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Jennifer S Brodbelt - One of the best experts on this subject based on the ideXlab platform.

  • differentiation and distributions of dna cisplatin crosslinks by liquid chromatography electrospray ionization Infrared Multiphoton Dissociation mass spectrometry
    Journal of the American Society for Mass Spectrometry, 2014
    Co-Authors: Jennifer S Brodbelt
    Abstract:

    Liquid chromatography-electrospray ionization-Infrared Multiphoton Dissociation (IRMPD) mass spectrometry was developed to investigate the distributions of intrastrand crosslinks formed between cisplatin and two oligodeoxynucleotides (ODNs), d(A1T2G3G4G5T6A7C8C9C10A11T12) (G3-D) and its analog d(A1T2G3G4G5T6T7C8C9C10A11T12) (G3-H), which have been reported to adopt different secondary structures in solution. Based on the formation of site-specific fragment ions upon IRMPD, two isobaric crosslink products were differentiated for each ODN. The preferential formation of G3G4 and G4G5 crosslinks was determined as a function of reaction conditions, including incubation temperature and presence of metal ions. G3-D consistently exhibited a greater preference for formation of the G4G5 crosslink compared with the G3-H ODN. The ratio of G3G4:G4G5 crosslinks increased for both G3-D and G3-H at higher incubation temperatures or when metal salts were added. Comparison of the IRMPD fragmentation patterns of the unmodified ODNs and the intramolecular platinated crosslinks indicated that backbone cleavage was significantly suppressed near the crosslink.

  • increased sequence coverage of thymine rich oligodeoxynucleotides by Infrared Multiphoton Dissociation compared to collision induced Dissociation
    Journal of Mass Spectrometry, 2010
    Co-Authors: Carol Parr, Jennifer S Brodbelt
    Abstract:

    Infrared Multiphoton Dissociation (IRMPD) of thymine-rich oligodeoxynucleotides in a linear ion-trap mass spectrometer affords far more extensive fragmentation than conventional collision-induced Dissociation (CID). For oligodeoxynucleotides containing one non-thymine base, CID results primarily in cleavage on the 3' side of the non-thymine nucleobase, whereas IRMPD results in cleavages between all the nucleobases and thus provides complete sequence coverage. Furthermore, for oligodeoxynucleotides containing a single non-thymine base, it is shown that the full series of diagnostic sequence ions observed in the IRMPD mass spectra arise from secondary Dissociation of the two primary products formed from the initial cleavage site located next to the non-thymine base.

  • Characterization of aziridinylbenzoquinone DNA cross-links by liquid chromatography-Infrared Multiphoton Dissociation-mass spectrometry
    Chemical research in toxicology, 2010
    Co-Authors: Sarah E. Pierce, Lynn J. Guziec, Frank S. Guziec, Jennifer S Brodbelt
    Abstract:

    DNA cross-linking was evaluated by liquid chromatography-tandem mass spectrometry to determine the relative cross-linking abilities of two aziridinylbenzoquinones. Reactivities of RH1 (2,5-diaziridinyl-3-[hydroxymethyl]-6-methyl-1,4-benzoquinone), a clinically studied antitumor cross-linking agent, and an analogue containing a phenyl group (2,5-diaziridinyl-3-[hydroxymethyl]-6-phenyl-1,4-benzoquinone, PhRH1) rather than a methyl group were compared. The bulky phenyl substituent was added to determine the impact of steric hindrance on the formation of cross-links within a double helical structure. Cross-links formed by RH1 and PhRH1 were observed at 5'-dGNC sites as well as 5'-dGAAC/dGTTC sites. RH1 was more effective at forming cross-links than PhRH1 for a variety of duplexes. Infrared Multiphoton Dissociation (IRMPD) and collision-induced Dissociation results confirmed the presence and the location of the cross-links within the duplexes, and IRMPD was used to identify the Dissociation pathways of the cross-linked duplexes.

