Towards liquid chromatography time-scale peptide sequencing and characterization of post-translational modifications in the negative-ion mode using electron detachment dissociation tandem mass spectrometry

Kjeldsen, Frank; Hørning, Ole; Jensen, Søren Skov; Giessing, Anders; Jensen, O.N.

doi:10.1016/j.jasms.2008.04.031

Cited by 26 publications

(45 citation statements)

References 38 publications

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“…In electron detachment dissociation (EDD) [23][24][25][26][27] the fragmentation of deprotonated peptides predominantly leads to cleavage of the peptide about the C ␣ -C backbone giving a • and x fragment ions, along with lower intensity c and y ions [28]. The 0-1 eV ionization afforded by PERCI bears some similarities as well as some notable differences to EDD, specifically in regards to fragmentation about the amide linkage.…”

Section: Comparison To Other Low Energy Ionization Processes: Edd Andmentioning

confidence: 99%

Low energy photoelectron resonance capture ionization aerosol mass spectrometry of small peptides with cysteine residues: Cys-Gly, γ-Glu-Cys, and glutathione (γ-Glu-Cys-Gly)

Geddes¹,

Zahardis²,

Eisenhauer³

et al. 2009

International Journal of Mass Spectrometry

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Section: Comparison To Other Low Energy Ionization Processes: Edd Andmentioning

confidence: 99%

Low energy photoelectron resonance capture ionization aerosol mass spectrometry of small peptides with cysteine residues: Cys-Gly, γ-Glu-Cys, and glutathione (γ-Glu-Cys-Gly)

Geddes¹,

Zahardis²,

Eisenhauer³

et al. 2009

International Journal of Mass Spectrometry

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“…Because of the known inadequacy of CID and the lack of feasibility of electron-capture dissociation and ETD for peptide anion sequencing, several alternative MS n methods have been developed recently. Electron detachment dissociation using highenergy electrons to induce backbone cleavages was developed for peptide anions (14,15). Another new technique, negative ETD, entails reactions of radical cation reagents with peptide anions to promote electron transfer from the peptide to the reagent that causes radical-directed dissociation (16,17).…”

mentioning

confidence: 99%

High-throughput Database Search and Large-scale Negative Polarity Liquid Chromatography–Tandem Mass Spectrometry with Ultraviolet Photodissociation for Complex Proteomic Samples

Madsen

Robinson

et al. 2013

Molecular & Cellular Proteomics

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The use of ultraviolet photodissociation (UVPD) for the activation and dissociation of peptide anions is evaluated for broader coverage of the proteome. To facilitate interpretation and assignment of the resulting UVPD mass spectra of peptide anions, the MassMatrix database search algorithm was modified to allow automated analysis of negative polarity MS/MS spectra. The new UVPD algorithms were developed based on the MassMatrix database search engine by adding specific fragmentation pathways for UVPD. The new UVPD fragmentation pathways in MassMatrix were rigorously and statistically optimized using two large data sets with high mass accuracy and high mass resolution for both MS 1 and MS 2 data acquired on an Orbitrap mass spectrometer for complex Halobacterium and HeLa proteome samples. Negative mode UVPD led to the identification of 3663 and 2350 peptides for the Halo and HeLa tryptic digests, respectively, corresponding to 655 and 645 peptides that were unique when compared with electron transfer dissociation (ETD), higher energy collision-induced dissociation, and collision-induced dissociation results for the same digests analyzed in the positive mode. In sum, 805 and 619 proteins were identified via UVPD for the Halobacterium and HeLa samples, respectively, with 49 and 50 unique proteins identified in contrast to the more conventional MS/MS methods. The algorithm also features automated charge determination for low mass accuracy data, precursor filtering (including intact charge-reduced peaks), and the ability to combine both positive and negative MS/MS spectra into a single search, and it is freely open to the public. The accuracy and specificity of the MassMatrix UVPD search algorithm was also assessed for low resolution, low mass accuracy data on a linear ion trap. Analysis of a known mixture of three mitogen-activated kinases yielded similar sequence coverage percentages for UVPD of peptide anions versus conventional collisioninduced dissociation of peptide cations, and when these methods were combined into a single search, an increase of up to 13% sequence coverage was observed for the kinases. The ability to sequence peptide anions and cations in alternating scans in the same chromatographic run was also demonstrated. Because ETD has a significant bias toward identifying highly basic peptides, negative UVPD was used to improve the identification of the more acidic peptides in conjunction with positive ETD for the more basic species. In this case, tryptic peptides from the cytosolic section of HeLa cells were analyzed by polarity switching nanoLC-MS/MS utilizing ETD for cation sequencing and UVPD for anion sequencing. Relative to searching using ETD alone, positive/negative polarity switching significantly improved sequence coverages across identified proteins, resulting in a 33% increase in unique peptide identifications and more than twice the number of peptide spectral matches. Molecular & Cellular Proteomics 12: 10.1074/mcp.O113.028258, 2604-2614, 2013.The advent of new high-performance tandem mas...

