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ProteomicsUnderstanding m/z range settings for MS/MS scans: a case study with intact glycopeptides
Several practical considerations dictate the scan range, or breadth of ion m/z values, that can be transmitted through ion guides in mass spectrometers (MS). Voltage settings must be balanced to minimize low m/z cutoffs while also generating effective pseudopotential wells for high m/z ions to maxim...
ORGANISM(S): Homo sapiens (Human) 
2026-06-08 | PXD062360 | Pride
Glycobiology Glycopeptides Mass spectrometry Mass range 
ProteomicsRevisiting the effect of trypsin digestion buffers on artificial deamidation
Deamidation of asparagine and glutamine residues occurs spontaneously, accelerated by adjacent amino acid residues and influenced by pH, temperature, and incubation time. Standard proteolytic digestion induces significant deamidation, which is especially problematic in bottom-up proteomic studies. T...
ORGANISM(S): Mus musculus (Mouse) 
2025-03-11 | PXD054603 | Pride
De-glycopeptides Chemical deamidation De-glycoproteomics 
ProteomicsCellular determinants of targeted membrane protein degradation by lysosome targeting chimeras
Targeted protein degradation is a powerful therapeutic strategy that offers benefits over canonical target inhibition. Lysosome targeting chimeras (LYTACs) harness lysosome trafficking receptors such as the cation-independent mannose-6-phosphate receptor (CI-M6PR) to direct secreted and membrane pro...
ORGANISM(S): Homo sapiens (Human) 
2024-01-26 | PXD037899 | Pride
Dia Lytac Quantitative proteomics Lysosome Crispri 
MetabolomicsGut microbiome dysbiosis drives metabolic dysfunction in Familial dysautonomia
Familial dysautonomia (FD) is a rare genetic neurologic disorder caused by impaired neuronal development and progressive degeneration of both the peripheral and central nervous systems. FD is monogenic, with >99.4% of patients sharing an identical point mutation in the elongator acetyltransferase co...
2022-12-06 | MTBLS5138 | MetaboLights
ProteomicsStructure-guided mutagenesis of a mucin-selective metalloprotease from Akkermansia muciniphila alters substrate preferences
Akkermansia muciniphila, a mucin-degrading microbe found in the human gut, is often associated with positive health outcomes. The abundance of Akkermansia muciniphila is modulated by the presence and accessibility of nutrients, which can be derived from diet or host glycoproteins. In particular, the...
ORGANISM(S): Homo sapiens (Human) 
2022-08-28 | PXD031225 | Pride
X-ray crystallography Mucin Mucinase Microbiome O-glycosylation Molecular docking Enzyme structure Metalloprotease 
ProteomicsModulation of immune cell reactivity with cis-binding Siglec-9 agonists
Primary inflammatory pathologies caused by phagocytes lead to numerous debilitating conditions, ranging from chronic pain to permanent blindness. Siglec-9 is an immunoinhibitory receptor expressed on many types of phagocytes and is a promising target for anti-inflammatory therapeutics. We developed ...
ORGANISM(S): Homo sapiens (Human) 
2021-01-14 | PXD018774 | Pride
Phosphoproteomics Tmt Lc-ms/ms 
ProteomicsDeciphering O-glycoprotease substrate preferences with O-Pair Search
O-glycoproteases are an emerging class of enzymes that selectively digest glycoproteins at positions decorated with specific O-linked glycans. O-glycoprotease substrates range from any O-glycoprotein (albeit with specific O-glycan modifications) to only glycoproteins harboring specific O-glycosylate...
ORGANISM(S): Homo sapiens (Human) 
2023-02-15 | PXD035775 | Pride
O-glycoproteomics Glycoproteins Cleavage Glycoproteomics Informatics O-pair search O-glycoprotease 
ProteomicsTMPRSS2-mediated coronavirus spike activation and inhibition
The human protease TMPRSS2 facilitates entry of many respiratory viruses into cells, including coronaviruses and influenza viruses, yet its mechanism or viral glycoprotein recognition remains unclear. Here, we show that following ACE2 engagement and formation of an early fusion intermediate SARS-CoV...
ORGANISM(S): Homo sapiens (Human) 
2026-03-27 | PXD069687 | Pride
Sars-cov-2 
ProteomicsSynthetic Siglec-9 agonists inhibit neutrophil activation associated with COVID-19
Severe cases of coronavirus disease 2019 (COVID-19) are characterized by a hyperinflammatory immune response that leads to numerous complications. Production of proinflammatory neutrophil extracellular traps (NETs) has been suggested to be a key factor in inducing a hyperinflammatory signaling casca...
ORGANISM(S): Homo sapiens (Human) 
2021-07-28 | PXD022990 | Pride
Neutrophil Siglec Netosis Sars-cov-2 Covid-19 
ProteomicsOptimal Dissociation Methods Differ for N- and O-glycopeptides
Site-specific characterization of glycosylation requires intact glycopeptide analysis, and recent efforts have focused on how to best interrogate glycopeptides using tandem mass spectrometry (MS/MS). Beam-type collisional activation, i.e., higher-energy collisional dissociation (HCD), has been a val...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) 
2020-07-20 | PXD017646 | Pride
Glycoproteomics N-glycopeptides Scehcd Ethcd O-glycopeptides Etd 
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