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ProteomicsCan we boost N-glycopeptide identification confidence? Smart collision energy choice taking into account structure and search engine
We investigated how the structural features of N-glycopeptides and the choice of the search engine influence the optimal collision energy, delivering highest identification confidence. We carried out LC-MS/MS measurements using a series of collision energies on a large set of N-glycopeptides with bo...
ORGANISM(S): Bos Taurus (ncbitaxon:9913) Homo Sapiens (ncbitaxon:9606) 
2023-10-14 | MSV000093110 | MassIVE
ProteomicsDiversity matters: Optimal collision energies for tandem mass spectrometric analysis of a large set of N-glycopeptides - part 2
a) Ratio of the lower and higher energy component. Tests were done on the mixture of AGP, fetuin and transferrin digests using 2.2 pmol from all glycoproteins in each run. Five different high CE setting was used which were 50%, 75%, 100%, 125% and 150% of the original method of Hinneburg et al. Thes...
ORGANISM(S): Bos Taurus (ncbitaxon:9913) Homo Sapiens (ncbitaxon:9606) 
2022-08-26 | MSV000090218 | MassIVE
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
ProteomicsBroadening the horizon of MS optimization for enzymatic digestions in proteomics
Collision energy dependent measurements on human protein exctract and human blood plasma samples digested with various enzymes (trypsin, Arg-C, Glu-C, chymotrypsin, Asp-N) and performance assessment at optimized energies on Bruker QTof instruments
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2024-06-18 | MSV000095066 | MassIVE
ProteomicsOptimum collision energies for proteomics: The impact of ion mobility separation
We performed LC-MS/MS measurements on a Waters Select Series Cyclic IMS QTof mass spectrometer with varied CE settings both with and without IMS. We investigated the CE dependence of identification score, using Byonic search engine, for more than 1000 tryptic peptides from HeLa digest standard. We d...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2022-12-20 | MSV000090944 | MassIVE
ProteomicsBottom-up proteomics with collision energies optimized for identification confidence
Collision energy dependent measurements on HeLa samples and performance assessment at optimized energies on QTof and Orbitrap instruments
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2020-10-28 | MSV000086379 | MassIVE
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