  • Infrared Multiphoton Dissociation of small-interfering RNA anions and cations
    Journal of the American Society for Mass Spectrometry, 2010
    Co-Authors: Myles W Gardner, Andrew D. Ellington, Jennifer S Brodbelt
    Abstract:

    Infrared Multiphoton Dissociation (IRMPD) on a linear ion trap mass spectrometer is applied for the sequencing of small interfering RNA (siRNA). Both single-strand siRNAs and duplex siRNA were characterized by IRMPD, and the results were compared with that obtained by traditional ion trap-based collision induced Dissociation (CID). The single-strand siRNA anions were observed to dissociate via cleavage of the 5′ P—O bonds yielding c- and y-type product ions as well as undergo neutral base loss. Full sequence coverage of the siRNA anions was obtained by both IRMPD and CID. While the CID mass spectra were dominated by base loss ions, accounting for ∼25% to 40% of the product ion current, these ions were eliminated through secondary Dissociation by increasing the irradiation time in the IRMPD mass spectra to produce higher abundances of informative sequence ions. With longer irradiation times, however, internal ions corresponding to cleavage of two 5′ P—O bonds began to populate the product ion mass spectra as well as higher abundances of [a − Base] and w-type ions. IRMPD of siRNA cations predominantly produced c- and y-type ions with minimal contributions of [a − Base] and w-type ions to the product ion current; the presence of only two complementary series of product ions in the IRMPD mass spectra simplified spectral interpretation. In addition, IRMPD produced high abundances of protonated nucleobases, [G + H]^+, [A + H]^+, and [C + H]^+, which were not detected in the CID mass spectra due to the low-mass cut-off associated with conventional CID in ion traps. CID and IRMPD using short irradiation times of duplex siRNA resulted in strand separation, similar to the Dissociation trends observed for duplex DNA. With longer irradiation times, however, the individual single-strands underwent secondary Dissociation to yield informative sequence ions not obtained by CID.

  • Infrared Multiphoton Dissociation of peptide cations in a dual pressure linear ion trap mass spectrometer
    Analytical Chemistry, 2009
    Co-Authors: Myles W Gardner, Aaron R. Ledvina, Joshua J. Coon, James A Madsen, Suncerae I Smith, Jae C Schwartz, George C Stafford, Jennifer S Brodbelt
    Abstract:

    A dual pressure linear ion trap mass spectrometer was modified to permit Infrared Multiphoton Dissociation (IRMPD) in each of the two cells—the first a high pressure cell operated at nominally 5 × 10−3 Torr and the second a low pressure cell operated at nominally 3 × 10−4 Torr. When IRMPD was performed in the high pressure cell, most peptide ions did not undergo significant photoDissociation; however, in the low pressure cell peptide cations were efficiently dissociated with less than 25 ms of IR irradiation regardless of charge state. IRMPD of peptide cations allowed the detection of low m/z product ions including the y1 fragments and immonium ions which are not typically observed by ion trap collision induced Dissociation (CID). PhotoDissociation efficiencies of ∼100% and MS/MS (tandem mass spectrometry) efficiencies of greater than 60% were observed for both multiply and singly protonated peptides. In general, higher sequence coverage of peptides was obtained using IRMPD over CID. Further, greater than...

Kristina Håkansson - One of the best experts on this subject based on the ideXlab platform.

  • electron detachment Dissociation and negative ion Infrared Multiphoton Dissociation of electrosprayed intact proteins
    Analytical Chemistry, 2012
    Co-Authors: Hangtian Song, Kristina Håkansson
    Abstract:

