Ion Mobility-Reframe Drug Library
Ontology highlight
ABSTRACT:
INSTRUMENT(S): timsTOF Pro 2
ORGANISM(S): Synthetic Construct (ncbitaxon:32630)
SUBMITTER: 
Pieter C. Dorrestein
PROVIDER: MSV000098263 | MassIVE | Wed Jun 18 18:57:00 BST 2025
REPOSITORIES: MassIVE
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Project description:Crude standards of reframe drug mixtures were analyzed on a TimsTOF Pro2 coupled to Agilent LC system for library generation.
2025-06-18 | MSV000098263 | GNPS
Project description:Spatial separation of ions in the gas-phase, providing information about their size as collisional cross-sections, can readily be achieved through ion mobility. The timsTOF Pro combines a trapped ion mobility device with a quadrupole, collision cell and a time-of-flight analyser to enable the analysis of ions at great speed. Here, we show that the timsTOF Pro is capable of physically separating N-glycopeptides from non-modified peptides and producing high-quality fragmentation spectra, both beneficial for glycoproteomics analyses of complex samples. The glycan moieties enlarge the size of glycopeptides compared to non-modified peptides, yielding a clear cluster in the mobilogram that, next to increased dynamic range from the physical separation of glycopeptides and non-modified peptides, can be used to make an effective selection filter for directing the mass spectrometer to analytes of interest. This new approach was applied to selected glycoproteins, human plasma- and neutrophil-derived glycopeptides. We show that the achieved physical separation, combined with the focussing of the mass spectrometer, allows for improved extraction of information from the samples, even at shorter LC gradients of 15 min. We validated our approach on human neutrophil and plasma samples of known make-up, in which we captured the anticipated glycan heterogeneity (paucimannose, phosphomannose, high mannose, hybrid and complex glycans) from diverse biological samples (plasma and neutrophils) at the expected abundances. As the method is compatible with off-the-shelve data acquisition routines and data analysis software, it can readily be applied by any laboratory with a timsTOF Pro and is reproducible as demonstrated by an inter-laboratory comparison between two laboratories.
2023-01-17 | PXD034845 | Pride
Project description:Mixtures and pure injections of 20 commercial standards collected in 4 different collection modes (DIA, DDA, HDDIA, and HDDDA). Initial MSMS eV testing of the standards is also included
2021-11-04 | MSV000088316 | MassIVE
Project description:Data independent acquisition (DIA or DIA/SWATH ) mass spectrometry has emerged as a primary measurement strategy in the field of quantitative proteomics. diaPASEF is a recent adaptation that leverages trapped ion mobility spectrometry (TIMS) to improve selectivity and increase sensitivity. The complex fragmentation spectra generated by co-isolation of peptides in DIA mode are most typically analyzed with reference to prior knowledge in the form of spectral libraries. The best established method for generating libraries uses data dependent acquisition (DDA) mode, or DIA mode if appropriately deconvoluted, often including offline fractionation to increase depth of coverage,to create spectral libraries. More recently strategies for spectral library generation based on gas phase fractionation (GPF), where a representative sample is injected serially using narrow window DIA methods designed to cover different slices of the precursor space, have been introduced and performed comparably to deep offline fractionation-based libraries for DIA data analysis. Here, we investigated whether an analogous GPF-based library building approach that accounts for the ion mobility (IM) dimension is useful for the analysis of diaPASEF data and can remove the need for offline fractionation. To enable a rapid library development approach for diaPASEF we designed a GPF acquisition scheme covering the majority of multiply charged precursors in the m/z vs 1/K0 space requiring 7 injections of a representative sample and compared this with libraries generated by direct deconvolution-based analysis of diaPASEF data or by deep offline fractionation and ddaPASEF. . We found that the GPF based library outperformed library generation by direct deconvolution of the diaPASEF data, and performed comparably to deep offline fractionation libraries, when analysing diaPASEF data acquired from 200ng of commercial HeLa digest. With the ion mobility integrated GPF scheme we establish a pragmatic approach to rapid and comprehensive library generation for the analysis of diaPASEF data.
