Peptide sequencing of charged derivatives by postsource decay MALDI mass spectrometry

Spengler, Bernhard; Luetzenkirchen, F; Metzger, Sabine; Chaurand, Pierre; Kaufmann, R.; Jeffery, W.; Bartlet-Jones, Michael; Pappin, Darryl

doi:10.1016/s0168-1176(97)00218-8

Cited by 75 publications

(65 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Questions about the internal energy content of precursor ions derived from DE MALDI (7,30,33) and the compelling arguments for the mobile proton model of peptide fragmentation (37, 39) led us to investigate an alternative approach to…”

Section: Introductionmentioning

confidence: 99%

“…An alternative strategy to increase the yield of sequence-specific fragment ions by PSD was developed by Dikler and coworkers (36), who modified the guanidine side chain of Arg-containing peptides. That modification was done to minimize charge localization on the basic Arg residue and to facilitate protonation of the backbone amide groups.Several previous studies (7,30,33,37) raise questions about the internal energy content of precursor ions derived from DE MALDI and whether there is enough energy to optimally produce sequence-specific products by the charge-remote fragmentation mechanisms that are required with fixed positivecharge derivatives. Wysocki and coworkers (37) showed that addition of a fixed positive charge at the N terminus of a peptide increased the internal energy needed to fragment the peptide.…”

mentioning

confidence: 99%

“…Those results are consistent with the electrospray ionization findings of Gaskell and coworkers (38), who showed that the formation of precharged derivatives was detrimental to the yield of sequence-specific fragment ions after lowenergy collisional activation of singly charged species. On the other hand, experimental (37) and theoretical (39) studies reveal that protonation of backbone amide nitrogen atoms enhance peptide fragmentation because amide bond orders are lowered dramatically by protonation.Questions about the internal energy content of precursor ions derived from DE MALDI (7,30,33) and the compelling arguments for the mobile proton model of peptide fragmentation (37, 39) led us to investigate an alternative approach toThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked ''advertisement'' in accordance with 18 U.S.C.…”

mentioning

confidence: 99%

See 2 more Smart Citations

A method for high-sensitivity peptide sequencing using postsource decay matrix-assisted laser desorption ionization mass spectrometry

Keough

Youngquist

Lacey

1999

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

225

262

View full text Add to dashboard Cite

A method has been developed for de novo peptide sequencing using matrix-assisted laser desorption ionization mass spectrometry. This method will facilitate biological studies that require rapid determination of peptide or protein sequences, e.g., determination of posttranslational modifications, identification of active compounds isolated from combinatorial peptide libraries, and the selective identification of proteins as part of proteome studies. The method involves fast, one-step addition of a sulfonic acid group to the N terminus of tryptic peptides followed by acquisition of postsource decay (PSD) fragment ion spectra. The derivatives are designed to promote efficient charge site-initiated fragmentation of the backbone amide bonds and to selectively enhance the detection of a single fragment ion series that contains the C terminus of the molecule (y-ions). The overall method has been applied to pmol quantities of peptides. The resulting PSD fragment ion spectra often exhibit uninterrupted sequences of 20 or more amino acid residues. However, fragmentation efficiency decreases considerably at amide bonds on the C-terminal side of Pro. The spectra are simple enough that de novo sequence tagging is routine. The technique has been successfully applied to peptide mixtures, to high-mass peptides (up to 3,600 Da) and to the unambiguous identification of proteins isolated from two-dimensional gel electrophoresis. The PSD spectra of these derivatized peptides often allow far more selective protein sequence database searches than those obtained from the spectra of native peptides.Knowledge of protein sequences is fundamentally important for understanding many physiological processes at the molecular level (1). Tandem mass spectrometry has become an increasingly essential tool for protein and peptide sequencing because of its speed, sensitivity, and applicability to complex mixtures (2). Recently, postsource decay (PSD) matrix-assisted laser desorption ionization (MALDI) mass spectrometry was developed for high-sensitivity peptide sequencing applications (3-8). Subpicomole limits of analysis were reported as a result of the high yield of fragment ions and the high ion transmission inherent with time-of-flight mass spectrometry (5). Kaufmann et al. (5) also noted several problems associated with PSD MALDI sequencing of peptides, including the complexity of the resulting fragmentation patterns and the lack of computer algorithms capable of interpreting the complex spectra. The recent incorporation of delayed extraction (DE) (9, 10), a technique designed to improve precursor-ion mass resolution and mass-measurement accuracy, reduced the rate of PSD fragmentation by at least an order of magnitude. As a result, many low-intensity precursor ions obtained by DE MALDI do not produce enough PSD fragmentation to allow derivation of even short sequence tags (7).Positively charged derivatives have been used in desorption mass spectrometry for many years to improve sensitivity by enhancing ionization efficiencies (11, 12...

