De Novo Peptide Sequencing Based on a Divide-and-Conquer Algorithm and Peptide Tandem Spectrum Simulation

Zhang, Zhongqi

doi:10.1021/ac0491206

Cited by 80 publications

(56 citation statements)

References 39 publications

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“…A program developed at Amgen, MassAnalyzer, was used to automatically assign the fragment ions [34,35] and to prepare the fragment coverage map [27]. It was also used to calculate the theoretical average masses of the antibodies and their fragments, using atomic weights of elements from organic sources listed in reference [3].…”

Section: Data Analysis Softwarementioning

confidence: 99%

Mass measurement and top-down HPLC/MS analysis of intact monoclonal antibodies on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer

Bondarenko

Second

Zabrouskov

et al. 2009

J. Am. Soc. Mass Spectrom.

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142

129

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Mass and top-down analyses of 150-kDa monoclonal immunoglobulin gamma (IgG) antibodies were performed on an Orbitrap analyzer. Three different sample delivery methods were tested including (1) infusion of an off-line desalted IgG sample using nano-electrospray; (2) on-line desalting followed by a step elution with a high percentage of organic solvent; and (3) reversed-phase HPLC separation and on-line mass and top-down analyses of disulfide isoforms of an IgG2 antibody. The accuracy of mass measurements of intact antibody was within Ϯ2 Da (15 ppm). The glycoforms of intact IgG antibodies separated by 162 Da were baseline resolved. In-source fragmentation of the intact antibodies produced mainly 115 residue fragments including N-terminal variable domains of heavy and light chains. The sequence coverage (the number of cleavages) was greatly increased after reduction of disulfide bonds and HPLC/MS/MS analysis of light and heavy chains using collisioninduced dissociation in the ion trap of the LTQ-Orbitrap. This is an attractive alternative to peptide mapping for characterization and monitoring of post-translational modifications attributed to minimal sample preparation, high speed of the mass/top-down analysis, and relatively minor method-induced sample modifications. [1,2]. This has resulted in a strong need for a highthroughput methods for analysis of different antibody drug candidates. Mass spectrometry has become one of the most powerful techniques for the structural characterization of monoclonal antibodies (mAbs) [3]. Traditionally, structural characterization of mAbs has been performed by a "bottom-up" approach after first digesting them to peptides [4 -6]. Unfortunately, enzymatic digestion is a laborious, time-consuming process and it often introduces artificial modifications, such as cyclization of N-terminal glutamine and deamidation [5,7]. Alternatively, protein molecular mass analysis is relatively fast, does not require lengthy sample preparation, and induces fewer, if any, modifications [8] compared with the peptide mapping [5,7]. Analysis of intact monoclonal IgG antibodies and their large domains has been reported for matrix-assisted laser desorption/ ionization (MALDI) and electrospray ionization (ESI) sources and almost all mass analyzers including MALDI-time of flight (TOF) [9 -11], ESI quadrupole (Q) [4,[12][13][14], ion trap [15], orthogonal TOF [8,11,16,17], and the LTQ-Orbitrap during direct infusion [18]. Although a mass change in a population of mAbs can be used to monitor post-translational modifications [8], it cannot reveal the site of modification. For that purpose, fragmentation of intact proteins, also known as "topdown" mass spectrometry, has been developed during the past decade [19 -25]

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Section: Data Analysis Softwarementioning

confidence: 99%

Mass measurement and top-down HPLC/MS analysis of intact monoclonal antibodies on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer

Bondarenko

Second

Zabrouskov

et al. 2009

J. Am. Soc. Mass Spectrom.

Self Cite

142

129

View full text Add to dashboard Cite

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“…Other algorithms like divide and conquer, for instance, are not in wide spread use. Zhang has used the divide and conquer algorithm for splitting the spectrum into successively smaller sub-spectra until they were solvable by the naïve approach and are then recursively re-integrated to solve the input spectrum [64]. The use of hidden Markov models, as an example for machine learning algorithms, has been used to tackle the de novo sequencing problem [37].…”