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Project description:Data independent acquisition (DIA or DIA/SWATH ) mass spectrometry has emerged as a primary measurement strategy in the field of quantitative proteomics. diaPASEF is a recent adaptation that leverages trapped ion mobility spectrometry (TIMS) to improve selectivity and increase sensitivity. The complex fragmentation spectra generated by co-isolation of peptides in DIA mode are most typically analyzed with reference to prior knowledge in the form of spectral libraries. The best established method for generating libraries uses data dependent acquisition (DDA) mode, or DIA mode if appropriately deconvoluted, often including offline fractionation to increase depth of coverage,to create spectral libraries. More recently strategies for spectral library generation based on gas phase fractionation (GPF), where a representative sample is injected serially using narrow window DIA methods designed to cover different slices of the precursor space, have been introduced and performed comparably to deep offline fractionation-based libraries for DIA data analysis. Here, we investigated whether an analogous GPF-based library building approach that accounts for the ion mobility (IM) dimension is useful for the analysis of diaPASEF data and can remove the need for offline fractionation. To enable a rapid library development approach for diaPASEF we designed a GPF acquisition scheme covering the majority of multiply charged precursors in the m/z vs 1/K0 space requiring 7 injections of a representative sample and compared this with libraries generated by direct deconvolution-based analysis of diaPASEF data or by deep offline fractionation and ddaPASEF. . We found that the GPF based library outperformed library generation by direct deconvolution of the diaPASEF data, and performed comparably to deep offline fractionation libraries, when analysing diaPASEF data acquired from 200ng of commercial HeLa digest. With the ion mobility integrated GPF scheme we establish a pragmatic approach to rapid and comprehensive library generation for the analysis of diaPASEF data.
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Project description:The combination of cross-linking/mass spectrometry (XL-MS) and ion mobility is still underexplored for conducting protein conformational and protein-protein interaction studies. We present a method for analyzing cross-linking mixtures on a timsTOF Pro mass spectrometer that allows separating ions based on their gas phase mobilities. Cross-linking was performed with three urea-based MS-cleavable cross-linkers that deliver distinct fragmentation patterns for cross-linked species upon collisional activation. The discrimination of cross-linked species from non-cross-linked peptides was readily performed based on their collisional cross sections. We demonstrate the general feasibility of our combined XL-MS/ion mobility approach for three protein systems of increasing complexity: (i) Bovine serum albumin, (ii) E. coli ribosome, and (iii) HEK293T cell nuclear extracts. We identified a total of 623 unique cross-linking sites for BSA, 670 for the E. coli ribosome, and 1,617 unique cross-links for nuclear extracts, corresponding to 1,088 intra- and 529 interprotein interactions and yielding 564 distinct protein-protein interactions. Our results underline the strength of combining XL-MS with ion mobility not only for deriving 3D-structures of single proteins, but also for performing system-wide protein interaction studies.
2022-03-17 | PXD027234 | Pride
Project description:This project developed electrophoresis-correlative (Eco) mass spectrometry (MS) to measure the proteome of single cells on a trapped ion mobility mass spectrometer (timsTOF PRO). Eco-MS identified 962 protein groups in a <20 min of electrophoresing a single-HeLa-cell-equivalent (~200 pg) proteome amount. Match-between-runs improved this number to 2,139 protein groups on the same dataset. We demonstrate the approach to measure the proteome of single cells in X. laevis embryos at stage 8 (blastula). Single cells were isolated from the animal cap and their proteomes digested on a fluorosilane-coated microplate. Less than 4% of the available single-cell proteome was analyzed on a custom-built capillary electrophoresis (CE) platform under classical and Eco-driven ddaPASEF. Eco-MS returned ~51% of more protein groups than the control, identifying 1,157 proteins from N = 9 different single cells (biological replicates) of the animal cap. Eco-MS deepens the detectable coverage of the single-cell proteome using ddaPASEF on a timsTOF MS.
2025-05-07 | PXD057685 | Pride
Project description:This project developed electrophoresis-correlative (Eco) mass spectrometry (MS) to measure the proteome of single cells on a trapped ion mobility mass spectrometer (timsTOF PRO). Eco-MS identified 962 protein groups in a <20 min of electrophoresing a single-HeLa-cell-equivalent (~200 pg) proteome amount. Match-between-runs improved this number to 2,139 protein groups on the same dataset. We demonstrate the approach to measure the proteome of single cells in X. laevis embryos at stage 8 (blastula). Single cells were isolated from the animal cap and their proteomes digested on a fluorosilane-coated microplate. Less than 4% of the available single-cell proteome was analyzed on a custom-built capillary electrophoresis (CE) platform under classical and Eco-driven ddaPASEF. Eco-MS returned ~51% of more protein groups than the control, identifying 1,157 proteins from N = 9 different single cells (biological replicates) of the animal cap. Eco-MS deepens the detectable coverage of the single-cell proteome using ddaPASEF on a timsTOF MS.
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Project description:Naphthenic acids (Nas) are carboxylic acids present in crude oil and classfied as emergent pollutants. The mechanisms underlaying the toxicity of such mixtures are unknown. Changes in gene expression are expected to reflect te teratogenenic effects of the exposure to NAs. The objective of these experiments is to determine the changes in the gene expression profile of Silurana (Xenopus) tropicalis embryos due to the exposition to two NA mixtures.
2018-11-29 | GSE118736 | GEO