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ProteomicsMorpheus Spectral Counter - Morpheus spectral counter: a computational tool for label-free quantitative mass spectrometry using the morpheus search engine
Label-free quantitative mass spectrometry (MS) based on the Normalized Spectral Abundance Factor (NSAF) has emerged as a simple and reasonably robust method to determine the relative abundance of individual proteins within complex mixtures. Here, we describe Morpheus Spectral Counter (MSpC) as the ...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2016-02-24 | PXD003002 | Pride
Proteomics Morpheus Software Bioinformatics Spectral count Label-free quantification Lc-ms/ms 
ProteomicsSTREAMLINE PROTOCOL FOR ARABIDOPSIS APOPLASTIC FLUID ISOLATION ENABLES A DETAILED PROTEOMIC VIEW OF THE EXTRACELLULAR SPACE SURROUNDING PLANT CELLS
The apoplastic space surrounding plant cells, encompassing the cell well matrix, extracellular spaces and xylem, is the least understood compartment within plant tissues due to its lack of limiting membranes and its unavoidable damage upon tissue homogenization. Using a streamlined vacuum-infiltrat...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2025-03-28 | PXD060844 | Pride
Apoplast Apf Mass spectrometary Proteomic Apoplastic fluid 
ProteomicsThe autophagy receptor NBR1 directs the clearance of photodamaged chloroplasts
The ubiquitin-binding NBR1 autophagy receptor plays a prominent role in recognizing ubiquitylated protein aggregates for vacuolar degradation during macroautophagy. Here, we show that upon exposing Arabidopsis plants to intense light, NBR1 associates with photodamaged chloroplasts independently of A...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2023-01-16 | PXD039183 | Pride
Microautophagy Ubiquitin. Nbr1 Chlorophagy 
ProteomicsProteomic Analysis of Affinity-Purified Proteasomes Identifies a Suite of Assembly Chaperones in Arabidopsis
The 26S proteasome is an essential protease for the selective elimination of dysfunctional and short-lived regulatory proteins in eukaryotes. To define the composition of this multi-catalytic, ATP-dependent proteolytic machine in plants, we exploited Arabidopsis particles tagged at either the core ...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2019-09-25 | PXD014610 | Pride
Chaperone  core protease  degradation  proteasome  proteolysis  regulatory particle  ubiquitin 
ProteomicsProteasomes Accumulate in the Plant Apoplast Where They Participate in Microbe-Associated Molecular Pattern (MAMP)-Triggered Pathogen Defense
Akin to mammalian extracellular fluids, the plant apoplastic fluid (APF) contains a unique collection of proteins, RNAs, and vesicles that drive many physiological processes ranging from cell wall assembly to defense against environmental challenges. Using an improved method to enrich for the Arabi...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2025-01-08 | PXD059522 | Pride
Arabidopsis Syringolin-a Reactive oxygen species Pathogen defense Pseudomonas syringae Apoplast Proteasome Microbe-associated molecular patterns Flagellin 
ProteomicsINTEGRATED MULTI-OMICS ANALYSES OF MAIZE REVEAL ROLES FOR AUTOPHAGIC DURING FIXED CARBON STARVATION
The turnover of cytoplasmic material via autophagic encapsulation and delivery to vacuoles is essential for recycling cellular constituents, especially under nutrient-limiting conditions. To determine how cells/tissues rely on autophagy, we applied in-depth multi-omic analyses to study maize (Zea m...
ORGANISM(S): Zea mays (Maize) 
2020-07-15 | PXD017077 | Pride
Autophagy Maize Lcms 
Proteomicsmaize mms21 seedling total proteome
Three maize mms21 mutant alleles and their normal siblings were harvested 10 days after planting for total proteome analysis.
ORGANISM(S): Zea mays (Maize) 
2021-10-07 | PXD026853 | Pride
Sumoylayion Smc5 Mms21 Maize 
ProteomicsTotal Proteome Analysis from Arabidopsis thaliana SUMO E3 Ligase Mutants
Proteomic Analysis of the total proteome from Arabidopsis thaliana SUMO E3 Ligase mutants siz1-2 and mms21-1 and wild-type (Col-0) 8-day old seedlings
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2018-04-23 | PXD009274 | Pride
Siz1 Arabidopsis Sumo e3 ligase Mms21 
ProteomicsSUMOylome Profiling in Arabidopsis of Targets Modified by the Sumo Ligase Siz1 During Heat Stress
Ligation is accomplished by a small set of SUMO E3 ligases, with the SAP-MIZ domain-containing (SIZ)-1 and METHYL METHANESULFONATE-SENSITIVE (MMS)-21 ligases having critical roles in stress protection and DNA endoreduplication, respectively. To help identify their corresponding Arabidopsis targets,...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2018-04-05 | PXD007054 | Pride
Sumo e3 ligases Siz1 Arabidopsis Heat stress Sumo 
ProteomicsVariation in upstream open reading frames contributes to allelic diversity in protein abundance
The 5' untranslated region (UTR) sequence of eukaryotic mRNAs may contain upstream open reading frames (uORFs), which can regulate translation of the main open reading frame (mORF). The current model of translational regulation by uORFs posits that when a ribosome scans an mRNA and encounters a uORF...
ORGANISM(S): Zea mays (Maize) 
2021-11-02 | PXD026378 | Pride
Proteomics Lc-ms Maize Snp Utr Rare alleles 
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