Derivatization procedures to facilitatede novo sequencing of lysine-terminated tryptic peptides using postsource decay matrix-assisted laser desorption/ionization mass spectrometry

Keough, T.; Lacey, Martin P.; Youngquist, R.S.

doi:10.1002/1097-0231(20001230)14:24<2348::aid-rcm175>3.0.co;2-8

Cited by 137 publications

(159 citation statements)

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“…It is known that the introduction of a strong acidic group at the N-terminus of tryptic peptides facilitates protonation of backbone amide bonds, leading to extensive structure-specific fragmentation under PSD MALDI and electrospray MS/MS conditions [11,12,26]. In the present study, the effect of the N-terminal sulfonation on the CID TOF/TOF fragmentation pattern was investigated.…”

Section: De Novo Sequence Analysismentioning

confidence: 99%

“…The formation of such derivatives was previously shown to be undesirable because they exhibit poor sensitivity in the positive-ion mode and relatively poor fragmentation under negative-ion analysis conditions. Negative-ion PSD spectra of several Lys-containing disulfonate derivatives showed both low-product ion yields and complex fragmentation patterns containing b-and y-type ions linked to the sulfonate group [26]. Therefore, this approach requires a preliminary modification of the -amino group of lysine residues.…”

Section: De Novo Sequence Analysismentioning

confidence: 99%

“…During PSD experiments with derivatized peptides, Keough et al observed enhanced fragmentation at Pro residues and a reduced abundance in fragmentation at the C-terminal side of Pro [26]. Therefore, a Pro residue near the N-terminus of a peptide can limit the amount of sequence information that can be derived from the peptide.…”

Section: Fragmentation Of Peptides Containing Proline Residuesmentioning

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: De Novo Sequence Analysismentioning

confidence: 99%

Section: De Novo Sequence Analysismentioning

confidence: 99%

Section: Fragmentation Of Peptides Containing Proline Residuesmentioning

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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“…MALDI-MS, ESI-MS, and ESI-MS/MS methods are now widely employed for the recognition and location of amino acid mutations in native and recombinant proteins and peptides. Recently, some N-terminal peptide derivatization procedures have been developed for subsequent MALDI analysis for the sequence determination of peptides obtained from the protein by enzymatic tryptic digestion (Keough, Lacey, & Youngquist, 2000). Those sulfonation reactions convert lysine-terminated tryptic peptides into modified peptides that are suitable for de novo sequencing by postsource decay matrix-assisted laser desorption/ionization (MALDI) mass spectrometry.…”

Section: A Proteins and Peptidesmentioning

confidence: 99%

“…In that case, the N-terminal amino acid series is mainly observed and the peptide sequence can be obtained from the N-terminus by the determination of the mass difference values among the fragment peaks. For instance, Figure 4A-C (Keough, Lacey, & Youngquist, 2000) shows the spectrum of the VGGY-GYGAK peptide obtained with the PSD technique with and without the derivatization approach. In that case, the fragmentation of the peptides without derivatization (Fig.…”

Section: A Proteins and Peptidesmentioning

confidence: 99%

Development of new methodologies for the mass spectrometry study of bioorganic macromolecules

Cristoni

Bernardi

2003

Mass Spectrometry Reviews

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I. Introduction 370 II. Techniques That Are Usually Employed in the Study of Bioorganic Macromolecules 371 A. Proteins and Peptides 371 B. Oligonucleotides 374 C. Oligosaccharides and Glycoconjugates 375 D. Various Complexes (DNA–Protein, Antigen–Antibody, Macromolecules–Metals) 377 III. Common Problems and Developments in the Analysis of Bioorganic Macromolecules by Mass Spectrometry 377 A. Ionization Source Problems and Developments 377 1. Sensitivity 377 2. Problems with Buffers 379 3. Multicharge Effect 381 B. Mass Analyzer Problems and Developments 381 1. Linear Dynamic Range 381 2. Tandem Mass Spectrometry 382 3. Sensitivity 382 4. Resolution 383 5. Mass Accuracy 383 IV. New Promising Technologies 384 A. Interfaces and Ionization Sources 384 1. Improvements in the Coupling of Liquid‐Phase Separation Systems to Mass Spectrometry 384 2. AP‐MALDI 384 3. Deprotonant Agents 385 4. Sonic Spray Ionization 388 5. APCI without Corona Discharge 391 B. Mass Analyzers 393 1. Linear Quadrupole Ion Trap 394 2. TOF Analyzers with New Detectors 395 3. Multiple Mass Analyzers 396 V. Software for Data Treatment 397 VI. Conclusions and Future Developments 399 Acknowledgments 400 References 400 In recent years, mass spectrometry has been increasingly used for the analysis of various macromolecules of biological, biomedical, and biochemical interest. This increase has been made possible by two key developments: the advent of electrospray ionization (ESI) and matrix‐assisted laser desorption ionization (MALDI) sources. The two new techniques produce a significant increase in mass range and in sensitivity that led to the development of new applications and of new analyzer designs, software, and robotics. This review, apart from the description of the status of mass spectrometry in the analysis of bioorganic macromolecules, is mainly devoted to the illustration of the more recent promising techniques and on their possible future evolution. © 2003 Wiley Periodicals, Inc., Mass Spec Rev 22:369–406, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mas.10062

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ICAT and other labeling strategies for semiquantitative LC ‐based expression profiling

Byrne

Cagney

2005

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

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Comprehensive proteome analysis requires efficient, robust, and practical methods for the identification and quantification of all proteins in complex biological samples. Mass spectrometry is a well‐established protein identification tool and semiquantitative proteomics has traditionally been performed using two‐dimensional gel electrophoresis (2‐DE) coupled with mass spectrometry. However, other separation strategies based on liquid chromatography now complement 2‐DE as a central method for analysis of proteins in complex biological systems. In this review, we discuss the most promising methodological developments in this area with particular attention to their merits and limitations.

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Derivatization procedures to facilitatede novo sequencing of lysine-terminated tryptic peptides using postsource decay matrix-assisted laser desorption/ionization mass spectrometry

Cited by 137 publications

References 23 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

Development of new methodologies for the mass spectrometry study of bioorganic macromolecules

ICAT and other labeling strategies for semiquantitative LC ‐based expression profiling

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