Low Energy Peptide Fragmentations in an ESI-Q-Tof Type Mass Spectrometer

Mouls, Laetitia; Aubagnac, Jean‐Louis; Martinez, Jean; Enjalbal, Christine

doi:10.1021/pr060574o

Cited by 63 publications

(75 citation statements)

References 53 publications

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“…The mechanism of deletion of the internal lysine residue has been investigated by multi stage CID, chemical, and isotopic modification of the peptides and energy resolved CID techniques. Our results suggest that this selective deletion of the lysine residue from the interior of the peptide may not follow the sequence scrambling fragmentation pathway as reported earlier [21,[27][28][29][30][31][32]. A novel gas-phase peptide ion degradation pathway has been shown to be responsible for the specific loss of the internal lysine residues in the peptide.…”

Section: Introductionsupporting

confidence: 53%

“…There are a few such nondirect sequence ions have been identified recently, such as scrambled fragments of the b/a type ions resulting in the loss of an amino acid residue from the interior of the peptide chain [21,26]. The first step of such loss of an internal amino acid by sequence scrambling fragmentation pathway was proposed [21,[27][28][29][30][31][32] to involve a nucleophilic attack by N-terminal α-NH 2 group on the acylium carbocation of the b-ion (a primary fragment) forming a protonated cyclicpeptide intermediate (CPI). This CPI subsequently undergoes ring opening at different amide bonds producing sequence scrambled linear b-ions.…”

Section: Introductionmentioning

confidence: 99%

“…This CPI subsequently undergoes ring opening at different amide bonds producing sequence scrambled linear b-ions. These scrambled linear b-ions undergo further dissociation by conventional fragmentation pathway to produce corresponding daughter ions that are not related to the original sequence of the peptide [21,[27][28][29][30][31][32]. Thus such ions, called the nondirect sequence ions, would be related to all the possible scrambled sequences of the peptide, and therefore would loss the memory of the original sequence.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Selective Deletion of the Internal Lysine Residue from the Peptide Sequence by Collisional Activation

Banerjee

Mazumdar

2012

J. Am. Soc. Mass Spectrom.

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The gas-phase peptide ion fragmentation chemistry is always the center of attraction in proteomics to analyze the amino acid sequence of peptides and proteins. In this work, we describe the formation of an anomalous fragment ion, which corresponds to the selective deletion of the internal lysine residue from a series of lysine containing peptides upon collisional activation in the ion trap. We detected several water-loss fragment ions and the maximum number of water molecules lost from a particular fragment ion was equal to the number of lysine residues in that fragment. As a consequence of this water-loss phenomenon, internal lysine residues were found to be deleted from the peptide ion. The N,N-dimethylation of all the amine functional groups of the peptide stopped the internal lysine deletion reaction, but selective Nterminal α-amino acetylation had no effect on this process indicating involvement of the side chains of the lysine residues. The detailed mechanism of the lysine deletion was investigated by multistage CID of the modified and unmodified peptides, by isotope labeling and by energy resolved CID studies. The results suggest that the lysine deletion might occur through a unimolecular multistep mechanism involving a seven-membered cyclic imine intermediate formed by the loss of water from a lysine residue in the protonated peptide. This intermediate subsequently undergoes degradation reaction to deplete the interior imine ring from the peptide backbone leading to the deletion of an internal lysine residue.

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Section: Introductionsupporting

confidence: 53%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Selective Deletion of the Internal Lysine Residue from the Peptide Sequence by Collisional Activation

Banerjee

Mazumdar

2012

J. Am. Soc. Mass Spectrom.

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“…27,28 The MS-Simulator method proposed in this study is largely based on the widely accepted mobile proton model for peptide fragmentation, 29 which is very briefly reviewed in the following. A better review of the mobile proton model can be found in refs 22 and 30.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

MS-Simulator: Predicting Y-Ion Intensities for Peptides with Two Charges Based on the Intensity Ratio of Neighboring Ions

