Traveling-wave ion mobility mass spectrometry analysis of isomeric modified peptides arising from chemical cross-linking

Santos, Luiz F. A.; Iglesias, Amadeu Hoshi; Pilau, Eduardo Jorge; Gomes, Alexandre F.; Gozzo, Fábio C.

doi:10.1016/j.jasms.2010.08.017

Cited by 22 publications

(15 citation statements)

References 62 publications

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“…It thus offers a complementary dimension of analysis to mass spectrometry and often provides the ability to separate isomers faster and with less effort than chromatography-based methods. [4][5][6][7][8][9][10][11][12][13] Specialized chromatographic methods that distinguish isomers frequently require a complex setup and long run times, while ion mobility filters for a set of isomers can be applied on a similar timescale as individual mass spectra.…”

Section: Introduction: Instrumentation Highlightsmentioning

confidence: 99%

Separation of biologically relevant isomers on an Orbitrap mass spectrometer using high‐resolution drift tube ion mobility and varied drift gas mixtures

Kaszycki

Rotta

Colsch

et al. 2019

Rapid Comm Mass Spectrometry

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Rationale Atmospheric pressure drift tube ion mobility is a powerful addition to the Orbitrap mass spectrometer enabling direct separation of isomers. Apart from offering high resolving power in a compact design, it also facilitates optimization of the separation gas, as shown here for a series of biologically relevant isomer pairs. Methods An Excellims MA3100 High‐Resolution Atmospheric Pressure Ion Mobility Spectrometer (HR‐IMS) was coupled to a Thermo Scientific™ Q Exactive™ Focus hybrid quadrupole–Orbitrap™ mass spectrometer, using an Excellims Directspray™ Electrospray Ionization source and a gas mixture setup to provide various drift gases (air, CO2 and mixtures). This instrument combination was used to separate isomers of eight pairs of metabolites and gangliosides, optimizing drift gas conditions for best separation of each set. Results All but one of the isomers pairs provided could be partially or fully separated by the HR‐IMS‐MS combination using ion mobility drift times. About half of the separated compounds showed significantly better analytical separation when analyzed in a mixture of CO2 and air rather than air or CO2 alone. Resolving power of up to 102 was achieved using the 10 cm atmospheric drift tube ion mobility add‐on for the Orbitrap mass spectrometer. Conclusions The present analysis demonstrates the usefulness of using atmospheric drift tube IMS on an Orbitrap mass spectrometer to characterize the isomeric composition of samples. It also highlights the potential benefits of being able to quickly optimize the drift gas composition to selectively maximize the mobility difference for isomer separation.

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Section: Introduction: Instrumentation Highlightsmentioning

confidence: 99%

Separation of biologically relevant isomers on an Orbitrap mass spectrometer using high‐resolution drift tube ion mobility and varied drift gas mixtures

Kaszycki

Rotta

Colsch

et al. 2019

Rapid Comm Mass Spectrometry

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“…The effect of modification groups on peptide structures in the gas phase has attracted some interest. 17–181920212223 For example, phosphorylation typically causes peptides to adopt structures that are more compact than non-phosphorylated peptide structures, even when differences in molecular weight are considered. 17,18 To date, IMS measurements have also been applied as a means of assessing locations of chemical cross-linking, 19 phosphorylation, 20,21 glycosylation 22 , and methylation.…”

Section: Introductionmentioning

confidence: 99%

“…17–181920212223 For example, phosphorylation typically causes peptides to adopt structures that are more compact than non-phosphorylated peptide structures, even when differences in molecular weight are considered. 17,18 To date, IMS measurements have also been applied as a means of assessing locations of chemical cross-linking, 19 phosphorylation, 20,21 glycosylation 22 , and methylation. 23 The work presented below focuses on two types of proteomics modifications found primarily on cysteine residues: carboxyamidomethylation 3,24,25 (designated as Cys Am or C Am ), and palmitoylation (designated as Cys Pal or C Pal ).…”

Section: Introductionmentioning

confidence: 99%

Intrinsic size parameters for palmitoylated and carboxyamidomethylated peptides

Dilger

Pejaver

et al. 2014

International Journal of Mass Spectrometry

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Cross sections for 61 palmitoylated peptides and 73 cysteine-unmodified peptides are determined and used together with a previously obtained tryptic peptide library to derive a set of intrinsic size parameters (ISPs) for the palmitoyl (Pal) group (1.26 ± 0.04), carboxyamidomethyl (Am) group (0.92 ± 0.04), and the 20 amino acid residues to assess the influence of Pal- and Am-modification on cysteine and other amino acid residues. These values highlight the influence of the intrinsic hydrophobic and hydrophilic nature of these modifications on the overall cross sections. As a part of this analysis, we find that ISPs derived from a database of a modifier on one amino acid residue (CysPal) can be applied on the same modification group on different amino acid residues (SerPal and TyrPal). Using these ISP values, we are able to calculate peptide cross sections to within ± 2% of experimental values for 83% of Pal-modified peptide ions and 63% of Am-modified peptide ions. We propose that modification groups should be treated as individual contribution factors, instead of treating the combination of the particular group and the amino acid residue they are on as a whole when considering their effects on the peptide ion mobility features.

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“…First, we have combined the MIX method with ion mobility spectrometry (IMS). IMS-MS has previously been used to separate positional isomers of “dead-end” cross-linker modified peptides [10], and to study complexes of a single amyloidogenic peptide [11], but not yet to study a digest of a cross-linked protein complex. The combination of IMS-MS with MIX is particularly powerful.…”

Section: Introductionmentioning

confidence: 99%

Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein–Protein Interactions by Chemical Cross-Linking

Merkley

Baker

Crowell

et al. 2013

J. Am. Soc. Mass Spectrom.

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Chemical cross-linking of proteins followed by proteolysis and mass spectrometric analysis of the resulting cross-linked peptides provides powerful insight into the quaternary structure of protein complexes. Mixed-isotope cross-linking (a method for distinguishing intermolecular cross-links) was coupled with liquid chromatography and ion mobility separations and mass spectrometry (LC-IMS-MS) to provide an additional separation dimension to the traditional cross-linking approach. This method produced multiplet m/z peaks that are aligned in the IMS drift time dimension and serve as signatures of intermolecular cross-linked peptides. We developed an informatics tool to use the amino acid sequence information inherent in the multiplet spacing for accurate identification of the cross-linked peptides. Because of the separation of peptides and cross-linked peptides in drift time, our LC-IMS-MS approach was able to confidently detect more intermolecular cross-linked peptides than LC-MS alone.

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Traveling-wave ion mobility mass spectrometry analysis of isomeric modified peptides arising from chemical cross-linking

Cited by 22 publications

References 62 publications

Separation of biologically relevant isomers on an Orbitrap mass spectrometer using high‐resolution drift tube ion mobility and varied drift gas mixtures

Separation of biologically relevant isomers on an Orbitrap mass spectrometer using high‐resolution drift tube ion mobility and varied drift gas mixtures

Intrinsic size parameters for palmitoylated and carboxyamidomethylated peptides

Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein–Protein Interactions by Chemical Cross-Linking

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