Biomolecule Mass Spectrometry

McLafferty, Fred W.; Fridriksson, Einar K.; Horn, David M.; Lewis, Mark A.; Zubarev, Roman A.

doi:10.1126/science.284.5418.1289

Cited by 167 publications

(117 citation statements)

References 19 publications

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“…A major aim in biological mass spectrometry has been the development of techniques to sequence peptides, proteins [1] and fragments of DNA [2][3][4]. A biomolecule sequence is generally obtained by tandem mass spectrometry (MS/MS) [5], in which a parent ion is first isolated from other ions of different mass-to-charge (m/z) ratio and then dissociated into sequence-specific fragment ions.…”

mentioning

confidence: 99%

Electron capture dissociation and infrared multiphoton dissociation of oligodeoxynucleotide dications

Håkansson

Hudgins

Marshall

et al. 2003

J. Am. Soc. Mass Spectrom.

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We report electron capture dissociation (ECD) and infrared multiphoton dissociation (IRMPD) of doubly protonated and protonated/alkali metal ionized oligodeoxynucleotides. Mass spectra following ECD of the homodeoxynucleotides polydC, polydG, and polydA contain w or d "sequence" ions. For polydC and polydA, the observed fragments are even-electron ions, whereas radical w/d ions are observed for polydG. Base loss is seen for polydG and polydA but is a minor fragmentation pathway in ECD of polydC. We also observe fragment ions corresponding to w/d plus water in the spectra of polydC and d(GCATGC). Although the structure of these ions is not clear, they are suggested to proceed through a pentavalent phosphorane intermediate. The major fragment in ECD of d(GCATGC) is a d ion. Radical a-or z-type fragment ions are observed in most cases. IRMPD primarily results in base loss, but backbone fragmentation is also observed. IRMPD provides more sequence information than ECD, but the spectra are more complex due to extensive base and water losses. It is proposed that the smaller degree of sequence coverage in ECD, with fragmentation mostly occurring close to the ends of the molecules, is a consequence of a mechanism in which the electron is captured at a P¢O bond, resulting in a negatively charged phosphate group. Consequently, at least two protons (or alkali metal cations) must be present to observe a w or d fragment ion, a requirement that is less likely for small fragments. , in which a parent ion is first isolated from other ions of different mass-to-charge (m/z) ratio and then dissociated into sequence-specific fragment ions. The fragmentation technique (e.g., collision induced dissociation (CID) [6], infrared multiphoton dissociation (IRMPD) [7,8], blackbody infrared radiative dissociation (BIRD) [9,10], surface induced dissociation (SID) [11], or ultraviolet photodissociation [12,13]) as well as the nature of the parent ion charge (singly versus multiply charged, protonation versus metal cation attachment, cation versus anion, etc.) play key roles in determining the major fragmentation processes.To date most attention has focused on the fragmentation reactions of even-electron ions, but electrospray ionization in combination with ion-ion reactions, ionelectron reactions, or ion-neutral reactions have opened up new opportunities to examine the fragmentation reactions of odd-electron ions. Examples include electron capture dissociation (ECD) of [M ϩ nH] nϩ ions of peptides and proteins [14,15], polymers [16,17] [24], and CID of a Cu(II)-amine-peptide complex [25]. In each case, the formation of the radical cation (or anion) results in new fragmentation pathways, which are complementary to those observed for even-electron fragmentation. For example, disulfide bond cleavage is observed as a major fragmentation pathway in ECD [26], whereas such cleavage is not observed in CID or IRMPD. In other instances, novel fragmentation chem-

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confidence: 99%

Electron capture dissociation and infrared multiphoton dissociation of oligodeoxynucleotide dications

Håkansson

Hudgins

Marshall

et al. 2003

J. Am. Soc. Mass Spectrom.

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“…Such gel-separated proteins can be identified rapidly by mass spectrometry (MS), and if genomic information is also available, such analyses permit the systematic identification of the protein complement of a genome, the proteome (Shevchenko et al, 1996;Dainese et al, 1997;Roepstorff, 1997;Yates, 1998). In addition, MS is a powerful tool for analysis of isoforms, secondary modifications of proteins (such as glycosylation, phosphorylation, or isoprenylation), and proteolysis requiring only low amounts (picomoles to attomoles) of proteins (Burlingame et al, 1998;Kuster and Mann, 1998;McLafferty et al, 1999;Wilkins et al, 1999). Such systematic analysis of protein populations is summarized by the term proteomics.…”

Section: Introductionmentioning

confidence: 99%

Proteomics of the Chloroplast: Systematic Identification and Targeting Analysis of Lumenal and Peripheral Thylakoid Proteins

Peltier

Friso

Kalume³

et al. 2000

Plant Cell

336

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The soluble and peripheral proteins in the thylakoids of pea were systematically analyzed by using two-dimensional electrophoresis, mass spectrometry, and N-terminal Edman sequencing, followed by database searching. After correcting to eliminate possible isoforms and post-translational modifications, we estimated that there are at least 200 to 230 different lumenal and peripheral proteins. Sixty-one proteins were identified; for 33 of these proteins, a clear function or functional domain could be identified, whereas for 10 proteins, no function could be assigned. For 18 proteins, no expressed sequence tag or full-length gene could be identified in the databases, despite experimental determination of a significant amount of amino acid sequence. Nine previously unidentified proteins with lumenal transit peptides are presented along with their full-length genes; seven of these proteins possess the twin arginine motif that is characteristic for substrates of the TAT pathway. Logoplots were used to provide a detailed analysis of the lumenal targeting signals, and all nuclear-encoded proteins identified on the two-dimensional gels were used to test predictions for chloroplast localization and transit peptides made by the software programs ChloroP, PSORT, and SignalP. A combination of these three programs was found to provide a useful tool for evaluating chloroplast localization and transit peptides and also could reveal possible alternative processing sites and dual targeting. The potential of proteomics for plant biology and homology-based searching with mass spectrometry data is discussed.

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“…I n the last decade, mass spectrometry has emerged as an important tool for the analysis of biomolecules [1]. While most of the attention has been focused on proteins, there is a growing interest in the analysis of carbohydrates.…”

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confidence: 99%

Structural analysis of κ-carrageenan sulfated oligosaccharides by positive mode Nano-ESI-FTICR-MS and MS/MS by SORI-CID

Aguilan

Dayrit

Zhang

et al. 2006

J. Am. Soc. Mass Spectrom.

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Structural analysis of sulfated oligosaccharides from -carrageenan of up to ten residues (MW Ͼ2 kDa) was successfully carried out by positive mode nano-ESI-FTICR-MS together with MS/MS using sustained off-resonance irradiation-collision induced dissociation (SORI-CID). Glycosidic bond cleavage reactions via the B-and Y-types of fragmentation were observed and enabled complete sequencing of the oligosaccharide samples. The positions of the labile sulfate substituents were observable using SORI-CID, enabling the determination of the sequence of the sulfated residues. (J Am Soc Mass Spectrom 2006, 17, 96 -103)

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Biomolecule Mass Spectrometry

Cited by 167 publications

References 19 publications

Electron capture dissociation and infrared multiphoton dissociation of oligodeoxynucleotide dications

Electron capture dissociation and infrared multiphoton dissociation of oligodeoxynucleotide dications

Proteomics of the Chloroplast: Systematic Identification and Targeting Analysis of Lumenal and Peripheral Thylakoid Proteins

Structural analysis of κ-carrageenan sulfated oligosaccharides by positive mode Nano-ESI-FTICR-MS and MS/MS by SORI-CID

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