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ProteomicsOne-STAGE Tip Method for TMT based Proteomic Analysis of Minimal Amount of Cells
LC-MS-based profiling of proteomes with isobaric tag labeling from low-quantity biological and clinical samples, including needle-core biopsies and laser capture microdissection, has been challenging due to limited amount and sample loss during preparation. To address this problem, we developed OnM ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2023-04-18 | MSV000091734 | MassIVE
ProteomicsDistinguishing N-Terminal Methylation from Near-isobaric Modifications by Statistical Analysis of Mass Error Distributions of Fragment Ions
alpha-N-terminal methylation is an understudied post-translational modification with presumed functions involving protein-protein and/or protein-DNA interaction. The covalent addition of mono-, di-, trimethyl groups to free alpha-amino group has proven to be difficult to profile globally by mass spe...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2024-11-14 | MSV000096415 | MassIVE
ProteomicstipNrich, a tip-based N-terminal proteome enrichment method
Protein N-termini provide valuable information such as half-life of protein, but one of hurdles to study N-terminome is that it requires large amount of sample, but this requirement might be problematic for analyzing the limited samples such as low number of cells of clinical biopsies. In this regar...
ORGANISM(S): Bos taurus (Bovine) Mus musculus (Mouse) Escherichia coli Bacillus subtilis 
2022-12-05 | PXD027961 | Pride
Human plasma Recombinant single proteins Protein mixture Lc-ms/ms 
ProteomicsQuantitative proteome for C.elegans by 3plex mTRAQ
Vesicle-mediated transport is a fundamental part of the secretory and endocytic pathways. In addition to their role in membrane protein trafficking, Arf-like protein subfamily of small GTPases also plays an important role in development, maintenance of Golgi structure and function. Proper protein tr...
ORGANISM(S): Caenorhabditis elegans 
2022-02-17 | PXD026411 | Pride
C. elegans Mtraq Lc-ms/ms 
ProteomicsPhosphoproteome profiling using the isobaric carrier without the need for phosphoenrichment
Phosphorylation is a crucial component of signaling cascades in a cell. It controls various biological cellular functions such as cell growth and apoptosis. Due to the low stoichiometry of phosphorylaion, enrichment of phosphopeptide prior to LC-MS/MS is necessary for comprehensive phosphoproteome a...
ORGANISM(S): Homo sapiens (Human) 
2022-03-07 | PXD028490 | Pride
Isobaric labeling Tmt Carrier Phosphoproteome Quantitative proteomics 
ProteomicsShift of EMT gradient in 3D spheroid MSCs for activation of mesenchymal niche function
This project is described about the detailed characterization of 3D spheroid mesenchymal stem cells (MSCs). Specifically, authors showed the dynamic action towards EMT in 3D MSCs and the potential of EMT-enhanced “naïve” mesenchymal phenotype.
ORGANISM(S): Homo sapiens (Human) 
2018-06-25 | PXD006653 | Pride
Human Cell 3d-cultured Mesenchymal stem cell Lc-ms/ms 
ProteomicsYeast N-terminome SILAC - Formyl-methionine as an N-degron of a eukaryotic N-end rule pathway
Discerning yeast N-termionome with SILAC method. To analyze qualitative and quantitative analysis of N-formyl-methionine when introducing environmental stress.
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2019-11-12 | PXD010780 | Pride
N-terminome Yeast Silac Formyl 
ProteomicsOptimized NHS-amine labeling for multiplexed phosphoproteome study.
In this project, we report the detrimental effect of hydroxylamine, a quenching reagent for NHS-amine reaction, on phosphopeptides. The degree of phosphopeptide enrichment was greatly improved by a desalting method compared with a vacuum-drying method right after quenching reaction. We demonstrate t...
ORGANISM(S): Homo sapiens (Human) 
2018-02-27 | PXD008082 | Pride
Phosphoproteome Β-elimination Hydroxylamine Phosphorylation Tandem mass tag N-hydroxysuccinamide-esters Isobaric tag 
ProteomicsMulti-layered proteomic analysis for colorectal cancer
Matrix metalloproteinase-2 (MMP-2) plays a role in cell migration and invasion that involve degradation of extracellular matrix proteins as well as vascular remodeling. Increased expression of MMP-2 has often been observed in the tumors of colorectal cancer (CRC) patients. In order to unveil the per...
ORGANISM(S): Homo sapiens (Human) 
2021-08-26 | PXD018304 | Pride
Mmp-2 Silac Plasma Label-free Focal adhesion kinase Secretome Colorectal cancer 
ProteomicsCommon Repository of FBS Proteins (cRFP) to be added to a search database for mass spectrometric analysis of cell secretome
We propose to use cRFP (common Repository of FBS Proteins) in the MS (mass spectrometry) raw data search of cell secretome. cRFP is a small supplementary sequence list of high abundant fetal bovine serum proteins added to the reference database in use. The aim behind using cRFP is to prevent the con...
ORGANISM(S): Homo sapiens (Human) 
2019-09-04 | PXD015143 | Pride
Common repository of fbs proteins Database search Secretome 
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