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ProteomicsDevelopment of a Mass Spectrometry-Based Quantitation Assay for Human Body Fluid Proteins using a Wheat Germ Cell-Free Synthesis System
In this study, we have developed a large-scale SRM assay targeting human body fluid proteins based on publicly available proteomics data. We first aimed to produce, in a high throughput manner, a peptide reference library. For this purpose, we selected 2,201 targeted peptides representing 1,215 prot...
ORGANISM(S): Homo sapiens (Human) 
2016-05-24 | PXD002090 | Pride
Wheat germ cell-free system Human body fluid proteins Targeted proteomics Reference peptide library 
ProteomicsMembers of the Plant CRK-superfamily are Capable of trans-/auto-Phosphorylation of Tyrosine Residues
Protein phosphorylation on Tyr residues is a key post-translational modification in mammals. In plants, recent studies have identified Tyr-specific protein phosphatase and Tyr-phosphorylated proteins in Arabidopsis by phosphoproteomic screenings, implying that plants have a Tyr phosphorylation signa...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2018-10-24 | PXD002158 | Pride
Arabidopsis  phosphotyrosine signaling 
ProteomicsBAC-DROP: Rapid digestion of proteome fractionated via dissolvable polyacrylamide gel electrophoresis and its application to bottom-up proteomics workflow
The GeLC-MS workflow, which combines low-cost, easy-to-use SDS-polyacrylamide gel electrophoresis (SDS-PAGE) with liquid chromatography-mass spectrometry (LC-MS), is very popular in current bottom-up proteomics. However, GeLC-MS requires that PAGE-separated proteins undergo overnight enzymatic diges...
ORGANISM(S): Homo Sapiens (human) 
PXD021523 | JPOST Repository
ProteomicsBAC-DROP: Rapid digestion of proteome fractionated via dissolvable polyacrylamide gel electrophoresis and its application to bottom-up proteomics workflow
The GeLC-MS workflow, which combines low-cost, easy-to-use SDS-polyacrylamide gel electrophoresis (SDS-PAGE) with liquid chromatography-mass spectrometry (LC-MS), is very popular in current bottom-up proteomics. However, GeLC-MS requires that PAGE-separated proteins undergo overnight enzymatic diges...
ORGANISM(S): Homo Sapiens Hepatitis B Virus Bos Taurus 
2021-01-24 | PXD021489 | panorama
ProteomicsDevelopment of sequential sample processing protocol on a single anion-exchange solid-phase extraction disc for bottom-up/cross-linking mass spectrometry
In this project, we developed a rapid enzymatic digestion protocol within an anion exchange StageTip named AnExSP (anion-exchange disc-assisted sequential sample preparation) and, using data-independent acquisition, analyzed its digestion performance of human cellular protein extracts (HCPE) using t...
ORGANISM(S): Homo Sapiens (human) 
PXD029444 | JPOST Repository
ProteomicsPEPPI-SP3: Robust and Simple Sample Prefractionation Workflow for Top-Down Proteomics
In this study, we developed a complete, robust, and simple sample preparation workflow named PEPPI-SP3 for top-down proteomics by combining PEPPI-MS with the magnetic bead-based protein purification approach used in SP3 (single-pot, solid-phase-enhanced sample preparation), now one of the standard s...
ORGANISM(S): Homo Sapiens (human) 
2025-01-23 | PXD056413 | JPOST Repository
ProteomicsSynthetic biology meets proteomics: Construction of à la carte QconCATs for absolute protein quantification
We report a new approach to the assembly and construction of QconCATs, quantitative concatamers for proteomic applications that yield stoichiometric quantities of sets of stable isotope-labelled internal standards. The new approach is based on synthetic biology precepts of biobricks, making use of l...
ORGANISM(S): Escherichia Coli 
2022-07-18 | PXD027047 | panorama
ProteomicsQuantitative assay of targeted proteome in trichome glandular cells using large-scale selected reaction monitoring strategy
Background: Glandular trichomes found in vascular plants are called natural cell factories because they synthesize and store secondary metabolites in the glandular cell. In order to systematically understand the metabolic processes in the glandular cells, it is indispensable to analyze the cellular ...
ORGANISM(S): Solanum Lycopersicum 
2019-08-13 | PXD012250 | panorama
ProteomicsDe novo reconstitution and isolation of nucleosomes using the wheat germ cell-free protein synthesis
DNA is packaged with histones and non-histone proteins to form chromatin that impinges on all nuclear processes such as transcription, replication and repair. A complete molecular understanding of these processes requires analysis of chromatin context. In this study, we report a simple and robust sy...
ORGANISM(S): Drosophila Melanogaster 
2026-06-17 | PXD011113 | panorama
ProteomicsPEPPI-MS- and GELFrEE-fractionated E. coli MG1655 whole cell lysate
Supplemental Files accompanying manuscript “PEPPI-MS: polyacrylamide gel-based prefractionation for analysis of intact proteoforms and protein complexes by mass spectrometry”.
ORGANISM(S): Escherichia Coli Str. K-12 Substr. Mg1655 (ncbitaxon:511145) 
2020-04-08 | MSV000085258 | MassIVE
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