Matrix‐assisted laser desorption/ionization‐ quadrupole ion trap‐time of flight mass spectrometry sequencing resolves structures of unidentified peptides obtained by in‐gel tryptic digestion of haptoglobin derivatives from human plasma proteomes

Koy, Cornelia; Mikkat, Stefan; Raptakis, E.; Sutton, Chris W.; Resch, Martin; Tanaka, Kōichi; Glocker, Michael O.

doi:10.1002/pmic.200300381

Cited by 67 publications

(46 citation statements)

References 22 publications

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“…However, several biochemical modifications appear to be superimposed on genetic polymorphisms. Using MS protein structure characterization, the cause of migrational differences of haptoglobin a chains in 2-DE was elucidated [35,36]. It was shown that at least three structurally different protein species can be differentiated and accounted for the most commonly observed spot patterns of haptoglobin a chains.…”

Section: Clinical Applications -Biomarker Identificationmentioning

confidence: 99%

Recent advances in blood‐related proteomics

et al. 2005

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Service régional vaudois de transfusion sanguine, Lausanne, SwitzerlandBlood is divided in two compartments, namely, plasma and cells. The latter contain red blood cells, leukocytes, and platelets. From a descriptive medical discipline, hematology has evolved towards a pioneering discipline where molecular biology has permitted the development of prognostic and diagnostic indicators for disease. The recent advance in MS and protein separation now allows similar progress in the analysis of proteins. Proteomics offers great promise for the study of proteins in plasma/serum, indeed a number of proteomics databases for plasma/ serum have been established. This is a very complex body fluid containing lipids, carbohydrates, amino acids, vitamins, nucleic acids, hormones, and proteins. About 1500 different proteins have recently been identified, and a number of potential new markers of diseases have been characterized. Here, examples of the enormous promise of plasma/serum proteomic analysis for diagnostic/prognostic markers and information on disease mechanism are given. Within the blood are also a large number of different blood cell types that potentially hold similar information. Proteomics of red blood cells, until now, has not improved our knowledge of these cells, in contrast to the major progresses achieved while studying platelets and leukocytes. In the future, proteomics will change several aspects of hematology.

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Section: Clinical Applications -Biomarker Identificationmentioning

confidence: 99%

Recent advances in blood‐related proteomics

et al. 2005

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“…The resulting IRMPD mass spectra afford more complete sequence coverage for both model peptides and tryptic peptides from cytochrome c. We compare the effectiveness of this derivatization/IRMPD approach to that of a common N-terminal sulfonation reaction that I n recent years, there has been tremendous effort devoted to the application of mass spectrometry to the field of proteomics [1, 2] in large part because of the success of tandem mass spectrometry for elucidation of primary sequences and modifications of peptides and proteins [3][4][5][6][7]. Several ion activation methods have been developed in this context, including collision induced dissociation (CID) [8,9], electron capture dissociation (ECD) [10]. electron-transfer dissociation (ETD) [11], pulsed-Q dissociation (PQD) [12], surface induced dissociation [13], and photodissociation (PD) [14 -19].…”

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“…Several ion activation methods have been developed in this context, including collision induced dissociation (CID) [8,9], electron capture dissociation (ECD) [10]. electron-transfer dissociation (ETD) [11], pulsed-Q dissociation (PQD) [12], surface induced dissociation [13], and photodissociation (PD) [14 -19].…”

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Improved infrared multiphoton dissociation of peptides through N-terminal phosphonite derivatization

