Charge derivatization by 4‐sulfophenyl isothiocyanate enhances peptide sequencing by post‐source decay matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry

Marekov, Lyuben N.; Steinert, Peter M.

doi:10.1002/jms.448

Cited by 64 publications

(79 citation statements)

References 29 publications

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“…The B30-generated muropeptides within peak A and B products from each strain were labeled with SPITC, which is an N-terminal label that has been used previously for peptide analysis (8,20) and for peptidoglycan analysis (12). The labeled fragments were analyzed using MALDI-tandem TOF collision-induced dissociation MS in the negative-ion mode.…”

Section: Resultsmentioning

confidence: 99%

Zif, the Zoocin A Immunity Factor, Is a FemABX-Like Immunity Protein with a Novel Mode of Action

Gargis

Heath

et al. 2009

Appl Environ Microbiol

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Producer cell immunity to the streptococcolytic enzyme zoocin A, which is a D-alanyl-L-alanine endopeptidase, is due to Zif, the zoocin A immunity factor. Zif has high degrees of similarity to MurM and MurN (members of the FemABX family of proteins), which are responsible for the addition of amino acids to cross bridges during peptidoglycan synthesis in streptococci. In this study, purified peptidoglycans from strains with and without zif were compared to determine how Zif modifies the peptidoglycan layer to cause resistance to zoocin A. The peptidoglycan from each strain was hydrolyzed using the streptococcolytic phage lysin B30, and the resulting muropeptides were separated by reverse-phase high-pressure liquid chromatography, labeled with 4-sulfophenyl isothiocyanate, and analyzed by tandem mass spectrometry in the negative-ion mode. It was determined that Zif alters the peptidoglycan by increasing the proportion of cross bridges containing three L-alanines instead of two. This modification decreased binding of the recombinant target recognition domain of zoocin A to peptidoglycan. Zif-modified peptidoglycan also was less susceptible to hydrolysis by the recombinant catalytic domain of zoocin A. Thus, Zif is a novel FemABX-like immunity factor because it provides resistance to a bacteriolytic endopeptidase by lengthening the peptidoglycan cross bridge rather than by causing an amino acid substitution.

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Section: Resultsmentioning

confidence: 99%

Zif, the Zoocin A Immunity Factor, Is a FemABX-Like Immunity Protein with a Novel Mode of Action

Gargis

Heath

et al. 2009

Appl Environ Microbiol

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“…To reduce misassignments, approaches have been suggested based on improved mass accuracy or precision (14,15), combining complementary fragmentation data (14,16,17) or the simplification of fragmentation spectra by using chemical derivatization to manipulate peptide behavior (18). Recently, we introduced a biochemical approach to simplify fragment spectra based on the protease Lys-N (19), which has enzymatic cleavage specificity for the N-terminal side of lysine residues.…”

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confidence: 99%

Database independent proteomics analysis of the ostrich and human proteome

Altelaar

Navarro²,

Boekhorst³

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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Mass spectrometry (MS)-based proteome analysis relies heavily on the presence of complete protein databases. Such a strategy is extremely powerful, albeit not adequate in the analysis of unpredicted postgenome events, such as posttranslational modifications, which exponentially increase the search space. Therefore, it is of interest to explore "database-free" approaches. Here, we sampled the ostrich and human proteomes with a method facilitating de novo sequencing, utilizing the protease Lys-N in combination with electron transfer dissociation. By implementing several validation steps, including the combined use of collision-induced dissociation/ electron transfer dissociation data and a cross-validation with conventional database search strategies, we identified approximately 2,500 unique de novo peptide sequences from the ostrich sample with over 900 peptides generating full backbone sequence coverage. This dataset allowed the appropriate positioning of ostrich in the evolutionary tree. The described database-free sequencing approach is generically applicable and has great potential in important proteomics applications such as in the analysis of variable parts of endogenous antibodies or proteins modified by a plethora of complex posttranslational modifications.

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“…Later, the method was refined by using a water-soluble, sulfopropionic acid NHS-ester [18], a reagent that recently became available in a commercial kit (Ettan CAF MALDI sequencing kit, Amersham Biosciences, Uppsala, Sweden) [19]. Very recently, a similar derivatization procedure was reported using 4-sulfophenyl isothiocyanate as the derivatization reagent [20,21].…”

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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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Charge derivatization by 4‐sulfophenyl isothiocyanate enhances peptide sequencing by post‐source decay matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry

Cited by 64 publications

References 29 publications

Zif, the Zoocin A Immunity Factor, Is a FemABX-Like Immunity Protein with a Novel Mode of Action

Zif, the Zoocin A Immunity Factor, Is a FemABX-Like Immunity Protein with a Novel Mode of Action

Database independent proteomics analysis of the ostrich and human proteome

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

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