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ProteomicsSequential N/O-glycosylation analysis of heavily glycosylated HIV-1 gp120 by combination of electron-transfer/higher-energy collisional dissociation and stepped collision energy/higher-energy collisional dissociation (EThcD-sceHCD)
The envelope (Env) glycoprotein on the surface of human immunodeficiency virus type 1 (HIV-1) which decorated with a dense array of glycans is a determinant for viral invasion and host immune response of HIV-1 and a major target for a preventive HIV-1 vaccine. Improved vaccine design requires an und...
ORGANISM(S): Homo sapiens (Human) 
2021-11-03 | PXD025078 | Pride
Envelope glycoprotein Human immunodeficiency virus Ethcd-scehcd-ms/ms N/o-glycosylation 
ProteomicsMS-based sequencing of the anti-FLAG-M2 antibody
We demonstrate a method for direct de novo sequencing of monoclonal IgG from the purified antibody products. The method uses a panel of multiple complementary proteases to generate suitable peptides for de novo sequencing by LC-MS/MS in a bottom-up fashion. Furthermore, we apply a dual fragmentation...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2021-01-11 | PXD023419 | Pride
Antibody Stepped hcd Ethcd De novo sequencing 
ProteomicsSite-specific N- and O-glycosylation Analysis of Human Plasma Fibronectin
Human plasma fibronectin is an adhesive protein that plays a crucial role in wound healing. Many studies had indicated that glycans may mediate the expression and functions of fibronectin, yet a comprehensive understanding of its glycosylation is still missing. Here, we performed a comprehensive N- ...
ORGANISM(S): Homo sapiens (Human) 
2022-02-17 | PXD025886 | Pride
Mass spectrometer Glycosylation Stepped normalized collision energy Operator Fibronectin 
ProteomicsDiversity matters: Optimal collision energies for tandem mass spectrometric analysis of a large set of N-glycopeptides
Detailed energy dependence investigations were carried out on AGP digest using 2.2 pmol glycoprotein per run and on the mixture of AGP, fetuin and transferrin digests injecting 2.2 pmol from all glycoproteins in each run. Stepped CE settings were applied with 80% of the time allocated to the higher ...
ORGANISM(S): Bos Taurus (ncbitaxon:9913) Homo Sapiens (ncbitaxon:9606) 
2022-06-15 | MSV000089657 | MassIVE
UnknownStepped collisional energy improves protein acylation identification by eliminating positional bias of cyclic immonium ions.
Not available
S-EPMC12800203 | biostudies-literature
ProteomicsSystems analysis of plasma IgG intact N-glycopeptides from pa-tients with chronic kidney diseases via combined electron-transfer/higher-energy collisional dissociation and stepped colli-sion energy/higher-energy collisional dissociation mass spectrom-etry within half an hour
Immunoglobulin G (IgG) molecules modulate an immune response. However, site-specific N-glycosylation signatures of plasma IgG in patients with chronic kidney disease (CKD) remain unclear. This study aimed to propose a novel method to explore the N-glycosylation pattern of IgG and to compare it with ...
ORGANISM(S): Homo sapiens (Human) 
2021-11-25 | PXD027174 | Pride
Glycosylation Immunoglobulin g Chronic kidney disease Lc-ms/ms 
MetabolomicsIntegrated multi-omics reveals Enterococcus faecalis JM263 alleviates high-concentrate diet-induced hepatic injury via the gut-liver axis in goats

This dataset contains raw liquid chromatography-tandem mass spectrometry (LC-MS/MS) data derived from the liver tissues of goats (Capra hircus). The purpose of this study is to explore the metabolic regulatory mechanism of the probiotic Enterococcus faecalis JM263 in goats fed a high-concentrate ...

2026-01-15 | MTBLS13688 | MetaboLights
ProteomicsEnrichment and Fragmentation Approaches for Enhanced Detection and Characterization of Endogenous Glycosylated Neuropeptides
Glycosylation, a common and heterogeneous post-translational modification plays a key role in altering biomolecule function and other properties. Prior to monitoring regulatory roles, basal glyconeuropeptide expression must be determined. Characterization is partially limited by the lower abundance ...
ORGANISM(S): Callinectes sapidus 
2022-08-19 | PXD033226 | Pride
Glycosylation Neuropeptides Endogenous peptides Mass spectrometry De novo sequencing 
ProteomicsLeveraging immonium ions for identifying and targeting acyl-lysine modifications in proteomic datasets
Acyl modifications vary greatly in terms of elemental composition and site of protein modification. Developing methods to identify these modifications more confidently can help assess the scope of these modifications in large proteomic datasets. Herein we analyze the utility of acyl-lysine immonium ...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) 
2020-09-09 | PXD018758 | Pride
Stepped collision energy Lysine acylation Immonium ion 3-hydroxypimelylation Lysine acetylation Bsa Lc-ms/ms 
ProteomicsStradard protein and yeast top-down data
We developed a novel dissociation strategy in the data acquisition process, the Mesh strategy to dissociate multiple charge states of one proteoform with stepped HCD (high collision energy dissociation). We proved that the ‘Mesh’ strategy could generate fragments with improved sequence coverage and...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2022-06-09 | PXD022941 | Pride
Stepped hcd Instrument control Real-time Mesh Top-down 
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