    In top-down proteomics, intact gaseous proteins are fragmented in a mass spectrometer by, e.g., electron capture Dissociation (ECD) to obtain structural information. By far, most top-down approaches involve Dissociation of protein cations. However, in electrospray ionization of phosphoproteins, the high acidity of phosphate may contribute to the formation of intramolecular hydrogen bonds or salt bridges, which influence subsequent fragmentation behavior. Other acidic proteins or proteins with regions containing multiple acidic residues may also be affected similarly. Negative ion mode, on the other hand, may enhance deprotonation and unfolding of multiply phosphorylated or highly acidic protein regions. Here, activated ion electron detachment Dissociation (AI-EDD) and negative ion Infrared Multiphoton Dissociation (IRMPD) were employed to investigate the fragmentation of intact proteins, including multiply phosphorylated β-casein, calmodulin, and glycosylated ribonuclease B. Compared to AI-ECD and positive ion IRMPD, AI-EDD and negative ion IRMPD provide complementary protein sequence information, particularly in regions with high acidity, including the multiply phosphorylated region of β-casein.

  • characterization of oligodeoxynucleotide fragmentation pathways in Infrared Multiphoton Dissociation and electron detachment Dissociation by fourier transform ion cyclotron double resonance
    European Journal of Mass Spectrometry, 2009
    Co-Authors: Jiong Yang, Kristina Håkansson
    Abstract:

    Infrared Multiphoton Dissociation (IRMPD) is a vibrational excitation tandem mass spectrometric fragmentation method valuable for sequencing of oligonucleotides. For oligodeoxynucleotides, typical product ions correspond to sequence-specific 5' (a-base) and their complementary 3' w-type ions from carbon-oxygen bond cleavage at the 3' position of the deoxyribose from which a nucleobase is lost. Such fragmentation patterns are also observed in collision activated Dissociation (CAD). The CAD oligodeoxynucleotide fragmentation mechanism has been characterized in detail. By contrast, fragmentation schemes in IRMPD have not been rigorously established. In this paper, we apply, for the first time, Fourier transform ion cyclotron double resonance (DR) experiments to characterize IRMPD fragmentation pathways of oligodeoxynucleotide anions. Our results suggest that neutral base loss precedes backbone fragmentation but that T-rich oligodeoxynucleotides fragment via a different mechanism, similar to the mechanisms proposed for CAD. We also extend the DR approach to characterize intermediates in electron detachment Dissociation of hexamer oligodeoxynucleotides. Here, we found that charge reduced radical precursor ions constitute major intermediates for dT(6), d(GCATAC) and d(GCATGC). Furthermore, (a/z-T) ions (z ions correspond to C-O bond cleavage on the other side of a backbone phosphate group as compared to the formation of a ions) mainly originate from secondary fragmentation of a/z radical ions for the oligodeoxynucleotide dT(6).

  • Infrared Multiphoton Dissociation and electron induced Dissociation as alternative ms ms strategies for metabolite identification
    Analytical Chemistry, 2007
    Co-Authors: Hyun Ju Yoo, Haichuan Liu, Kristina Håkansson
    Abstract:

    A major challenge encountered in mass spectrometric metabolite analysis is the identification and structural characterization of metabolites. Fourier transform ion cyclotron resonance mass spectrometry is a valuable technique for metabolite structural determination because it provides accurate masses and allows for multiple MS/MS fragmentation strategies, including Infrared Multiphoton Dissociation (IRMPD) and electron-induced Dissociation (EID). Collision activated Dissociation (CAD) is currently the most commonly used MS/MS technique for metabolite structural characterization. In contrast, IRMPD and EID have had very limited, if any, application for metabolite characterization. Here, we explore IRMPD and EID of phosphate-containing metabolites and compare the resulting fragmentation patterns to those of CAD. Our results show that CAD, IRMPD, and EID provide complementary structural information for phosphate-containing metabolites. Overall, CAD provided the most extensive fragmentation for smaller (<600 ...

