Dataset Information

TimsTOF Pro datasets for CCS prediction

ABSTRACT: Tryptic digested E. coli dataset fractionated by SCX stagetip and applied to test the CCS prediction model.

ORGANISM(S): Escherichia Coli

SUBMITTER: Yasushi Ishihama

PROVIDER: PXD022800 | JPOST Repository | Mon Sep 06 00:00:00 BST 2021

REPOSITORIES: jPOST

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Dataset's files

Source:

			Action	DRS
	201020ko17EColi_Fr02_Slot1-01_1_13272.maxqFin.txt	Txt
	201020ko17EColi_Fr02_Slot1-01_1_13272.tdf	Other
	201020ko17EColi_Fr02_Slot1-01_1_13272.tdf_bin	Other
	201020ko18EColi_Fr03_Slot1-01_1_13273.maxqFin.txt	Txt
	201020ko18EColi_Fr03_Slot1-01_1_13273.tdf	Other

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Publications

Sequence-Specific Model for Predicting Peptide Collision Cross Section Values in Proteomic Ion Mobility Spectrometry.

Chang Chih-Hsiang CH Yeung Darien D Spicer Victor V Ogata Kosuke K Krokhin Oleg O Ishihama Yasushi Y

Journal of proteome research 20210616

The contribution of peptide amino acid sequence to collision cross section values (CCS) has been investigated using a dataset of ∼134 000 peptides of four different charge states (1+ to 4+). The migration data were acquired using a two-dimensional liquid chromatography (LC)/trapped ion mobility spectrometry/quadrupole/time-of-flight mass spectrometry (MS) analysis of HeLa cell digests created using seven different proteases and was converted to CCS values. Following the previously reported model ...[more]

PMID: 34133192

Similar Datasets

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 (Bruker Daltonics) series combines a trapped ion mobility device with a quadrupole, collision cell, and a time-of-flight analyzer to enable the analysis of ions at great speed. Here, we show that the timsTOF Pro is capable of physically separating N-glycopeptides from nonmodified peptides and producing high-quality fragmentation spectra, both beneficial for glycoproteomics analyses of complex samples. The glycan moieties enlarge the size of glycopeptides compared with nonmodified peptides, yielding a clear cluster in the mobilogram that, next to increased dynamic range from the physical separation of glycopeptides and nonmodified peptides, can be used to make an effective selection filter for directing the mass spectrometer to analytes of interest. We designed an approach where we (1) focused on a region of interest in the ion mobilogram and (2) applied stepped collision energies to obtain informative glycopeptide tandem mass spectra on the timsTOF Pro:glyco-polygon-stepped collision energy-parallel accumulation serial fragmentation. This method was applied to selected glycoproteins, human plasma- and neutrophil-derived glycopeptides. We show that the achieved physical separation in the region of interest allows for improved extraction of information from the samples, even at shorter liquid chromatography gradients of 15 min. We validated our approach on human neutrophil and plasma samples of known makeup, in which we captured the anticipated glycan heterogeneity (paucimannose, phosphomannose, high mannose, hybrid and complex glycans) from plasma and neutrophil samples 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 a comparison between two laboratories.