Section: Other Algorithmsmentioning

confidence: 99%

Algorithms for thede novosequencing of peptides from tandem mass spectra

Allmer¹

2011

Expert Review of Proteomics

107

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Proteomics is the study of the proteins, their time and location dependent expression profiles as well as their modifications and interactions. Mass spectrometry is useful to investigate many of the questions asked in proteomics. Typically database search methods are employed to identify proteins from complex mixtures. However, often databases are not available or despite their availability some sequences are not readily found therein. To overcome this problem de novo sequencing can be used to directly assign a peptide sequence to an MS/MS spectrum. Many algorithms have been proposed for de novo sequencing and a selection of them is detailed in this review. Although a standard accuracy measure has not been agreed upon in the field, relative algorithm performance is discussed. The current state of the de novo sequencing is assessed thereafter and finally, examples are used to construct possible future perspectives of the field. Running title:De novo sequencing of MS/MS spectra

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“…Using ion trap data, peptides were identified automatically by software developed in-house which correlated the experimental tandem mass spectra against theoretical tandem mass spectra generated from the known antibody amino acid sequence for peptide identification [14,15]. All disulfide-linked peptides were identified manually using accurate mass information from both ESI-IT and ESI-TOF.…”

Section: Mass Spectrometry Analysis Of Lyc-c Peptidesmentioning

confidence: 99%

Reversed-phase liquid chromatography in-line with negative ionization electrospray mass spectrometry for the characterization of the disulfide-linkages of an immunoglobulin gamma antibody

Chelius

Wimer

Bondarenko

2006

J. Am. Soc. Mass Spectrom.

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In this report, we present a new approach for the determination of the disulfide bond connectivity in proteins using negative ionization mass spectrometry of nonreduced enzymatic digests. The mass spectrometric analysis in negative ion mode was optimized to allow in-line analysis coupled directly to the HPLC system used for the separation of the peptides resulting from enzymatic digestion. We determined the disulfide structure of a human immunoglobulin gamma 2 (IgG2) antibody containing 18 unique cysteine residues linked via 11 unique disulfide bonds. The efficiency of the gas-phase dissociation of disulfide-linked peptides using negative electrospray ionization was evaluated for an ion trap mass spectrometer and an orthogonal acceleration time-of-flight mass spectrometer. Both mass spectrometry techniques provided efficient in-source fragmentation for the identification of the disulfide-linked peptides of the antibody. Both instruments were limited in the number of disulfide bonds that could be dissociated. Seven of the 11 unique disulfide linkages have been determined, including the linkage of the light chain to the heavy chain. Only the disulfide connectivity of the hinge peptide H6H7H8H9 (C 6 C 7 VEC 8 PPC 9 PAPPVAGPSVFLFPPKPK) could not be determined (numbering the cysteine residues sequentially from the N-terminus and labeling the heavy chain cysteines "H" and the light chain cysteines "L"). However, we identified the dimer of peptide C 6 C 7 VEC 8 PPC 9 PAPPVAGPSVFLFPPKPK linked via four disulfide bonds based on the unique molecular weight of this dipeptide. The established linkages were H1 to H2, H10 to H11, H12 to H13, L1 to L2, L3 to L4, and L5 to H3H4. The intrachain linkages of the light chain (L1 to L2, L3 to L4), and heavy chain (H10 to H11, H12 to H13) domains were identical to the linkages found in IgG1 antibodies. (J Am Soc Mass Spectrom 2006, 17, 1590 -1598

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De Novo Peptide Sequencing Based on a Divide-and-Conquer Algorithm and Peptide Tandem Spectrum Simulation

Cited by 80 publications

References 39 publications

Mass measurement and top-down HPLC/MS analysis of intact monoclonal antibodies on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer

Mass measurement and top-down HPLC/MS analysis of intact monoclonal antibodies on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer

Algorithms for thede novosequencing of peptides from tandem mass spectra

Reversed-phase liquid chromatography in-line with negative ionization electrospray mass spectrometry for the characterization of the disulfide-linkages of an immunoglobulin gamma antibody

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