  • preferential cleavage of ss and cs bonds in electron detachment Dissociation and Infrared Multiphoton Dissociation of disulfide linked peptide anions
    International Journal of Mass Spectrometry, 2007
    Co-Authors: Anastasia Kalli, Kristina Håkansson
    Abstract:

    Abstract Disulfide bonds generally show only limited cleavage in positive ion mode collision activated Dissociation (CAD). However, it has been demonstrated that a reverse situation exists in negative ion mode in which preferential S S and C S bond cleavage occurs. Here, we show that electron detachment Dissociation (EDD) and Infrared Multiphoton Dissociation (IRMPD) of peptide anions containing disulfide linkages also result in preferential cleavage of S S and C S bonds. Resulting products are mainly radical ions in EDD whereas IRMPD produces even-electron product ions, as expected, thereby supporting different disulfide cleavage mechanisms for these two fragmentation processes. We also show that, in EDD, the presence of tryptophan can result in abundant side chain loss (129 Da), which effectively can compete with disulfide bond cleavage.

  • Collision-activated Dissociation, Infrared Multiphoton Dissociation, and electron capture Dissociation of the Bacillus anthracis siderophore petrobactin and its metal ion complexes
    Journal of the American Society for Mass Spectrometry, 2007
    Co-Authors: Haichuan Liu, Kristina Håkansson, Jung Yeop Lee, David H. Sherman
    Abstract:

    Siderophores are high-affinity iron-chelating ligands produced by microorganisms to scavenge vital Fe3+ from the environment. Thus, siderophores constitute potential therapeutic targets and their structural determination is important for exploiting their therapeutic value. Here, the virulence-associated siderophore petrobactin from Bacillus anthracis was characterized with electron capture Dissociation (ECD). Fragmentation of doubly protonated petrobactin was investigated and compared to sustained off-resonance irradiation collision-activated Dissociation (SORI CAD) and Infrared Multiphoton Dissociation (IRMPD) of both the singly and doubly protonated species. These experiments demonstrate that ECD provides additional information (complementary bond cleavages) on the structure of petrobactin compared to both SORI CAD and IRMPD. Furthermore, complexes of petrobactin with divalent (Ca2+, Fe2+, and Co2+) and trivalent (Fe3+ and Ga3+) metal cations were also subjected to SORI CAD and ECD. Again, most structural information was obtained from the ECD spectra. However, significant differences were found in both SORI CAD and ECD of metal complexes, dependent on the nature of the metal ion. Intriguingly, unique behavior, consistent with a recently proposed solution-phase structure, was observed for the highly preferred Fe3+—petrobactin complex.

Alan G. Marshall - One of the best experts on this subject based on the ideXlab platform.

  • structural characterization of the gm1 ganglioside by Infrared Multiphoton Dissociation electron capture Dissociation and electron detachment Dissociation electrospray ionization ft icr ms ms
    Journal of the American Society for Mass Spectrometry, 2005
    Co-Authors: Melinda A Mcfarland, Alan G. Marshall, Carol L Nilsson, Christopher L Hendrickson, Pam Fredman, Janeric Mansson
    Abstract:

    Gangliosides play important biological roles and structural characterization of both the carbohydrate and the lipid moieties is important. The FT-ICR MS/MS techniques of electron capture Dissociation (ECD), electron detachment Dissociation (EDD), and Infrared Multiphoton Dissociation (IRMPD) provide extensive fragmentation of the protonated and deprotonated GM1 ganglioside. ECD provides extensive structural information, including identification of both halves of the ceramide and cleavage of the acetyl moiety of the N-acetylated sugars. IRMPD provides similar glycan fragmentation but no cleavage of the acetyl moiety. Cleavage between the fatty acid and the long-chain base of the ceramide moiety is seen in negative-ion IRMPD but not in positive-ion IRMPD of GM1. Furthermore, this extent of fragmentation requires a range of laser powers, whereas all information is available from a single ECD experiment. However, stepwise fragmentation by IRMPD may be used to map the relative labilities for a series of cleavages. EDD provides the alternative of electron-induced fragmentation for negative ions with extensive fragmentation, but suffers from low efficiency as well as complication of data analysis by frequent loss of hydrogen atoms. We also show that analysis of MS/MS data for glycolipids is greatly simplified by classification of product ion masses to specific regions of the ganglioside based solely on mass defect graphical analysis.

