Fragmentation of amidinated peptide ions

Beardsley, Richard L.; Reilly, James P.

doi:10.1016/j.jasms.2003.10.007

Cited by 27 publications

(54 citation statements)

References 36 publications

(69 reference statements)

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“…The samples were allowed to air-dry at room temperature and were then inserted into the mass spectrometer and subjected to MALDI-MS analysis. Prior to analysis, the mass spectrometer was externally calibrated with a mixture of Angiotensin I, Glu-fibrino-peptide B, ACTH (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17), and ACTH . For MS/MS experiments, the instrument was externally calibrated with fragments of Glu-fibrino-peptide.…”

Section: Matrix-assisted Laser Desorption/ionization Tof/ Tof Mass Spmentioning

confidence: 99%

“…This modification induces selective dissociation of Nterminal peptide bonds in gas phase fragmentation experiments, enabling the facile identification of N-terminal residues. More recently, Beardsley and Reilly [16] illustrated that the use of the N-terminal residue of a peptide as a search constraint reduced the number of candidates extracted from a sequence database and improved database-matching techniques by reducing the occurrence of false-positive assignments. In their study, free amino groups were selectively modified with an amidine label, a form of labeling that has also been employed as a tag in comparative proteomics [17].…”

mentioning

confidence: 99%

“…CID analysis of singly charged acetamidinated peptides indicated a predominance of b-NH 3 fragment ions in the fragmentation spectra. While this unique type of fragmentation may facilitate de novo sequencing, the authors noted that not every peptide generated continuous (b-NH 3 )-ion series [16].…”

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confidence: 99%

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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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Section: Matrix-assisted Laser Desorption/ionization Tof/ Tof Mass Spmentioning

confidence: 99%

mentioning

confidence: 99%

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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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“…Bergquist and co-workers [114] obtained very large deviations from the expected ratios when using LC-FTICR-MS. In a recent paper, the effect of this amidination procedure on peptide fragmentation patterns was also examined [115].…”

Section: Tagging Methods Specific For Other Amino Acidsmentioning

confidence: 99%

Current chemical tagging strategies for proteome analysis by mass spectrometry

Leitner¹,

Lindner²

2004

Journal of Chromatography B

107

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“…Beardsley and Reilly and coworkers reported that peptide bond of the Nterminal amino acid of an amidinated peptide is preferentially dissociated in the MS/MS process, and, therefore, b 1 and y n-1 ions are the most abundant among fragment ions [35,36]. In the case of a picolinamidinated tryptic peptide like AENDVGDK, where the C-terminal lysine residue is picolinamidinated, all of the y-series ions should have a picolinamidination tag at the C-terminal and thus would yield a strong signal.…”

Section: Sequencing Picolinamidinated Tryptic Peptide By Ms/msmentioning

confidence: 99%

Picolinamidination of phosphopeptides for MALDI-TOF-TOF mass spectrometric sequencing with enhanced sensitivity

Kim

Cui

Kim

2009

J. Am. Soc. Mass Spectrom.

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Two orders of magnitude matrix-assisted laser desorption/ionization (MALDI) signal enhancement of phosphopeptides has been achieved by picolinamidination of N-terminal amine group and -amine group of lysine residues. Due to the presence of picolinamidination tag at the N-terminal amine of peptides, MS/MS spectra with a strong b-ion series was obtained, which greatly facilitated sequencing and identification of the phosphorylation site. Phosphorylation site of a phosphopeptide could be identified from MALDI TOF/TOF spectrum obtained from a tryptic or a chymotryptic phosphopeptide, which was not even detected in the positive ion mode, without signal enhancement by picolinamidination, due to the negative charge of the phosphate group in the presence of other peptides. (J Am Soc Mass

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Fragmentation of amidinated peptide ions

Cited by 27 publications

References 36 publications

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

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

Current chemical tagging strategies for proteome analysis by mass spectrometry

Picolinamidination of phosphopeptides for MALDI-TOF-TOF mass spectrometric sequencing with enhanced sensitivity

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