Dataset Information

Spectral quality guided optimization of hybrid EAciD fragmentation on the ZenoTOF 7600 system

ABSTRACT: Systematically optimized N-glycoproteomics method combining EAD and CID on the ZenoTOF 7600. Several dynamic CID parameters were optimized, next EAD was added using different kinetic energy values. Optimization was performed on glycopeptide enriched human plasma. After optimization, the method was tested on a small cohort of cancer patient sera.

INSTRUMENT(S): ZenoTOF 7600

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: A.J.R. Heck

PROVIDER: MSV000098519 | MassIVE | Tue Jul 15 02:54:00 BST 2025

REPOSITORIES: MassIVE

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Publications

Spectral Quality-Guided Optimization of Hybrid EAciD Fragmentation on the ZenoTOF 7600 System Enables Efficient Characterization of the Serum <i>N</i>-Glycoproteome.

Jager Shelley S Shamorkina Tatiana M TM Heidelberger Sibylle M SM Pribil Patrick A PA Schulte Douwe D Reiding Karli R KR Heck Albert J R AJR

Analytical chemistry 20260129 5

The analysis of <i>N</i>-glycopeptides using mass spectrometry comes with numerous challenges, one of which is the unique fragmentation features associated with glycopeptides. Generally, low energy collision-based fragmentation can provide valuable information by the glycan-related B- and Y-ions but often at the expense of peptide backbone coverage. On the other hand, while electron-based fragmentation methods provide good peptide backbone coverage and allow glycan localization, they do not gene ...[more]

PMID: 41609577

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Project description:Ischemia-reperfusion injury during liver transplantation is responsible for early allograft dysfunction (EAD) and failure, both of which are associated with a high risk of morbidity and mortality in the recipient. The purpose of this study was to study major transcriptional alterations in livers procured from different types of human liver donors in order to identify genetic profiles predictive of post-implantation function. We have analyzed samples form living donors (LD), donors after cardiac death (DCD), donors after brain death, with subsequent post-implantation EAD in the recipient (DBD-EAD); and donors after brain death without EAD (DBD). Two samples were obtained from each donor: sample A was taken immediately before cold perfusion (baseline) and sample B 2h after portal reperfusion. We identified clear differences in gene expression patterns according to donor source. Both samples A and B from DBD-EAD and DCD demonstrated over-expression of pro-apoptotic and inflammatory transcripts. However, in DBD and LD, expression of these genes was low at baseline and rose only after reperfusion. DBD and LD demonstrated the greatest increase in overall genetic expression after reperfusion when sample B was contrasted with A, indicating less baseline graft injury in these two groups. Grafts from LD were characterized by activation of transcripts related to anti-ischemic and regenerative processes and fewer pro-inflammatory gene transcripts. This transcriptional events occurring in liver allografts could allow for the prediction of post-transplant function. Pro-inflammatory and ischemic transcriptional changes in the grafts are directly related to donor type and may be useful targets for the development of future therapeutic strategies. The complete database comprised the expression for samples taken from 33 liver grafts. Sample A was taken immediately before cold perfusion (baseline) and sample B 2 h after portal reperfusion. Donors were from one of four groups: living (LD); after cardiac death (DCD); after brain death, with subsequent post-implantation EAD in the recipient (DBD-EAD); and after brain death without EAD (DBD). RNA was extracted from the 66 samples and analyzed using Illumina Beadarray technology. A group of 3 samples from healthy volunteers and 3 samples form LD taken at the start of surgery are included as controls or reference samples. This dataset is part of the TransQST collection.

Dataset Information

Spectral quality guided optimization of hybrid EAciD fragmentation on the ZenoTOF 7600 system

Dataset's files

Publications

Spectral Quality-Guided Optimization of Hybrid EAciD Fragmentation on the ZenoTOF 7600 System Enables Efficient Characterization of the Serum <i>N</i>-Glycoproteome.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

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Dataset Information

Spectral quality guided optimization of hybrid EAciD fragmentation on the ZenoTOF 7600 system

Dataset's files

Publications

Spectral Quality-Guided Optimization of Hybrid EAciD Fragmentation on the ZenoTOF 7600 System Enables Efficient Characterization of the Serum &lt;i&gt;N&lt;/i&gt;-Glycoproteome.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Spectral Quality-Guided Optimization of Hybrid EAciD Fragmentation on the ZenoTOF 7600 System Enables Efficient Characterization of the Serum <i>N</i>-Glycoproteome.