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ProteomicsLarge-scale discovery of non-canonical peptides in monocot and dicot plants through an integrated peptidogenomic pipelineLarge-scale discovery of non-canonical peptides in monocot and dicot plants through an integrated peptidogenomic pipeline
Non-canonical peptides (NCPs) have been shown to play critical roles in fundamental biological processes. Despite their importance, NCPs have been rarely identified and characterized in plants. Here we developed an integrated peptidogenomic pipeline using high-throughput mass spectra to probe custom...
ORGANISM(S): Zea mays (Maize) 
2020-08-11 | PXD017081 | Pride
Plants Six-frame translation Mass spectrometry Peptidogenomics Non-canonical peptides 
ProteomicsA Temporal Proteomic Map of Epstein-Barr Virus Lytic Replication in B-cells
Epstein Barr virus (EBV) replication contributes to multiple human diseases, including infectious mononucleosis, nasopharyngeal carcinoma, B-cell lymphomas, and oral hairy leukoplakia. We performed systematic quantitative analyses of temporal changes in host and EBV proteins during lytic replication...
ORGANISM(S): Homo sapiens (Human) 
2017-05-19 | PXD006317 | Pride
B-cell receptor Immune evasion Herpesvirus Complement Viral evasion Epstein-barr virus Lytic replication Host-pathogen interaction Quantitative proteomics Tandem mass tag 
ProteomicsEpstein-Barr Virus Induced One-Carbon Metabolism Drives B-Cell Transformation
Epstein-Barr virus (EBV) causes Burkitt, Hodgkin, and post-transplant B-cell lymphomas. How EBV remodels metabolic pathways to support rapid B-cell outgrowth remains largely unknown. To gain insights, primary human B-cells were profiled by tandem-mass-tag based proteomics at rest and at 9 time point...
ORGANISM(S): Homo sapiens (Human) Epstein-barr virus strain p3hr-1 
2019-06-28 | PXD013034 | Pride
Herpesvirus One-carbon metabolism Epstein-barr virus Host-pathogen interaction Quantitative proteomics Tandem mass tag 
ProteomicsTranslation of bi-directional transcripts generates peptides for the MHC-I pathway.
Antisense transcripts play an important role in generating regulatory non-coding RNAs but if these transcripts are also translated and for what purpose is yet poorly understood. Isolation of polysome fractions followed by RNA sequencing and mass spectrometry analysis of a six frame data-base reveale...
ORGANISM(S): Homo sapiens (Human) 
2025-05-07 | PXD057573 | Pride
Human Mass spectrometry Polysomes Mhc-i pathway 
ProteomicsN-terminomics Proteogenomics - N-terminal proteomics assisted profiling of the unexplored translation initiation landscape in Arabidopsis thaliana
Proteogenomics is a research field where proteome data is used to improve gene annotation. To achieve this, customized protein databases are constructed to match proteomic data. We perform a proteogenomic analysis using N-terminal COFRADIC data in order to identify novel translational initiation sta...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2017-04-24 | PXD004896 | Pride
Arabidopsis thaliana Proteogenomics N-terminal cofradic Ribosome profiling Positional proteomics Ribo-seq 
ProteomicsSmall Proteome of Haloferax volcanii - Proteogenomic database search strategy
The small proteome has already been well explored in eukaryal and bacterial species, but so far, archaeal genomes have not yet been analysed broadly with a dedicated focus on small proteins. Here, we present a combinatorial approach, integrating experimental information from small protein-optimized ...
ORGANISM(S): Haloferax volcanii (Halobacterium volcanii) 
2023-02-01 | PXD031691 | Pride
Sep Archaea Sprotein Proteogenomics Database search Sorf Small protein enrichment Top-down Ribosome profiling Haloferax volcanii Small protein Proteolytic digest 
ProteomicsLarge-scale discovery of non-canonical peptides in monocot and dicot plants through an integrated peptidogenomic pipeline
Non-canonical peptides (NCPs) have been shown to play critical roles in fundamental biological processes. Despite their importance, NCPs have been rarely identified and characterized in plants. Here we developed an integrated peptidogenomic pipeline using high-throughput mass spectra to probe custom...
ORGANISM(S): Zea mays (Maize) 
2020-08-11 | PXD017080 | Pride
Plant peptide lc-ms/ms 
UnknownTranslation of bi-directional transcripts enhances MHC-I peptide diversity.
Not available
S-EPMC11956742 | biostudies-literature
ProteomicsJUMPg: an Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells
Proteogenomics is an emerging approach to improve gene annotation and interpretation of proteomics data. Here we present JUMPg, an integrative proteogenomics pipeline including customized database construction, tag-based database search, peptide-spectrum match filtering, and data visualization. JUMP...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-16 | MSV000080641 | MassIVE
ProteomicsThe generation of cancer-specific ribosomes by the lncRNA LISR suppresses melanoma anti-tumour immunity
Gains of chromosome 12p11.21, encoding for the cancer-specific lncRNA LISR, correlate with poor survival in the PanCancer Atlas. In melanoma, LISR is highly expressed by patients resistant to immunotherapy and it contributes to the generation of drug-tolerant persister cells by activating an immune...
ORGANISM(S): Homo sapiens (Human) 
2025-09-17 | PXD046528 | Pride
Ribosomes Long non coding rna 
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