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“…An alternative method that was reported to actually give higher yields of sequenceinformative fragment ions from more highly and negatively charged precursors [28,29] is electron detachment dissociation (EDD), which was introduced by Zubarev and coworkers as a new technique for dissociation of peptide anions [30]. In EDD, bombardment of multiply deprotonated peptides [31][32][33], oligonucleotides [29, 34 -38], or oligosaccharides [28, 39 -43] with Ͼ10 eV electrons results in electron detachment, producing (M Ϫ nH) (n-1)-• radical ions that can undergo backbone dissociation [37,38]. To date, only one study on EDD of RNA (6 nt) has been published [44], with only one of the sequences (GCAUAC) allowing for unambiguous assignment of fragment ion identity (in 3=-and 5=-OH terminated homonucleotides, e.g., A 6 , the following ions cannot be distinguished from each other based on their mass values: a from z, b from y, c from x, and d from w).…”

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confidence: 99%

Top-down mass spectrometry for sequencing of larger (up to 61 nt) RNA by CAD and EDD

Taucher

Breuker

2010

J. Am. Soc. Mass Spectrom.

109

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We have studied the effect of solution additives on hydrolysis and charge state distribution in ESI MS of RNA. Lower and higher charge state ions can be electrosprayed from solutions containing 25 mM piperidine/25 mM imidazole and 1% vol. triethylamine, respectively, with base-catalyzed hydrolysis rates that are sufficiently slow to perform MS/MS experiments. These lower and higher charge state ions are suitable as precursors for CAD and EDD, respectively. We demonstrate nearly complete sequence coverage for 61 nt RNA dissociated by CAD, and 34 nt RNA dissociated by EDD, and suggest a mechanism for backbone fragmentation in EDD of RNA. (J Am Soc Mass Spectrom 2010, 21, 918 -929) © 2010 American Society for Mass Spectrometry T he "top-down" approach is increasingly being applied in mass spectrometry (MS) studies of proteins [1][2][3][4][5], using mostly collisionally activated dissociation (CAD) [6 -8], electron capture dissociation (ECD) [9 -12], or electron-transfer dissociation (ETD) [13] for generation of sequence-informative fragment ions from backbone cleavage in multiply protonated precursor ions. First examples of top-down mass spectrometry of smaller (up to 25 nt) multiply deprotonated desoxyribonucleic acids (DNA) were reported in the early 1990s [14 -16], and the concept was soon extended to larger (up to 108 nt) DNA [17].For ribonucleic acids (RNAs), the development and application of mass spectrometry-based methodology has been much slower than for DNA [18], possibly because the significance of RNA in regulation of gene expression was recognized only recently [19]. Topdown MS has been applied to study RNA modified by structural probes [20], for characterization of conserved domains of the HIV-1 packaging signal RNA [21], for investigating aptamer/ligand complexes [22], and binding of antibiotics to ribosomal RNA subdomains [23]. However, sequencing by top-down mass spectrometry of RNA Ͼ 20 nt has been demonstrated only recently, as discussed below.Collisionally activated dissociation of multiply deprotonated RNA from electrospray ionization (ESI) [24] has lately provided full sequence coverage for small interfering RNA (siRNA) [25] and a riboswitch aptamer domain sequence [26] consisting of 21 and 34 nucleotides (nt), respectively. Mass spectral quality, particularly with regard to undesired secondary fragmentation, was shown to critically depend on precursor ion charge [25,27] and collisional cooling of primary fragments [26]. Our rationale for the decrease in secondary fragmentation was that reduced net charge and collisional cooling minimize the internal energy of fragment ions from primary backbone cleavage, which makes them less prone to secondary fragmentation [26]. In our study of 34 nt RNA, we used ions of relatively low net charge, (M Ϫ 7H) 7Ϫ , which were electrosprayed from acidified solutions [26].However, mass spectrometer performance generally decreases with increasing mass-to-charge ratio, i.e., lower ion charge. An alternative method that was reported to actually give higher yields...

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Towards liquid chromatography time-scale peptide sequencing and characterization of post-translational modifications in the negative-ion mode using electron detachment dissociation tandem mass spectrometry

Cited by 26 publications

References 38 publications

Low energy photoelectron resonance capture ionization aerosol mass spectrometry of small peptides with cysteine residues: Cys-Gly, γ-Glu-Cys, and glutathione (γ-Glu-Cys-Gly)

Low energy photoelectron resonance capture ionization aerosol mass spectrometry of small peptides with cysteine residues: Cys-Gly, γ-Glu-Cys, and glutathione (γ-Glu-Cys-Gly)

High-throughput Database Search and Large-scale Negative Polarity Liquid Chromatography–Tandem Mass Spectrometry with Ultraviolet Photodissociation for Complex Proteomic Samples

Top-down mass spectrometry for sequencing of larger (up to 61 nt) RNA by CAD and EDD

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