Enhancing the intensities of lysine-terminated tryptic peptide ions in matrix-assisted laser desorption/ionization mass spectrometry

Beardsley, Richard L.; Karty, Jonathan A.; Reilly, James P.

doi:10.1002/1097-0231(20001215)14:23<2147::aid-rcm145>3.0.co;2-m

Cited by 110 publications

(124 citation statements)

References 15 publications

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“…Therefore, in early study, the method by converting lysine into homoarginine (guanidination derivatization) was established to increase the gas-phase basicity of lysine-containing peptides [14,15] . Hale et al [16] applied O-methylisourea to converting the İ-amino group of lysine into homoarginine and obtained a higher detection sensitivity in detecting peptides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS).…”

Section: Derivatization Of Amino Groupsupporting

confidence: 80%

Recent Advancement of Chemical Derivatization and Its Applications to High Sensitive Analysis of Peptide in Mass Spectrometry

Qiao

Rui

Zhang

et al. 2012

Chinese Journal of Analytical Chemistry

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Section: Derivatization Of Amino Groupsupporting

confidence: 80%

Recent Advancement of Chemical Derivatization and Its Applications to High Sensitive Analysis of Peptide in Mass Spectrometry

Qiao

Rui

Zhang

et al. 2012

Chinese Journal of Analytical Chemistry

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“…The other side-chain cleavage fragments are also observed from the free radical-induced decomposition of the lithium adduct of the lysine modified peptide 2a. It is of note that the fragment 2h ([a 5 ϩ Li] ϩ , m/z 463) may be derived from a radical that migrates along the peptide backbone from the radical on the ␣-carbon of the lysine side chain [16]. Fragments 2e, 2i, and 2j have also been observed in the decomposition of Li adduct of 1a (Scheme 2).…”

Section: Cid Experiments Of Modified Peptides At Lysine Sites Using Ementioning

confidence: 99%

“…The sequencing is often accomplished using tandem mass spectrometry (MS/MS) by collision-induced dissociation (CID) or electron capture dissociation (ECD) of protonated species [3,4]. Chemical modification of peptides or proteins has also provided strategies that are helpful in assignment of peptide sequence, enhancement of the MS sensitivity [5], and, importantly, in protein quantification [6]. Even though database searches for protein identification are primarily based on b-and y-ions observed in MS/MS spectra, complex fragmentation patterns can result from the ECD process and improve the sequence coverage in protein identification [7,8].…”

mentioning

confidence: 99%

Free radical-induced site-specific peptide cleavage in the gas phase: Low-energy collision-induced dissociation in ESI- and MALDI mass spectrometry

Yin

Chacon

Porter

et al. 2007

J. Am. Soc. Mass Spectrom.

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Protein identification is routinely accomplished by peptide sequencing using mass spectrometry (MS) after enzymatic digestion. Site-specific chemical modification may improve peptide ionization efficiency or sequence coverage in mass spectrometry. We report herein that amino group of lysine residue in peptides can be selectively modified by reaction with a peroxycarbonate and the resulting lysine peroxycarbamates undergo homolytic fragmentation under conditions of low-energy collision-induced dissociation (CID) in electrospray ionization (ESI) and matrix-assisted laser desorption and ionization (MALDI) MS. Selective modification of lysine residue in peptides by our strategy can induce specific peptide cleavage at or near the lysine site. Studies using deuterated analogues of modified lysine indicate that fragmentation of the modified peptides involves apparent free-radical processes that lead to peptide chain fragmentation and side-chain loss. The formation of a-, c-, or z-types of ions in MS is reminiscent of the proposed free-radical mechanisms in low-energy electron capture dissociation (ECD) processes that may have better sequence coverage than that of the conventional CID method. This site-specific cleavage of peptides by free radical-promoted processes is feasible and such strategies may aid the protein sequencing analysis and have potential applications in top-down proteomics. . The sequencing is often accomplished using tandem mass spectrometry (MS/MS) by collision-induced dissociation (CID) or electron capture dissociation (ECD) of protonated species [3,4]. Chemical modification of peptides or proteins has also provided strategies that are helpful in assignment of peptide sequence, enhancement of the MS sensitivity [5], and, importantly, in protein quantification [6]. Even though database searches for protein identification are primarily based on b-and y-ions observed in MS/MS spectra, complex fragmentation patterns can result from the ECD process and improve the sequence coverage in protein identification [7,8]. The typical a-, c-, and z-fragments in ECD are postulated to arise from free-radical intermediates. The nomenclature of the fragments as proposed by Roestorff is shown in Scheme 1 [9].In a recent communication we reported a method to generate radicals in a site-specific manner on peptides in the gas phase, after modification of lysine residues as peroxycarbamates [10]. Fragmentation appears to result from initial free-radical dissociation of the peroxide bond followed by decarboxylation. The chemistry can

