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ProteomicsExtending the coverage of Lys-C/trypsin-based bottom-up proteomics using cysteine S-aminoethylation
In this study, S-aminoethylation of Cys (AE-Cys) was carried out with 2-bromoethylamine to form pseudo-Lys, which was then digested with Lys-C or trypsin to improve proteome coverage in bottom-up proteomics. A model study with bovine serum albumin showed that the C-terminal side of Cys was successfu...
ORGANISM(S): Homo Sapiens (human) Bos Taurus 
2023-09-27 | PXD045433 | JPOST Repository
ProteomicsUbiquitination at the Parkin ubiquitin-like domain suggests a new mechanism for Parkin activation
The mitochondrial kinase PINK1 and the cytosolic ubiquitin ligase (E3) Parkin is involved in mitochondrial quality control. PINK1, which phosphorylates ubiquitin at serine 65 residue and the ubiquitin-like (Ubl) domain of Parkin at serine 65 residue, promotes the Parkin activation and translocation ...
ORGANISM(S): Homo Sapiens (human) 
2022-08-24 | PXD026554 | JPOST Repository
ProteomicsIn vitro reconstitution of epigenetic reprogramming in the human germ line
M1-BTAG iPSCs or TET1-KO iPSCs were analyzed by 8% SDS-PAGE, followed by trypsin digestion and LC/MS/MS with an Orbitrap Fusion Lumos linked with an Ultimate 3000 pump and HTC-PAL autosampler. Acquired data files were processed using FragPipe v20.0 (MSFragger v3.8, Philosopher v5.0.0, IonQuant v1.9....
ORGANISM(S): Homo Sapiens (human) 
2024-04-25 | PXD048118 | JPOST Repository
ProteomicsTargeted Quantitation of Host Cell Proteins by Capillary LC/IMS/MS/MS in Combination with Rapid Digestion on Immobilized Trypsin Column Under Native Conditions
Host cell protein (HCP) impurities are considered a critical quality attribute of biopharmaceuticals because of their potential to compromise safety and efficacy, and LC/MS-based analytical methods have been developed to identify and quantify individual proteins instead of employing enzyme-linked im...
ORGANISM(S): Cricetulus Griseus 
2025-05-02 | PXD053135 | JPOST Repository
ProteomicsEffect of Phosphorylation on the Collision Cross Sections of Peptide Ions in Ion Mobility Spectrometry
The insertion of ion mobility spectrometry (IMS) between LC and MS can improve peptide identification in both proteomics and phosphoproteomics by providing structural information that is complementary to LC and MS, because IMS separates ions on the basis of differences in their shapes and charge sta...
ORGANISM(S): Homo Sapiens (human) 
2021-01-14 | PXD019746 | JPOST Repository
ProteomicsNano-scale solid-phase isobaric labeling for multiplexed quantitative phosphoproteomics
We established a workflow for highly sensitive multiplexed quantitative phosphoproteomics using a nano-scale solid-phase tandem mass tag (TMT) labeling reactor. Phosphopeptides were firstly enriched by titanium oxide chromatography and then labeled with isobaric TMT reagents in a StageTip packed wit...
ORGANISM(S): Homo Sapiens (human) 
2021-07-23 | PXD025536 | JPOST Repository
ProteomicsMotif-centric phosphoproteomics to target kinase-mediated signaling pathways
Identifying cellular phosphorylation pathways based on kinase-substrate relationships is a critical step to understanding the regulation of physiological functions in cells. Mass spectrometry-based phosphoproteomics workflows have made it possible to comprehensively collect information on individual...
ORGANISM(S): Homo Sapiens (human) 
2021-12-01 | PXD026996 | JPOST Repository
ProteomicsFormic acid and Acetic acid for peptide LC-MS
Despite the general acceptance of formic acid as the additive of choice for peptide reversed-phase LC-MS/MS applications, some still argue that the selection of acetic acid represents a better option. To settle this debate, we investigated both the difference in MS sensitivity and chromatographic be...
ORGANISM(S): Homo Sapiens (human) 
2022-12-10 | PXD029416 | JPOST Repository
ProteomicstimsTOF Pro datasets for CCS prediction with Mascot-Percolator.
Tryptic digested E. coli dataset fractionated by SCX stagetip and applied to test the CCS prediction model. The Peaklist from the MS/MS spectra as mascot generic format (MGF) was created by compass DataAnalysis 5.2.216.271.5315. Protein and peptides were identified by by Mascot-Percolator.
ORGANISM(S): Escherichia Coli 
2021-09-06 | PXD026087 | JPOST Repository
ProteomicstimsTOF Pro datasets for CCS prediction
Tryptic digested E. coli dataset fractionated by SCX stagetip and applied to test the CCS prediction model.
ORGANISM(S): Escherichia Coli 
2021-09-06 | PXD022800 | JPOST Repository
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