show abstract

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

A method for high-sensitivity peptide sequencing using postsource decay matrix-assisted laser desorption ionization mass spectrometry

Keough

Youngquist

Lacey

1999

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

225

262

View full text Add to dashboard Cite

show abstract

“…5) The introduction of a positively charged group, such as quaternary and tertiary ammonium, 6) or quaternary phosphonium groups, 7) at the N-terminus is known to enhance the relative intensity of N-terminal fragments in product ion spectra, facilitating the formation of a consecutive series of a-or b-ions. Recently, our group introduced another type of derivatization to improve fragmentation under low-energy CID conditions, in which a substructure with a high proton affinity, such as a guanidino or amidino group, is included.…”

Section: )mentioning

confidence: 99%

Differential 14N/15N-Labeling of Peptides Using N-Terminal Charge Derivatization with a High-Proton Affinity for Straightforward de novo Peptide Sequencing

et al. 2013

View full text Add to dashboard Cite

While de novo peptide sequencing is essential in many situations, it remains a difficult task. This is because peptide fragmentation results in complicated and often incomplete product ion spectra. In a previous study, we demonstrated that N-terminal charge derivatization with 4-amidinobenzoic acid (Aba) resulted in improved peptide fragmentation under lowenergy CID conditions. However, even with this derivatization, some ambiguity exists, due to difficulties in discriminating between N-and C-terminal fragments. In this study, to specifically identify b-ions from complex product ion spectra, the differential 14 N/ 15 N-labeling of peptides was performed using Aba derivatization. 15 N-Labeled Aba was synthesized in the form of a succinimide ester. Peptides were derivatized individually with 14 N-Aba or 15 N-Aba and analyzed by ESI-MS/MS using a linear ion trap-Orbitrap hybrid FTMS system. The N-terminal fragments (i.e., b-ions) were then identified based on m/z differences arising from isotope labeling. By comparing the spectra between 14 N-and 15 N-Aba derivatized peptides, b-ions could be successfully identified based on the m/z shifts, which provided reliable sequencing results for all of the peptides examined in this study. The method developed in this study allows the easy and reliable de novo sequencing of peptides, which is useful in peptidomics and proteomics studies.

show abstract

“…In addition, different peptides have various fragmentation capabilities making the spectra difficult to interpret. To overcome this, attempts have been made to induce biased fragmentations by peptide modifications, in order to produce 'cleaner' PSD spectra [12][13][14][15][16]. We applied the 2-methoxy-4,5-dihydro-1H-imidazol (KTAG) modification [17,18] to one set of 2-D PAGE separated proteins.…”

Section: Introductionmentioning

confidence: 99%

Parallel post‐source decay for increasing protein identification confidence levels from 2‐D gels

et al. 2008

View full text Add to dashboard Cite

Peptide mass fingerprinting (PMF) has over the years become one of the most commonly used tools for high-throughput analysis and identification of proteins. This method is applicable when relatively simple samples have to be analysed and it is commonly used for analysing proteins previously separated by 2-DE. The most common type of instrument used for this approach is the MALDI-TOF that has proved to be particularly suitable for the PMF analysis because of its characteristics of speed, robustness, sensitivity and automation. We have used a MALDI-TOF equipped with a novel parallel PSD capability (MALDI micro MX), to perform the analysis of two sets of different biological samples isolated by 2-DE. By using a method that integrates the data obtained by PMF analysis with the PSD data obtained in the same experiment, we show that the new multiplexed PSD solution increases the protein identification rate compared to the normal PMF approach. We also investigated the use of a charge-directed fragmentation modification reagent to improve the identification rate and confidence levels.

show abstract

Peptide sequencing of charged derivatives by postsource decay MALDI mass spectrometry

Cited by 75 publications

References 19 publications

A method for high-sensitivity peptide sequencing using postsource decay matrix-assisted laser desorption ionization mass spectrometry

A method for high-sensitivity peptide sequencing using postsource decay matrix-assisted laser desorption ionization mass spectrometry

Differential 14N/15N-Labeling of Peptides Using N-Terminal Charge Derivatization with a High-Proton Affinity for Straightforward de novo Peptide Sequencing

Parallel post‐source decay for increasing protein identification confidence levels from 2‐D gels

Contact Info

Product

Resources

About