  • combined electron capture and Infrared Multiphoton Dissociation for multistage ms ms in a fourier transform ion cyclotron resonance mass spectrometer
    Analytical Chemistry, 2003
    Co-Authors: Kristina Håkansson, Michael J Chalmers, John P Quinn, Melinda A Mcfarland, Christopher L Hendrickson, Alan G. Marshall
    Abstract:

    We have mounted a permanent on-axis dispenser cathode electron source inside the magnet bore of a 9.4-T Fourier transform ion cyclotron resonance mass spectrometer. This configuration allows electron capture Dissociation (ECD) to be performed reliably on a millisecond time scale. We have also implemented an off-axis laser geometry that enables simultaneous access to ECD and Infrared Multiphoton Dissociation (IRMPD). Optimum performance of both fragmentation techniques is maintained. The analytical utility of performing either ECD or IRMPD on a given precursor ion population is demonstrated by structural characterization of several posttranslationally modified peptides:  IRMPD of phosphorylated peptides results in few backbone (b- and y-type) cleavages, and product ion spectra are dominated by neutral loss of H3PO4. In contrast, ECD provides significantly more backbone (c- and z•-type) cleavages without loss of H3PO4. For N-glycosylated tryptic peptides, IRMPD causes extensive cleavage of the glycosidic bo...

  • electron capture Dissociation and Infrared Multiphoton Dissociation of oligodeoxynucleotide dications
    Journal of the American Society for Mass Spectrometry, 2003
    Co-Authors: Kristina Håkansson, Robert R. Hudgins, Alan G. Marshall, Richard A J Ohair
    Abstract:

    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 fragmention, a requirement that is less likely for small fragments.

  • structural validation of saccharomicins by high resolution and high mass accuracy fourier transform ion cyclotron resonance mass spectrometry and Infrared Multiphoton Dissociation tandem mass spectrometry
    Journal of the American Society for Mass Spectrometry, 1999
    Co-Authors: Stone D H Shi, Alan G. Marshall, Christopher L Hendrickson, Marshall M Siegel, Fangming Kong, Guy T Carter
    Abstract:

    Exceptionally high mass resolving power and mass accuracy combined with tandem mass spectrometry (MSn) capability make Fourier transform ion cyclotron resonance mass spectrometry a powerful tool for structure verification and determination of biological macromolecules. By means of local internal calibration and electron mass correction, mass accuracy better than ±0.5 ppm was achieved for two oligosaccharide antibiotics, Saccharomicins A and B, consistent with the proposed elemental compositions based upon NMR data. High resolution and high mass accuracy MS/MS data were obtained for both oligosaccharides by use of Infrared Multiphoton Dissociation (IRMPD) with a 40 W continuous-wave CO2 laser. The spectra were charge-state deconvolved by the “Z-score” algorithm to yield much simpler mass-only spectra. Sequences of 15 sugar residues could be confirmed from the charge state deconvolved accurate mass MS/MS spectra for Saccharomicins A and B, even without use of traditional prior permethylation. A fragment corresponding to an internal sugar loss rearrangement was observed by IRMPD and studied by collision activated Dissociation MS4.

  • identification of intact proteins in mixtures by alternated capillary liquid chromatography electrospray ionization and lc esi Infrared Multiphoton Dissociation fourier transform ion cyclotron resonance mass spectrometry
    Analytical Chemistry, 1999
    Co-Authors: Christopher L Hendrickson, Mark R Emmett, Alan G. Marshall
    Abstract:

    Here we propose a novel method for rapidly identifying proteins in complex mixtures. A list of candidate proteins (including provision for posttranslational modifications) is obtained by database searching, within a specified mass range about the accurately measured mass (e.g., ±0.1 Da at 10 kDa) of the intact protein, by capillary liquid chromatography electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (LC ESI FT-ICR MS). On alternate scans, LC ESI Infrared Multiphoton Dissociation (IRMPD) FT-ICR MS yields mostly b and y fragment ions for each protein, from which the correct candidate is identified as the one with the highest “hit” score (i.e., most b and y fragments matching the candidate database protein amino acid sequence masses) and sequence “tag” score (based on a series of fragment sequences differing in mass by 1 or 2 amino acids). The method succeeds in uniquely identifying each of a mixture of five proteins treated as unknowns (melittin, ubiquitin, GroES, myoglo...

