
Microbiome Ptm Lysine acylation Metaproteomics 
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