Sun

Yang

et al. 2012

J. Proteome Res.

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For the identification of peptides with tandem mass spectrometry (MS/MS), many software tools rely on the comparison between an experimental spectrum and a theoretically predicted spectrum. Consequently, the accurate prediction of the theoretical spectrum from a peptide sequence can potentially improve the peptide identification performance and is an important problem for mass spectrometry based proteomics. In this study a new approach, called MS-Simulator, is presented for predicting the y-ion intensities in the spectrum of a given peptide. The new approach focuses on the accurate prediction of the relative intensity ratio between every two adjacent y-ions. The theoretical spectrum can then be derived from these ratios. The prediction of a ratio is a closed-form equation that involves up to five consecutive amino acids nearby the two y-ions and the two peptide termini. Compared with another existing spectrum prediction tool MassAnalyzer, the new approach not only simplifies the computation, but also improves the prediction accuracy.

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“…Besides, peptide chains terminated by a C-terminal carboxylic acid as well as a C-terminal amide were also prepared to mimic the proteolysis of naturally occurring amidated proteins [25,26].…”

Section: Studied Peptidesmentioning

confidence: 99%

Laser desorption/ionization mass spectrometry on porous silica and alumina for peptide mass fingerprinting

Shenar

Martinez

Enjalbal

2008

J. Am. Soc. Mass Spectrom.

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We investigated a variant of desorption/ionization on porous silicon (DIOS) mass spectrometry utilizing an aqueous suspension of either porous silica gel or porous alumina (pore size of 60 and 90 Å, respectively). Laser desorption/ionization (LDI) from samples directly deposited on a stainless steel surface without any inorganic substrates was also achieved. Synthetic peptides designed to cover large sequence diversity constituted our model compounds. Sample preparation, including material conditioning, peptide solubilization, and deposition protocol onto standard matrix-assisted laser desorption/ionization (MALDI) probe, as well as ionization source tuning were optimized to perform sensitive reproducible LDI analyses. The addition of either a cationizing agent or an alkali metal scavenger to the sample suspension allowed modification of the ionization output. Comparing hydrophilic silica gel to hydrophobic reversed-phase silica gel as well as increasing material pore size provided further insights into desorption/ionization processes. Furthermore, mixtures of peptides were analyzed to probe the spectral suppression phenomenon when no interfering organic matrix was present. The results gathered from synthetic peptide cocktails indicated that LDI mass spectrometry on silica gel or alumina constitutes a promising complementary method to MALDI in proteomics for peptide mass fingerprinting. [19]. These LDI methods, sometimes referred to as "matrix-free", produce mass spectra that exhibit less matrix ions in the low mass range compared with the chemical noise generated by the organic matrices used in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. Such chemical noise that usually pollutes the low mass range of MALDI mass spectra and that may complicate the detection of small molecules is less pronounced in the DIOS mass spectra.Nevertheless, the drawback of such an approach is in the preparation of the silicon material. To present adequate physical properties [20], silicon surfaces are conditioned via a galvanostatic etching procedure from Si wafer to produce pores with nanometer diameters. Commercially available ready-to-use DIOS-chips can also be mounted on modified MALDI plates [20]. Otherwise, silicon powders (5 to 50 nm particle size) were investigated as a substitute to DIOS chips to make the overall sample preparation simpler and safer [18]. Provided that the appropriate powder preparation was performed (including particle etching by HF, oxidation by HNO 3 , and derivatization of the generated SiOH groups), such silicon nanopowder method was found to exhibit the same characteristics as DIOS mass spectrometry.Porous silicon is a material that presents (1) a large active surface and (2) a strong absorbance in the UV range. Such a form of silicon was thus found particularly suitable for LDI mass spectrometry with irradiation at 337 nm, the pore size and the surface chemical nature being the most important parameters as stated by Siuzdak and coworkers in their early publications on DIOS [20...

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Low Energy Peptide Fragmentations in an ESI-Q-Tof Type Mass Spectrometer

Cited by 63 publications

References 53 publications

Selective Deletion of the Internal Lysine Residue from the Peptide Sequence by Collisional Activation

Selective Deletion of the Internal Lysine Residue from the Peptide Sequence by Collisional Activation

MS-Simulator: Predicting Y-Ion Intensities for Peptides with Two Charges Based on the Intensity Ratio of Neighboring Ions

Laser desorption/ionization mass spectrometry on porous silica and alumina for peptide mass fingerprinting

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