Dataset Information

Sequencing and Identification of Endogenous Neuropeptides with Matrix-Enhanced Secondary Ion Mass Spectrometry Tandem Mass Spectrometry.

ABSTRACT: Matrix-enhanced secondary ion mass spectrometry (ME-SIMS) has overcome one of the biggest disadvantages of SIMS analysis by providing the ability to detect intact biomolecules at high spatial resolution. By increasing ionization efficiency and minimizing primary ion beam-induced fragmentation of analytes, ME-SIMS has proven useful for detection of numerous biorelevant species, now including peptides. We report here the first demonstration of tandem ME-SIMS for de novo sequencing of endogenous neuropeptides from tissue in situ (i.e., rat pituitary gland). The peptide ions were isolated for tandem MS analysis using a 1 Da mass isolation window, followed by collision-induced dissociation (CID) at 1.5 keV in a collision cell filled with argon gas, for confident identification of the detected peptide. Using this method, neuropeptides up to m/z 2000 were detected and sequenced from the posterior lobe of the rat pituitary gland. These results demonstrate the potential for ME-SIMS tandem MS development in bottom-up proteomics imaging at high-spatial resolution.

SUBMITTER: Ogrinc Potocnik N

PROVIDER: S-EPMC5566790 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Sequencing and Identification of Endogenous Neuropeptides with Matrix-Enhanced Secondary Ion Mass Spectrometry Tandem Mass Spectrometry.

Ogrinc Potočnik Nina N Fisher Gregory L GL Prop Arnoud A Heeren Ron M A RMA

Analytical chemistry 20170803 16

Matrix-enhanced secondary ion mass spectrometry (ME-SIMS) has overcome one of the biggest disadvantages of SIMS analysis by providing the ability to detect intact biomolecules at high spatial resolution. By increasing ionization efficiency and minimizing primary ion beam-induced fragmentation of analytes, ME-SIMS has proven useful for detection of numerous biorelevant species, now including peptides. We report here the first demonstration of tandem ME-SIMS for de novo sequencing of endogenous ne ...[more]

PMID: 28753276

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Project description:In a bottom-up shotgun approach, the proteins of a mixture are enzymatically digested, separated, and analyzed via tandem mass spectrometry. The mass spectra relating fragment ion intensities (abundance) to the mass-to-charge are used to deduce the amino acid sequence and identify the peptides and proteins. The variables that influence intensity were characterized using a multi-factorial mixed-effects model, a ten-fold cross-validation, and stepwise feature selection on 6,352,528 fragment ions from 61,543 peptide ions. Intensity was higher in fragment ions that did not have neutral mass loss relative to any mass loss or that had a +1 charge state. Peptide ions classified for proton mobility as non-mobile had lowest intensity of all mobility levels. Higher basic residue (arginine, lysine or histidine) counts in the peptide ion and low counts in the fragment ion were associated with lower fragment ion intensities. Higher counts of proline in peptide and fragment ions were associated with lower intensities. These results are consistent with the mobile proton theory. Opposite trends between peptide and fragment ion counts and intensity may be due to the different impact of factor under consideration at different stages of the MS/MS experiment or to the different distribution of observations across peptide and fragment ion levels. Presence of basic residues at all three positions next to the fragmentation site was associated with lower fragment ion intensity. The presence of proline proximal to the fragmentation site enhanced fragmentation and had the opposite trend when located distant from the site. A positive association between fragment ion intensity and presence of sulfur residues (cysteine and methionine) on the vicinity of the fragmentation site was identified. These results highlight the multi-factorial nature of fragment ion intensity and could improve the algorithms for peptide identification and the simulation in tandem mass spectrometry experiments.

Dataset Information

Sequencing and Identification of Endogenous Neuropeptides with Matrix-Enhanced Secondary Ion Mass Spectrometry Tandem Mass Spectrometry.

Publications

Sequencing and Identification of Endogenous Neuropeptides with Matrix-Enhanced Secondary Ion Mass Spectrometry Tandem Mass Spectrometry.

Similar Datasets

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