Investigation of the influence of charge derivatization on the fragmentation of multiply protonated peptides

Sonsmann, Guido; Römer, Axel; Schomburg, Dietmar

doi:10.1016/s1044-0305(01)00328-2

Cited by 31 publications

(23 citation statements)

References 32 publications

(45 reference statements)

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“…tris(2,4,6-trimethoxyphenyl)-phosphonium or TMPP) has been used for a long time in MS to improve ionization. The presence of a permanent charge at the N-or C-terminus in a peptide greatly favors the formation and prominence of b-and y-ions, respectively [77]. While most commonly used for N-terminal derivatization [78], C-terminal derivatization with TMPP has been shown to improve peptide fragmentation [79], in particular of the C-terminal peptide of proteins and GluC-derived peptides.…”

Section: Derivatization Methodsmentioning

confidence: 99%

Genomic variability and protein species — Improving sequence coverage for proteogenomics

Bischoff

Permentier

Guryev

et al. 2016

Journal of Proteomics

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Section: Derivatization Methodsmentioning

confidence: 99%

Genomic variability and protein species — Improving sequence coverage for proteogenomics

Bischoff

Permentier

Guryev

et al. 2016

Journal of Proteomics

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“…Notable in this regard is the use of 18 O incorporation at the carboxyl-termini of peptides during protein hydrolysis [14 -17]. For underivatized peptides, ESI has found use for de novo sequencing under a variety of conditions, which include collision-induced dissociation (CID) in the triple quadrupole mass analyzer [18 -20] and the QqTOF mass analyzer [18,19,[21][22][23][24][25][26], resonant excitation in the quadrupole ion trap mass analyzer [14,[27][28][29], and electron capture dissociation in the Fourier transform ion cyclotron resonance mass analyzer [30 -34]. MALDI de novo sequencing has been carried out using CID and metastable decay in single- [35] and double-stage [36 -39] TOF instruments and with CID in QqTOF instruments [40 -44].…”

mentioning

confidence: 99%

“De novo” peptide sequencing by MALDI-quadrupole-ion trap mass spectrometry: A preliminary study

Zhang

Krutchinsky

Chait

2003

J. Am. Soc. Mass Spectrom.

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Collision-induced dissociation of singly charged peptide ions produced by resonant excitation in a matrix-assisted laser desorption/ionization (MALDI) ion trap mass spectrometer yields relatively low complexity MS/MS spectra that exhibit highly preferential fragmentation, typically occurring adjacent to aspartyl, glutamyl, and prolyl residues. Although these spectra have proven to be of considerable utility for database-driven protein identification, they have generally been considered to contain insufficient information to be useful for extensive de novo sequencing. Here, we report a procedure for de novo sequencing of peptides that uses MS/MS data generated by an in-house assembled MALDI-quadrupole-ion trap mass spectrometer (Krutchinsky, Kalkum, and Chait Anal. Chem. 2001, 73, 5066 -5077). Peptide sequences of up 14 amino acid residues in length have been deduced from digests of proteins separated by SDS-PAGE. Key to the success of the current procedure is an ability to obtain MS/MS spectra with high signal-to-noise ratios and to efficiently detect relatively low abundance fragment ions that result from the less favorable fragmentation pathways. The high signal-tonoise ratio yields sufficiently accurate mass differences to allow unambiguous amino acid sequence assignments (with a few exceptions), and the efficient detection of low abundance fragment ions allows continuous reads through moderately long stretches of sequence. Finally, we show how the aforementioned preferential cleavage property of singly charged ions can be used to facilitate the de novo sequencing process. T he use of mass spectrometry combined with database searching has gained wide acceptance for rapid, sensitive protein identification [1]. This method requires the availability of extensive protein, cDNA, or genomic sequence from the organism of interest (or at least from a closely related species). If such sequence information is not available, as remains the case for the vast majority of extant organisms, it is desirable to utilize de novo peptide sequencing to identify and obtain information about their protein(s). Although Edman sequencing has for a long time been a method of choice for de novo sequencing of peptides and proteins, mass spectrometry (MS) has also been shown to have considerable utility for this purpose.Indeed, mass spectrometric de novo sequencing based on the fragmentation of derivitized peptide ions dates back to the late 1960s and on underivatized peptide ions to the early 1980s (reviewed in [2] and [3]). More recently, MS sequencing has been given considerable impetus by the development of ESI and MALDI, ionization techniques whose efficiencies for producing intact peptide ions are far higher than those that were previously available. Again, both derivitized and underivatized peptides have been used in this newer work. Thus, chemical derivatization has been applied to simplify/enhance the fragmentation spectra and/or to differentiate N-from C-terminal fragment ions [4 -13]. Notable in this regard is the use of 18 O i...