Myles W Gardner - One of the best experts on this subject based on the ideXlab platform.

  • Infrared Multiphoton Dissociation of small-interfering RNA anions and cations
    Journal of the American Society for Mass Spectrometry, 2010
    Co-Authors: Myles W Gardner, Andrew D. Ellington, Jennifer S Brodbelt
    Abstract:

    Infrared Multiphoton Dissociation (IRMPD) on a linear ion trap mass spectrometer is applied for the sequencing of small interfering RNA (siRNA). Both single-strand siRNAs and duplex siRNA were characterized by IRMPD, and the results were compared with that obtained by traditional ion trap-based collision induced Dissociation (CID). The single-strand siRNA anions were observed to dissociate via cleavage of the 5′ P—O bonds yielding c- and y-type product ions as well as undergo neutral base loss. Full sequence coverage of the siRNA anions was obtained by both IRMPD and CID. While the CID mass spectra were dominated by base loss ions, accounting for ∼25% to 40% of the product ion current, these ions were eliminated through secondary Dissociation by increasing the irradiation time in the IRMPD mass spectra to produce higher abundances of informative sequence ions. With longer irradiation times, however, internal ions corresponding to cleavage of two 5′ P—O bonds began to populate the product ion mass spectra as well as higher abundances of [a − Base] and w-type ions. IRMPD of siRNA cations predominantly produced c- and y-type ions with minimal contributions of [a − Base] and w-type ions to the product ion current; the presence of only two complementary series of product ions in the IRMPD mass spectra simplified spectral interpretation. In addition, IRMPD produced high abundances of protonated nucleobases, [G + H]^+, [A + H]^+, and [C + H]^+, which were not detected in the CID mass spectra due to the low-mass cut-off associated with conventional CID in ion traps. CID and IRMPD using short irradiation times of duplex siRNA resulted in strand separation, similar to the Dissociation trends observed for duplex DNA. With longer irradiation times, however, the individual single-strands underwent secondary Dissociation to yield informative sequence ions not obtained by CID.

  • Infrared Multiphoton Dissociation of peptide cations in a dual pressure linear ion trap mass spectrometer
    Analytical Chemistry, 2009
    Co-Authors: Myles W Gardner, Aaron R. Ledvina, Joshua J. Coon, James A Madsen, Suncerae I Smith, Jae C Schwartz, George C Stafford, Jennifer S Brodbelt
    Abstract:

    A dual pressure linear ion trap mass spectrometer was modified to permit Infrared Multiphoton Dissociation (IRMPD) in each of the two cells—the first a high pressure cell operated at nominally 5 × 10−3 Torr and the second a low pressure cell operated at nominally 3 × 10−4 Torr. When IRMPD was performed in the high pressure cell, most peptide ions did not undergo significant photoDissociation; however, in the low pressure cell peptide cations were efficiently dissociated with less than 25 ms of IR irradiation regardless of charge state. IRMPD of peptide cations allowed the detection of low m/z product ions including the y1 fragments and immonium ions which are not typically observed by ion trap collision induced Dissociation (CID). PhotoDissociation efficiencies of ∼100% and MS/MS (tandem mass spectrometry) efficiencies of greater than 60% were observed for both multiply and singly protonated peptides. In general, higher sequence coverage of peptides was obtained using IRMPD over CID. Further, greater than...

