Protein sequence and structural studies employing matrix-assisted laser desorption ionization-high energy collision-induced dissociation

Medzihradszky, Katalin F.; Maltby, David; Qiu, Yongchang; Yu, Zhonghua; Hall, Steven C.; Chen, Y.; Burlingame, Alma L.

doi:10.1016/s0168-1176(96)04525-9

Cited by 21 publications

(19 citation statements)

References 26 publications

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“…PSD spectra show much less predictable fragmentation patterns than those obtained with the competing electrospray methods [13,14,19]. Previous attempts to improve the reliability of MALDI-PSD MS/MS for peptide sequencing used high-energy collisional activation [26,27] or various N-terminal dervatization chemistries that add fixed cationic groups to the peptides [28]. Neither of the latter methods have proven to be generally effective in the context of proteomics research, and most peptide tagging still relies on low-energy collisional activation of doubly protonated molecules formed by electrospray ionization [13,14,19].…”

Section: Introductionmentioning

confidence: 99%

Tandem mass spectrometry methods for definitive protein identification in proteomics research

et al. 2000

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Optimized procedures have been developed for the addition of sulfonic acid groups to the N-termini of low-level peptides. These procedures have been applied to peptides produced by tryptic digestion of proteins that have been separated by two-dimensional (2-D) gel electrophoresis. The derivatized peptides were sequenced using matrix-assisted laser desorption/ionization (MALDI) post-source decay (PSD) and electrospray ionization-tandem mass spectrometry methods. Reliable PSD sequencing results have been obtained starting with sub-picomole quantities of protein. We estimate that the current PSD sequencing limit is about 300 fmol of protein in the gel. The PSD mass spectra of the derivatized peptides usually allow much more specific protein sequence database searches than those obtained without derivatization. We also report initial automated electrospray ionization-tandem mass spectrometry sequencing of these novel peptide derivatives. Both types of tandem mass spectra provide predictable fragmentation patterns for arginine-terminated peptides. The spectra are easily interpreted de novo, and they facilitate error-tolerant identification of proteins whose sequences have been entered into databases.

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Section: Introductionmentioning

confidence: 99%

Tandem mass spectrometry methods for definitive protein identification in proteomics research

et al. 2000

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“…Matrix assisted laser desorption ionization (MALDI) in conjunction with MS/MS analysis has also been used to acquire product ion spectra from proteomic samples, generating data sets both analogous to and complementary with those produced by LC/ESI/MS/MS [8 -12]. While differences in the spectral content of MALDI/MS/MS and ESI/MS/MS of the same peptides have been described [9,10,13], there has been less discussion focused on findings that analysis of the same sample by both LC/ESI/MS/MS and LC/MALDI/MS/MS gives rise to improved proteome coverage at both the peptide and protein level.…”

mentioning

confidence: 99%

Exploiting the complementary nature of LC/MALDI/MS/MS and LC/ESI/MS/MS for increased proteome coverage

Bodnar

Blackburn

Krise

et al. 2003

J. Am. Soc. Mass Spectrom.

175

127

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The goal of this work was to evaluate the improvement in proteome coverage of complex protein mixtures gained by analyzing samples using both LC/ESI/MS/MS and LC/MALDI/ MS/MS. Parallel analyses of a single sample were accomplished by interfacing a Probot fractionation system with a nanoscale LC system. The Probot was configured to perform a post-column split such that a fraction (20%) of the column effluent was sent for on-line LC/ESI/MS/MS data acquisition, and the majority of the sample (80%) was mixed with a matrix solution and deposited onto the MALDI target plate. The split-flow approach takes advantage of the concentration sensitive nature of ESI and provides sufficient quantity of sample for MALDI/MS/MS. Hybrid quadrupole time-of-flight mass spectrometers were used to acquire LC/ESI/MS/MS data and LC/MALDI/MS/MS data from a tryptic digest of a preparation of mammalian mitochondrial ribosomes. The mass spectrometers were configured to operate in a data dependent acquisition mode in which precursor ions observed in MS survey scans are automatically selected for interrogation by MS/MS. This type of acquisition scheme maximizes the number of peptide fragmentation spectra obtained and is commonly referred to as shotgun analysis. While a significant degree of overlap (63%) was observed between the proteins identified in the LC/ESI/MS/MS and LC/MALDI/MS/MS data sets, both unique peptides and unique proteins were observed by each method. These results demonstrate that improved proteome coverage can be obtained using a combination of these ionization techniques. (J Am Soc Mass Spectrom 2003, 14, 971-979)

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“…Post-source decay therefore allows for fragmentation and sequencing studies on a single peptide without previous separation of the analyte mixture. The implementation of a collision cell into the first field-free region, i.e., into the flight path prior to the reflector, significantly enhances the fragmentation yield in a PSD experiment on a MALDI-TOF instrument [46].…”

Section: Principles and Recent Developments In Maldi-ms Instrumentationmentioning

confidence: 99%

“…Due to the restriction on the spontaneity of the process, the yield of fragment ions is highly dependent on the nature of the parent ion. As mentioned in Section 2.1, this limitation can be partially overcome by the installation of a collision cell in the first field-free region, i.e., prior to the reflector [46]. Furthermore, as there is no control of the energetic input on the parent ion like in collision-induced dissociation (CID) [80][81][82] and ion trap [38,39] technique (most commonly coupled to electrospray sources), usually many different kinds of fragments (a-, b-, c-, x-, y-and z-ions [83]) occur simultaneously.…”

Section: Protein Primary Structure Characterisationmentioning

confidence: 99%

Characterisation of the covalent structure of proteins from biological material by MALDI mass spectrometry ‣ possibilities and limitations

Kussmann¹,

Roepstorff²

1998

Journal of Spectroscopy

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Abstract. Matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-MS) has become a primary tool for the detailed characterisation of the covalent structure of proteins isolated from biological material, mainly because of its following potentials: high sensitivity and specificity, speed of analysis, appropriateness for mixture analysis, high tolerance towards contaminants, and compatibility with separation techniques, e.g., gel electrophoresis. These characteristics enable the structural analysis of proteins even if they are only available in limited amounts and/or in mixtures, and even if the protein preparations contain large amounts of salts, buffers, detergents and denaturants. Additionally, structural data can be generated within a relatively short time.Whereas X-ray crystallography and multidimensional NMR techniques can provide "absolute" structural data, i.e., a threedimensional "picture" of the protein of interest, MALDI-MS -especially in combination with selective protein chemistryyields information on particular aspects of the entire protein structure, e.g., primary structure, active site(s), binding sites, and posttranslational modifications, all of which are often of crucial interest for the understanding of the protein function. Taking into account that protein crystallography and protein NMR studies require large quantities of highly purified sample, MALDI-MS can be even more regarded as a powerful complement in protein structure analysis.This review aims at describing the state-of-the-art of MALDI-MS for characterisation of proteins from biological material by evaluating its potential and limitations.

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Protein sequence and structural studies employing matrix-assisted laser desorption ionization-high energy collision-induced dissociation

Cited by 21 publications

References 26 publications

Tandem mass spectrometry methods for definitive protein identification in proteomics research

Tandem mass spectrometry methods for definitive protein identification in proteomics research

Exploiting the complementary nature of LC/MALDI/MS/MS and LC/ESI/MS/MS for increased proteome coverage

Characterisation of the covalent structure of proteins from biological material by MALDI mass spectrometry ‣ possibilities and limitations

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