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“…All matches to a given peptide regardless of precursor ion charge state are reduced to a single identification, and the highest ion score (S) is used in the PRO-FDR calculation. Although spectra from multiple precursor ion charge states may exhibit distinct fragmentation patterns, these peptides are not considered as independent peptide matches by PROVALT and are not allowed to contribute to the peptide coverage (c) (44). We have adopted this approach because of the fact that during database searching precursor ions of multiple charge states will be converted to their singly charged precursor masses prior to comparison with the in silico derived peptides.…”

Section: Resultsmentioning

confidence: 99%

A Heuristic Method for Assigning a False-discovery Rate for Protein Identifications from Mascot Database Search Results

Weatherly¹,

Atwood

Minning³

et al. 2005

Molecular & Cellular Proteomics

188

208

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MS/MS and database searching has emerged as a valuable technology for rapidly analyzing protein expression, localization, and post-translational modifications. The probability-based search engine Mascot has found widespread use as a tool to correlate tandem mass spectra with peptides in a sequence database. Although the Mascot scoring algorithm provides a probability-based model for peptide identification, the independent peptide scores do not correlate with the significance of the proteins to which they match. Herein, we describe a heuristic method for organizing proteins identified at a specified false-discovery rate using Mascot-matched peptides. We call this method PROVALT, and it uses peptide matches from a random database to calculate false-discovery rates for protein identifications and reduces a complex list of peptide matches to a nonredundant list of homologous protein groups. This method was evaluated using Mascotidentified peptides from a Trypanosoma cruzi epimastigote whole-cell lysate, which was separated by multidimensional LC and analyzed by MS/MS. PROVALT was then compared with the two traditional methods of protein identification when using Mascot, the single peptide score and cumulative protein score methods, and was shown to be superior to both in regards to the number of proteins identified and the inclusion of lower scoring nonrandom peptide matches. Molecular & Cellular Proteomics 4:762-772, 2005.As a complement to gene expression profiling, proteomics is the analysis of gene and cellular function at the protein level. The definition of proteomics has expanded to include not simply the proteins encoded by a genome but the analysis of protein isoforms, post-translational modifications, and protein-protein interactions (1-4). Although two-dimensional gel electrophoresis and MS have been the dominant techniques used in this field, LC-MS/MS has emerged as a valuable technology for the analysis of complex protein mixtures (5).Typical LC-MS/MS experiments are subdivided into five stages. First, the proteins are extracted from the biological material followed by enzymatic digestions to produce peptides. The peptides are partitioned through multiple separations followed by analysis with LC-MS/MS. Two methods can then be employed to correlate an MS/MS spectrum with the peptide and protein from which it originated. The MS/MS spectrum is either sequenced de novo, yielding a complete amino acid sequence or sequence tag (6 -13), which is then searched against a protein database, or software algorithms are used to directly match experimental with theoretical MS/MS spectra generated from peptides in a protein database (14 -21).All software designed for matching MS/MS spectra to peptide sequences function in a similar manner. The experimental peptide masses are first compared with theoretical peptide masses derived from in silico enzymatic digestion of the specified protein database. The subsets of theoretical peptides with similar masses (within a user-defined mass tolerance) to the experimental peptides...

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Investigation of the influence of charge derivatization on the fragmentation of multiply protonated peptides

Cited by 31 publications

References 32 publications

Genomic variability and protein species — Improving sequence coverage for proteogenomics

Genomic variability and protein species — Improving sequence coverage for proteogenomics

“De novo” peptide sequencing by MALDI-quadrupole-ion trap mass spectrometry: A preliminary study

A Heuristic Method for Assigning a False-discovery Rate for Protein Identifications from Mascot Database Search Results

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