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“…The guanidination, leading to C-terminal lysines being converted into homoarginines (ϩ42 Da), can be selectively and quantitatively performed with O-methylisourea at high pH and does not affect the peptide amino terminus or other side groups. The resulting homoarginine has an even higher pKa than arginine, and it has previously been shown that a rise of the basicity of lysines increases their relative abundances in MALDI mass spectra by enabling enhanced charge retention [27,28]. Furthermore, it allows unambiguous differentiation of Lys (128.18 Da) and Gln (128.13 Da) by mass spectrometry.…”

Section: De Novo Sequence Analysismentioning

confidence: 99%

A case study of de novo sequence analysis of N-sulfonated peptides by MALDI TOF/TOF mass spectrometry

Samyn

Debyser

Sergeant

et al. 2004

J. Am. Soc. Mass Spectrom.

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The simplicity and sensitivity of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry have increased its application in recent years. The most common method of "peptide mass fingerprint" analysis often does not provide robust identification. Additional sequence information, obtained by post-source decay or collision induced dissociation, provides additional constraints for database searches. However, de novo sequencing by mass spectrometry is not yet common practice, most likely because of the difficulties associated with the interpretation of high and low energy CID spectra. Success with this type of sequencing requires full sequence coverage and demands better quality spectra than those typically used for data base searching. In this report we show that full-length de novo sequencing is possible using MALDI TOF/TOF analysis. The interpretation of MS/MS data is facilitated by N-terminal sulfonation after protection of lysine side chains (Keough et al., Proc. Natl. Acad. Sci. U.S. A. 1999, 96, 7131-7136). Reliable de novo sequence analysis has been obtained using sub-picomol quantities of peptides and peptide sequences of up to 16 amino acid residues in length have been determined. The simple, predictable fragmentation pattern allows routine de novo interpretation, either manually or using software. Characterization of the complete primary structure of a peptide is often hindered because of differences in fragmentation efficiencies and in specific fragmentation patterns for different peptides. These differences are controlled by various structural parameters including the nature of the residues present. The influence of the presence of internal Pro, acidic and basic residues on the TOF/TOF fragmentation pattern will be discussed, both for underivatized and guanidinated/sulfonated peptides. (J Am Soc Mass Spectrom 2004, 15, 1838 -1852) © 2004 American Society for Mass Spectrometry P rotein identification protocols in proteomics currently rely on the peptide mass fingerprinting (PMF) technique in which a (mostly gel-purified) protein is digested with an endoprotease of known cleavage specificity. The masses of the resulting peptides are measured by mass spectrometry, usually matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF), and matched to peptide masses that have been generated theoretically from proteins in databases. Notwithstanding the fact that the PMF approach is useful for identifying proteins in simple mixtures (e.g., 2D-PAGE gel spots), the identification of proteins in more complex mixtures often requires partial peptide sequence data obtained by tandem mass spectrometry (MS/MS) methods. If accurate genome sequence information is available, database search algorithms can be used in conjunction with MS/MS to readily identify proteins. For proteins not contained within sequence databases, it is necessary to determine partial or complete amino acid sequences using either manual or automated de novo peptide sequence analysis methods. This genera...

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Enhancing the intensities of lysine-terminated tryptic peptide ions in matrix-assisted laser desorption/ionization mass spectrometry

Cited by 110 publications

References 15 publications

Recent Advancement of Chemical Derivatization and Its Applications to High Sensitive Analysis of Peptide in Mass Spectrometry

Recent Advancement of Chemical Derivatization and Its Applications to High Sensitive Analysis of Peptide in Mass Spectrometry

Free radical-induced site-specific peptide cleavage in the gas phase: Low-energy collision-induced dissociation in ESI- and MALDI mass spectrometry

A case study of de novo sequence analysis of N-sulfonated peptides by MALDI TOF/TOF mass spectrometry

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