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ProteomicsComputational prediction combined with proteogenomics unveils widespread non-AUG translation initiation events in plants
Non-AUG translation initiation is crucial for regulating translation, which can generate N-terminally extended protein isoforms with diverse biological functions. However, a comprehensive view of non-AUG translation initiation events with N-terminal extensions (NTEs) across monocots and dicots remai...
ORGANISM(S): Glycine max Zea mays (Maize) Oryza sativa (Rice) 
2026-04-27 | PXD058528 | Pride
Non-aug translation initiation  n-terminally extended protein isoforms  n-terminal extensions (ntes)  upstream translation initiation sites (utiss)  proteogenomics  monocots and dicots 
UnknownCotton pedigree genome reveals restriction of cultivar-driven strategy in cotton breeding.
Not available
S-EPMC10704732 | biostudies-literature
ProteomicsReadthrough Events in Plants Reveal Unprecedented Plasticity of Stop Codons
Stop codon readthrough (SCR) has important biological implications but remains largely uncharacterized. Here, we identify 1,009 SCR events in plants using a proteogenomic strategy. Plant SCR candidates tend to have shorter transcript lengths and fewer exons and splice variants than non-SCR transcrip...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) Glycine max Zea mays (Maize) Oryza sativa (Rice) 
2024-02-02 | PXD035958 | Pride
Proteogenomics Mass spectrometry Stop codon readthrough Recoding plasticity Amino acids Plants 
ProteomicsReadthrough Events in Plants Reveal Unprecedented Plasticity of Stop Codons
Stop codon readthrough (SCR) has important biological implications but remains largely uncharacterized. Here, we identify 1,009 SCR events in plants using a proteogenomic strategy. Plant SCR candidates tend to have shorter transcript lengths and fewer exons and splice variants than non-SCR transcrip...
ORGANISM(S): Glycine max Arabidopsis thaliana (Mouse-ear cress) Zea mays (Maize) Oryza sativa (Rice) 
2024-02-02 | PXD038762 | Pride
Proteogenomics Mass spectrometry Stop codon readthrough Recoding plasticity Amino acids Plants 
ProteomicsDevelopmental dynamics of endogenous peptides in maize
In this study, we present a comprehensive peptidomic atlas of 13 tissues in maize spanning the vegetative and reproductive phases. Using 3-frame translation of canonical coding sequences (CDSs), we identified 6,100 non-redundant endogenous peptides, significantly expanding the known repertoire of pe...
ORGANISM(S): Zea mays (Maize) 
2025-05-07 | PXD055863 | Pride
Peptides Maize Lc-ms/ms 
ProteomicsComparative proteomic analysis of susceptible and resistance maize lines to southern corn rust
Southern corn rust (SCR) is one of destructive diseases in maize caused by Puccinia polysora Undrew. (P. polysara), widely occurring in warm-temperate and tropical regions globally. To identify candidate SCR resistance-related proteins and understand the molecular mechanism underlaying the maize and...
ORGANISM(S): Zea mays (Maize) 
2019-04-18 | PXD008904 | Pride
Southern corn rust Maize Proteomic 
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 
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 
UnknownAn all-in-one plant virus-based vector toolkit for streamlined gene silencing, overexpression, and genome editing.
Not available
S-EPMC12365833 | biostudies-literature
UnknownCotton transposon-related variome reveals roles of transposon-related variations in modern cotton cultivation.
Not available
S-EPMC12126696 | biostudies-literature
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