Vasicek

Wilson

Brodbelt

2009

J. Am. Soc. Mass Spectrom.

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A strategy for improving the sequencing of peptides by infrared multiphoton dissociation (IRMPD) in a linear ion trap mass spectrometer is described. We have developed an N-terminal derivatization reagent, 4-methylphosphonophenylisothiocyanate (PPITC), which allows the attachment of an IR-chromogenic phosphonite group to the N-terminus of peptides, thus enhancing their IRMPD efficiencies. After the facile derivatization process, the PPITCmodified peptides require shorter irradiation times for efficient IRMPD and yield extensive series of y ions, including those of low m/z that are not detected upon traditional CID. The resulting IRMPD mass spectra afford more complete sequence coverage for both model peptides and tryptic peptides from cytochrome c. We compare the effectiveness of this derivatization/IRMPD approach to that of a common N-terminal sulfonation reaction that I n recent years, there has been tremendous effort devoted to the application of mass spectrometry to the field of proteomics [1, 2] in large part because of the success of tandem mass spectrometry for elucidation of primary sequences and modifications of peptides and proteins [3][4][5][6][7]. Several ion activation methods have been developed in this context, including collision induced dissociation (CID) [8,9], electron capture dissociation (ECD) [10]. electron-transfer dissociation (ETD) [11], pulsed-Q dissociation (PQD) [12], surface induced dissociation [13], and photodissociation (PD) [14 -19]. Each method has its own particular strengths and shortcomings, with CID being the most widely used due to its relatively well-understood underpinnings. However, the resulting CID mass spectra can be cluttered with redundant b and y ions, as well as ions created by uninformative losses of small organic molecules like water and ammonia. Hence, the interpretation of such data manually or via de novo algorithms remains challenging [20,21]. ECD and ETD provide complementary c and z ions and have proven more useful for tracking post-translational modifications (PTMs); however, these activation methods generally offer lower dissociation efficiencies than CID and are highly dependent on the charge state of the selected precursor ion [10,11]. PD methods, including both infrared multiphoton dissociation (IRMPD) and ultraviolet photodissociation (UVPD), have also shown promise because of their potential for high-energy deposition and tunability [14 -19, 22-35]. Since photoabsorption is not a collision-based process, it does not alter the kinetic energies of ions and thus minimizes any ion losses due to scattering.Photodissociation also offers particular advantages for ion trap mass spectrometers. For example, photoactivation is independent of the trapping voltage, unlike CID. In CID, the rf voltage during ion activation influences the energy deposition of collisional activation as well as defines the lower m/z range. The potential for greater energy deposition in CID occurs at the expense of storage of lower m/z ions, ones which might be key diagnostic ions for...

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“…Concatenating the differences between successive entries in compositional series yields peptide sequences that can be scored and ranked according to signal intensity. , examples persist of demand for fast and reliable peptide sequencing due to incomplete or inadequate databases [5][6][7][8][9]. De novo peptide sequencing algorithms also abound [5, 10 -17], but objective assessments of de novo peptide sequencing capabilities with unknowns [18] indicate that much work remains.…”

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De novo peptide sequencing using exhaustive enumeration of peptide composition

Olson

Epstein

Yergey

2006

J. Am. Soc. Mass Spectrom.

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We introduce the use of a peptide composition lookup table indexed by residual mass and number of amino acids for de novo sequencing of polypeptides. Polypeptides of 1600 Daltons (Da) or more can be sequenced effectively through exhaustive compositional analysis of MS/MS spectra obtained by unimolecular decomposition (without CID) in a MALDI TOF/ TOF despite a fragment mass accuracy of 50 mDa. Peaks are referenced against the lookup table to obtain a complete profile of amino acid combinations, and combinations are assembled into series of increasing length. Concatenating the differences between successive entries in compositional series yields peptide sequences that can be scored and ranked according to signal intensity. , examples persist of demand for fast and reliable peptide sequencing due to incomplete or inadequate databases [5][6][7][8][9]. De novo peptide sequencing algorithms also abound [5, 10 -17], but objective assessments of de novo peptide sequencing capabilities with unknowns [18] indicate that much work remains.One recently described de novo sequencing method has taken an approach that is wholly different from others reported to date [15]. It employs logical processing of all amino acid combinations from the parent ion and prominent fragments to obtain several relevant amino acid combinations, which are permuted into sequences; the presence of other peaks guides the selection of a final sequence. This method presents a straightforward and desirable means for sequence validation and for obtaining sequences of peptides independently of how well they fragment. However, the resolution and mass accuracy specifications for this method rely completely on the desirable performance characteristics of Fourier transform mass spectrometry (FTMS).The use of exhaustive peptide-relevant elemental combinations, as Spengler [15] has done, represents one particular understated advantage: it allows the inherent distinction of the correct ion type for use in sequence analysis. Thus, the generation of a sequence de novo is not misguided by neutral losses and/or high-energy fragmentation (x-, w-, c-, or d-) ions. Nearly all previously published de novo peptide sequencing methods [10 -16] incorporate neutral loss, high-energy fragmentation, and a-type ions into the scoring and selection of the ultimate sequence. Extensive variability in any solution generated by them appears to stem from the implementation of this feature; a robust comparison of the advantages and shortcomings in these various scoring schemes, involving fragmentation simulations [16,19], arbitrary values [13,15], empirical assignment functions [14], or a combination, seems a worthwhile venture, especially in view of peptide and instrumental variability. While the importance of these nonsequence ions to the reinforcement of sequence validation cannot be underestimated, their highly variable frequency and intensity present significant obstacles to their accurate

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Matrix‐assisted laser desorption/ionization‐ quadrupole ion trap‐time of flight mass spectrometry sequencing resolves structures of unidentified peptides obtained by in‐gel tryptic digestion of haptoglobin derivatives from human plasma proteomes

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Cited by 67 publications

References 22 publications

Recent advances in blood‐related proteomics

Recent advances in blood‐related proteomics

Improved infrared multiphoton dissociation of peptides through N-terminal phosphonite derivatization

De novo peptide sequencing using exhaustive enumeration of peptide composition

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