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ProteomicsImpact of alternative splicing on Arabidopsis proteome (Part III, TMT RT-SPS-MS3)
Alternative splicing (AS) is a key regulatory process in eukaryotes. Despite its importance, the impact of AS on plant protein diversity and its global effect on the proteome remain largely unexplored. To address this, we included the AS acinus pinin mutant in our qualitative proteomic analysis to i...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2026-06-08 | PXD068593 | Pride
Tandem mass tags (tmt) Proteome Transcriptomics Alternative splicing 
ProteomicsComparison of DIA and TMT based protein quantification in complex background
Label free quantification (LFQ) and isobaric labelling quantification (ILQ) are among the most popular protein quantification workflows in discovery proteomics. Here, we compared the TMT 10-plex workflow to label free single shot data-independent acquisition (DIA) method on a controlled sample set. ...
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
2020-01-29 | MSV000084859 | MassIVE
ProteomicsComparison of TMT6plex MS3 IT vs OT
This dataset is associated with a manuscript where the SPS MS3 method was used for quantifying peptides and a comparison was made between using the ion trap or Orbitrap for the MS3 analysis
ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932) 
2016-05-03 | MSV000079696 | MassIVE
ProteomicsMouse liver sinusoidal endothelial cell responses to the glucocorticoid receptor agonist dexamethasone
Liver sinusoidal endothelial cells (LSECs) from C57Bl/6J male mice obtained from Charles River Laboratory (Sulzfeld, Germany) were cultured on fibronectin coated plates in 5% oxygen atmosphere in AIM-V with serum-free supplements for 1h, 10h, or 48h. Data from quantitative proteomics using a tandem ...
ORGANISM(S): Mus musculus (Mouse) 
2024-09-25 | PXD041381 | Pride
Mus musculus Tmt sps ms3 method Orbitrap fusion lumos mass spectrometer 
ProteomicsOptimized TMT-based quantitative cross-linking mass spectrometry strategy for large-scale interactomic studies
Cross-linking mass spectrometry is a powerful method for the investigation of protein-protein interactions from highly complex samples. XL-MS combined with tandem mass tag labeling holds the promise of large-scale PPI quantification. However, a robust and efficient TMT-based XL-MS quantification met...
ORGANISM(S): Homo sapiens (Human) Escherichia coli Bacteria 
2022-04-07 | PXD031114 | Pride
Faims Hek Ratio distortion E. coli Mass spectrometry Lumos Dsso Xl-ms Interactome Stepped hcd Cross-linking Interference Sps 
ProteomicsTKO6: A Peptide Standard to Assess Interference for Unit-Resolved Isobaric Labeling Platforms
Protein abundance profiling using isobaric labeling is a well-established quantitative mass spectrometry technique. However, ratio distortion resulting from co-isolated and co-fragmented ions - commonly referred to as interference - remains a caveat of this technique. Tribrid mass spectrometers, suc...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2019-03-07 | PXD011653 | Pride
Tko  interference  tmt  itraq  sps-ms3 
ProteomicsAnastrepha ludens antenna proteome in response to CeraTrap®
Anastrepha ludens (Loew) is one of the most important pestiferous fruit fly species infesting citrus and mangoes from Texas to Costa Rica. Despite the latter, the mechanisms of odorant perception in this specie have been poorly studied. In most of the cases, the detection of semiochemicals in inse...
ORGANISM(S): Anastrepha ludens 
2021-09-09 | PXD020012 | Pride
Tmt Anastrepha ludens Odorant binging proteins Lc-ms Fruit fly Sps Antenna proteome 
ProteomicsProteomics study in somatic embryogenesis in avocado
To understand the molecular foundation of the SE induction and development in avocado, we compared by proteomics approach, the embryogenic (EC) and non-embryogenic (NEC) cultures of two avocado varieties. Although Criollo and Hass EC exhibits particularities in the proteome and metabolome profile, i...
ORGANISM(S): Persea americana 
2020-08-14 | PXD019705 | Pride
Sps-ms3 Plant proteomics Tmt Avocado 
ProteomicsTMT10 controlled mixtures - SILAC HeLa UPS1, acquired using SPS-MS3
The controlled mixtures were prepared to evaluate the ability of our proposed approach when dealing with the complicated design, e.g. multiple TMT mixtures with technical replicates. 500, 333, 250, and 62.5 fmol UPS1 peptides were spiked-into 50 g SILAC HeLa peptides in duplicate. It produced a dilu...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2019-08-30 | MSV000084264 | MassIVE
UnknownMultiNotch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes.
Not available
S-EPMC4215866 | biostudies-literature
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