  • top down protein fragmentation by Infrared Multiphoton Dissociation in a dual pressure linear ion trap
    Analytical Chemistry, 2009
    Co-Authors: James A Madsen, Aaron R. Ledvina, Joshua J. Coon, Myles W Gardner, Suncerae I Smith, Jae C Schwartz, George C Stafford, Jennifer S Brodbelt
    Abstract:

    Infrared Multiphoton Dissociation (IRMPD) was implemented in a novel dual pressure linear ion trap for rapid top-down proteomics. The high pressure cell provided improved trapping and isolation efficiencies while the isotopic profiles of 10+ charged ions could be resolved by mass analysis in the low pressure cell that enabled effective top down protein identification. Striking differences between IRMPD in the low pressure cell and CID in the high pressure cell were observed for proteins ranging from 8.6 to 29 kDa. Because of secondary Dissociation, IRMPD yielded product ions in significantly lower charge states as compared to CID, thus facilitating more accurate mass identification and streamlining product ion assignment. This outcome was especially useful for database searching of larger proteins (∼29 kDa) as IRMPD substantially improved protein identification and scoring confidence. Also, IRMPD showed an increased selectivity toward backbone cleavages N-terminal to proline and C-terminal to acidic resid...

  • chromogenic cross linker for the characterization of protein structure by Infrared Multiphoton Dissociation mass spectrometry
    Analytical Chemistry, 2008
    Co-Authors: Myles W Gardner, Shagufta H Shabbir, Eric V Anslyn, Lisa Vasicek, Jennifer S Brodbelt
    Abstract:

    We have developed a new IR chromogenic cross-linker (IRCX) to aid in rapidly distinguishing cross-linked peptides from unmodified species in complex mixtures. By incorporating a phosphate functional group into the cross-linker, one can take advantage of its unique IR absorption properties, affording selective Infrared Multiphoton Dissociation (IRMPD) of the cross-linked peptides. In a mock mixture of unmodified peptides and IRCX-cross-linked peptides (intramolecularly and intermolecularly cross-linked), only the peptides containing the IRCX modification were shown to dissociate upon exposure to 50 ms of 10.6-μm radiation. LC-IRMPD-MS proved to be an effective method to distinguish the cross-linked peptides in a tryptic digest of IRCX-cross-linked ubiquitin. A total of four intermolecular cross-links and two dead-end modifications were identified using IRCX and LC-IRMPD-MS. IRMPD of these cross-linked peptides resulted in secondary Dissociation of all primary fragment ions containing the chromophore, produ...

Christopher L Hendrickson - One of the best experts on this subject based on the ideXlab platform.

  • structural characterization of the gm1 ganglioside by Infrared Multiphoton Dissociation electron capture Dissociation and electron detachment Dissociation electrospray ionization ft icr ms ms
    Journal of the American Society for Mass Spectrometry, 2005
    Co-Authors: Melinda A Mcfarland, Alan G. Marshall, Carol L Nilsson, Christopher L Hendrickson, Pam Fredman, Janeric Mansson
    Abstract:

    Gangliosides play important biological roles and structural characterization of both the carbohydrate and the lipid moieties is important. The FT-ICR MS/MS techniques of electron capture Dissociation (ECD), electron detachment Dissociation (EDD), and Infrared Multiphoton Dissociation (IRMPD) provide extensive fragmentation of the protonated and deprotonated GM1 ganglioside. ECD provides extensive structural information, including identification of both halves of the ceramide and cleavage of the acetyl moiety of the N-acetylated sugars. IRMPD provides similar glycan fragmentation but no cleavage of the acetyl moiety. Cleavage between the fatty acid and the long-chain base of the ceramide moiety is seen in negative-ion IRMPD but not in positive-ion IRMPD of GM1. Furthermore, this extent of fragmentation requires a range of laser powers, whereas all information is available from a single ECD experiment. However, stepwise fragmentation by IRMPD may be used to map the relative labilities for a series of cleavages. EDD provides the alternative of electron-induced fragmentation for negative ions with extensive fragmentation, but suffers from low efficiency as well as complication of data analysis by frequent loss of hydrogen atoms. We also show that analysis of MS/MS data for glycolipids is greatly simplified by classification of product ion masses to specific regions of the ganglioside based solely on mass defect graphical analysis.

