<i>De novo</i> sequencing of peptides by MS/MS

Seidler, Joerg; Zinn, Nico; Boehm, Martin E.; Lehmann, Wolf D.

doi:10.1002/pmic.200900459

Cited by 197 publications

(155 citation statements)

References 134 publications

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“…Even separating differentially phosphorylated protein isoforms is possible, provided the samples are not too complex [21]. The last phosphoprotein-enrichment method that should be mentioned is hydroxyapatite chromatography; a type of "pseudo-affinity" chromatography or "mixed-mode" ion exchange using a form of calcium phosphate with the formula Ca 10 (PO 4 ) 6 (OH) 2 . Several types of hydroxyapatite resins have been designed for protein and DNA separation.…”

Section: Phosphoproteome Enrichment By Affinity Chromatographymentioning

confidence: 99%

Advances in purification and separation of posttranslationally modified proteins

Černý

Skalák

Cerná

et al. 2013

Journal of Proteomics

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Posttranslational modifications (PTMs) of proteins represent fascinating extensions of the dynamic complexity of living cells' proteomes. The results of enzymatically catalyzed or spontaneous chemical reactions, PTMs form a fourth tier in the gene -transcript -protein cascade, and contribute not only to proteins' biological functions, but also to challenges in their analysis. There have been tremendous advances in proteomics during the last decade. Identification and mapping of PTMs in proteins have improved dramatically, mainly due to constant increases in the sensitivity, speed, accuracy and resolution of mass spectrometry (MS). However, it is also becoming increasingly evident that simple gel-free shotgun MS profiling is unlikely to suffice for comprehensive detection and characterization of proteins and/or protein modifications present in low amounts. Here, we review current approaches for enriching and separating posttranslationally modified proteins, and their MS-independent detection. First, we discuss general approaches for proteome separation, fractionation and enrichment. We then consider the commonest forms of PTMs (phosphorylation, glycosylation and glycation, lipidation, methylation, acetylation, deamidation, ubiquitination and various redox modifications), and the best available methods for detecting and purifying proteins carrying these PTMs.

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Section: Phosphoproteome Enrichment By Affinity Chromatographymentioning

confidence: 99%

Advances in purification and separation of posttranslationally modified proteins

Černý

Skalák

Cerná

et al. 2013

Journal of Proteomics

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“…T andem mass spectrometry has been used with great success to elucidate the sequences of biomolecules such as nucleic acids [1], peptides [2][3][4][5], and oligosaccharides [6,7]. Both the well-explored dynamics and mechanisms of collision induced dissociation (CID) [8][9][10] and extensively developed computer algorithms that have facilitated spectral interpretation [11,12] have cemented the landmark status of CID for tandem mass spectrometry.…”

Section: Introductionmentioning

confidence: 99%

Enhanced Electron Transfer Dissociation of Peptides Modified at C-terminus with Fixed Charges

Brodbelt

2012

J. Am. Soc. Mass Spectrom.

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The impact of the conversion of carboxylates in peptides to basic or fixed charge sites on the outcome of electron transfer dissociation (ETD) is evaluated with respect to ETD efficiency and the number of diagnostic sequence ions. Four reagents, including benzylamine (BA), 1-benzylpiperazine (BZP), carboxymethyl trimethylammonium chloride hydrazide (GT), and (2-aminoethyl)trimethylammonium chloride hydrochloride (AETMA), were used for the carboxylate derivatization, with the first two replacing the acidic carboxylate groups with basic functionalities and the latter two introducing fixed charge sites. The ETD efficiencies and Xcorr scores were compared for both nonderivatized and derivatized tryptic and Glu-C peptides from cytochrome c. Derivatization of the carboxylate increases the average charge states, the number of fragment ions, and the dissociation efficiencies of peptides, especially for the fixed charge reagent, AETMA.

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“…The de novo sequencing by mS dates back more than 30 years and was firstly used in combination with edman degradation, and then on its own (Biemann, 2002). The development of "soft" ionization techniques, such as the electrospray ionization, high resolution and accuracy mass spectrometry greatly improved the results from de novo sequencing (Standing, 2003, Seidler et al, 2010. with improved mass resolution capacity of FTiCr instruments, detection of more fragments was made possible.…”

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confidence: 99%

“…Proteins of organisms with unknown genome often show sequence homologies to functionally related homologues in other completely sequenced organisms. Therefore, existing sequences databases may be helpful through homology-based searches of peptide candidates suggested by the automated de novo engines (Seidler et al, 2010). it is important to notice that peptide sequence candidates cannot be directly used to BLAST and FASTA engines without compromising search specificity.…”

mentioning

confidence: 99%

Challenges in proteome analyses of tropical plants

Balbuena¹,

Dias²,

Martins³

et al. 2011

Braz. J. Plant Physiol.

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Genome sequencing of various organisms allow global analysis of gene expression, providing numerous clues on the biological function and involvement in the biological processes studied. Proteomics is a branch of molecular biology and biotechnology that has undergone considerable development in the post-genomic era. Despite the recent significant advancements in proteomics techniques, still there is much to be improved. Due to peculiarities to the plant kingdom, proteomics approaches require adaptations, so as to improve efficiency and accuracy of results in plants. Data generated by proteomics can substantially contribute to the understanding and monitoring of plant physiological events and development of biotechnological strategies. especially for tropical species, challenges are even greater, in the light of the abundance of secondary metabolites, as well as of the lack of complete genome sequences. This review discusses current topics in proteomics concerning challenges and perspectives, with emphasis on the proteomics of tropical plant species.Key words: 2-De, mass spectrometry, recalcitrant species, proteomics, unknown genome resuMo O sequenciamento dos genomas de diversos organismos tornou praticável a análise global da expressão gênica, fornecendo numerosas pistas quanto à função biológica e envolvimento de inúmeros genes nos processos biológicos estudados. A proteômica é um dos ramos da biologia molecular e da biotecnologia que passou por expressivo desenvolvimento na era pós-genômica. Apesar dos recentes avanços nas técnicas em proteômica, muito resta a ser aprimorado. Devido às particularidades do reino vegetal, várias abordagens devem ser adaptadas no sentido de aumentar a eficiência e a acurácia de resultados das análises proteômicas em plantas. nesse sentido, os dados gerados pela proteômica podem contribuir substancialmente para a compreensão e acompanhamento de eventos fisiológicos e para o desenvolvimento de estratégias biotecnológicas. no que tange às espécies tropicais, as dificuldades são ainda maiores, devido ao fato de serem ricas em metabólitos secundários e ainda não terem seus genomas totalmente sequenciados. esta revisão trata de tópicos atuais em estudos de proteômica de plantas, desafios e perspectivas, com ênfase em espécies tropicais. palavras-chave: 2-De, espectrometria de massas, espécies recalcitrantes, genomas desconhecidos, proteômica.

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De novo sequencing of peptides by MS/MS

Cited by 197 publications

References 134 publications

Advances in purification and separation of posttranslationally modified proteins

Advances in purification and separation of posttranslationally modified proteins

Enhanced Electron Transfer Dissociation of Peptides Modified at C-terminus with Fixed Charges

Challenges in proteome analyses of tropical plants

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