  • combined electron capture and Infrared Multiphoton Dissociation for multistage ms ms in a fourier transform ion cyclotron resonance mass spectrometer
    Analytical Chemistry, 2003
    Co-Authors: Kristina Håkansson, Michael J Chalmers, John P Quinn, Melinda A Mcfarland, Christopher L Hendrickson, Alan G. Marshall
    Abstract:

    We have mounted a permanent on-axis dispenser cathode electron source inside the magnet bore of a 9.4-T Fourier transform ion cyclotron resonance mass spectrometer. This configuration allows electron capture Dissociation (ECD) to be performed reliably on a millisecond time scale. We have also implemented an off-axis laser geometry that enables simultaneous access to ECD and Infrared Multiphoton Dissociation (IRMPD). Optimum performance of both fragmentation techniques is maintained. The analytical utility of performing either ECD or IRMPD on a given precursor ion population is demonstrated by structural characterization of several posttranslationally modified peptides:  IRMPD of phosphorylated peptides results in few backbone (b- and y-type) cleavages, and product ion spectra are dominated by neutral loss of H3PO4. In contrast, ECD provides significantly more backbone (c- and z•-type) cleavages without loss of H3PO4. For N-glycosylated tryptic peptides, IRMPD causes extensive cleavage of the glycosidic bo...

  • structural validation of saccharomicins by high resolution and high mass accuracy fourier transform ion cyclotron resonance mass spectrometry and Infrared Multiphoton Dissociation tandem mass spectrometry
    Journal of the American Society for Mass Spectrometry, 1999
    Co-Authors: Stone D H Shi, Alan G. Marshall, Christopher L Hendrickson, Marshall M Siegel, Fangming Kong, Guy T Carter
    Abstract:

    Exceptionally high mass resolving power and mass accuracy combined with tandem mass spectrometry (MSn) capability make Fourier transform ion cyclotron resonance mass spectrometry a powerful tool for structure verification and determination of biological macromolecules. By means of local internal calibration and electron mass correction, mass accuracy better than ±0.5 ppm was achieved for two oligosaccharide antibiotics, Saccharomicins A and B, consistent with the proposed elemental compositions based upon NMR data. High resolution and high mass accuracy MS/MS data were obtained for both oligosaccharides by use of Infrared Multiphoton Dissociation (IRMPD) with a 40 W continuous-wave CO2 laser. The spectra were charge-state deconvolved by the “Z-score” algorithm to yield much simpler mass-only spectra. Sequences of 15 sugar residues could be confirmed from the charge state deconvolved accurate mass MS/MS spectra for Saccharomicins A and B, even without use of traditional prior permethylation. A fragment corresponding to an internal sugar loss rearrangement was observed by IRMPD and studied by collision activated Dissociation MS4.

  • identification of intact proteins in mixtures by alternated capillary liquid chromatography electrospray ionization and lc esi Infrared Multiphoton Dissociation fourier transform ion cyclotron resonance mass spectrometry
    Analytical Chemistry, 1999
    Co-Authors: Christopher L Hendrickson, Mark R Emmett, Alan G. Marshall
    Abstract:

    Here we propose a novel method for rapidly identifying proteins in complex mixtures. A list of candidate proteins (including provision for posttranslational modifications) is obtained by database searching, within a specified mass range about the accurately measured mass (e.g., ±0.1 Da at 10 kDa) of the intact protein, by capillary liquid chromatography electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (LC ESI FT-ICR MS). On alternate scans, LC ESI Infrared Multiphoton Dissociation (IRMPD) FT-ICR MS yields mostly b and y fragment ions for each protein, from which the correct candidate is identified as the one with the highest “hit” score (i.e., most b and y fragments matching the candidate database protein amino acid sequence masses) and sequence “tag” score (based on a series of fragment sequences differing in mass by 1 or 2 amino acids). The method succeeds in uniquely identifying each of a mixture of five proteins treated as unknowns (melittin, ubiquitin, GroES, myoglo...