Matrix-assisted laser desorption/ionization-tandem mass spectrometry with high resolution and sensitivity for identification and characterization of proteins

Bienvenut, Willy V.; Déon, Catherine; Pasquarello, Carla; Campbell, J. M.; Sanchez, Jean‐Charles; Vestal, Marvin L.; Hochstrasser, Denis F.

doi:10.1002/1615-9861(200207)2:7<868::aid-prot868>3.0.co;2-d

Cited by 142 publications

(86 citation statements)

References 24 publications

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“…Three subunits with oxidized tryptophan residues were observed in complex V, the most oxidized being subunit d. Interestingly, a homologous peptide from subunit d was also reported to contain N-formylkynurenine by Bienvenut and co-workers (17) in bovine heart, suggesting that there may be a specificity for tryptophan oxidation in certain sequences across species as observed in Fig. 2A for NDUFS4.…”

Section: Oxidized Tryptophan Residues In Mitochondrial Proteins 19588mentioning

confidence: 71%

Oxidative Post-translational Modification of Tryptophan Residues in Cardiac Mitochondrial Proteins

Taylor¹,

Fahy²,

Murray

et al. 2003

Journal of Biological Chemistry

171

127

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We examined the distribution of N-formylkynurenine, a product of the dioxidation of tryptophan residues in proteins, throughout the human heart mitochondrial proteome. This oxidized amino acid is associated with a distinct subset of proteins, including an over-representation of complex I subunits as well as complex V subunits and enzymes involved in redox metabolism. No relationship was observed between the tryptophan modification and methionine oxidation, a known artifact of sample handling. As the mitochondria were isolated from normal human heart tissue and not subject to any artificially induced oxidative stress, we suggest that the susceptible tryptophan residues in this group of proteins are "hot spots" for oxidation in close proximity to a source of reactive oxygen species in respiring mitochondria.

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Section: Oxidized Tryptophan Residues In Mitochondrial Proteins 19588mentioning

confidence: 71%

Oxidative Post-translational Modification of Tryptophan Residues in Cardiac Mitochondrial Proteins

Taylor¹,

Fahy²,

Murray

et al. 2003

Journal of Biological Chemistry

171

127

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“…Elevated Mascot scores indicate higher probability and thus greater confidence that the proteins identified are not merely random matches in the database. It has been noted that analysis of peptides using MALDI/TOF/TOF instruments using high energy collisions (Ͼ1 kV) gives rise to a significant number of similar fragments [10,21]. The d and w ions generated in high energy collisions were not observed however in the MALDI Q-TOF data.…”

Section: Resultsmentioning

confidence: 99%

“…Matrix assisted laser desorption ionization (MALDI) in conjunction with MS/MS analysis has also been used to acquire product ion spectra from proteomic samples, generating data sets both analogous to and complementary with those produced by LC/ESI/MS/MS [8 -12]. While differences in the spectral content of MALDI/MS/MS and ESI/MS/MS of the same peptides have been described [9,10,13], there has been less discussion focused on findings that analysis of the same sample by both LC/ESI/MS/MS and LC/MALDI/MS/MS gives rise to improved proteome coverage at both the peptide and protein level.…”

mentioning

confidence: 99%

Exploiting the complementary nature of LC/MALDI/MS/MS and LC/ESI/MS/MS for increased proteome coverage

Bodnar

Blackburn

Krise

et al. 2003

J. Am. Soc. Mass Spectrom.

175

127

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The goal of this work was to evaluate the improvement in proteome coverage of complex protein mixtures gained by analyzing samples using both LC/ESI/MS/MS and LC/MALDI/ MS/MS. Parallel analyses of a single sample were accomplished by interfacing a Probot fractionation system with a nanoscale LC system. The Probot was configured to perform a post-column split such that a fraction (20%) of the column effluent was sent for on-line LC/ESI/MS/MS data acquisition, and the majority of the sample (80%) was mixed with a matrix solution and deposited onto the MALDI target plate. The split-flow approach takes advantage of the concentration sensitive nature of ESI and provides sufficient quantity of sample for MALDI/MS/MS. Hybrid quadrupole time-of-flight mass spectrometers were used to acquire LC/ESI/MS/MS data and LC/MALDI/MS/MS data from a tryptic digest of a preparation of mammalian mitochondrial ribosomes. The mass spectrometers were configured to operate in a data dependent acquisition mode in which precursor ions observed in MS survey scans are automatically selected for interrogation by MS/MS. This type of acquisition scheme maximizes the number of peptide fragmentation spectra obtained and is commonly referred to as shotgun analysis. While a significant degree of overlap (63%) was observed between the proteins identified in the LC/ESI/MS/MS and LC/MALDI/MS/MS data sets, both unique peptides and unique proteins were observed by each method. These results demonstrate that improved proteome coverage can be obtained using a combination of these ionization techniques. (J Am Soc Mass Spectrom 2003, 14, 971-979)

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“…After electrophoresis, the protein spots of interest were digested with trypsin in situ, and the recovered peptides were purified using C 18 ZipTip pipette tips (Millipore). Mass spectrometric measurements were performed on an Applied Biosystems 4700 Proteomics Analyzer, which is a tandem time-of-flight instrument with a matrix-assisted laser desorption ionization ion source (35). Peptide sequences were determined by manual interpretation of the tandem spectra.…”

Section: Methodsmentioning

confidence: 99%

“…Aliquots of the culture, the growth of which is shown in Fig. 3A, were withdrawn on days 0, 1, 2, 3, and 6 after induction, and the cells were labeled for two hours with 35 S-amino acids in the presence of cycloheximide, followed by two-dimensional gel electrophoresis to visualize the labeled Cyb and COI spots (Fig. 3B).…”

Section: Mitochondrial Biosynthesis Of Coi and Cyb Proteins Decreasesmentioning

confidence: 99%

The Effect of RNA Interference Down-regulation of RNA Editing 3′-Terminal Uridylyl Transferase (TUTase) 1 on Mitochondrial de Novo Protein Synthesis and Stability of Respiratory Complexes in Trypanosoma brucei

Neboháčová

Maslov

Falick

et al. 2004

Journal of Biological Chemistry

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Inhibition of RNA editing by down-regulation of expression of the mitochondrial RNA editing TUTase 1 by RNA interference had profound effects on kinetoplast biogenesis in Trypanosoma brucei procyclic cells. De novo synthesis of the apocytochrome b and cytochrome oxidase subunit I proteins was no longer detectable after 3 days of RNAi. The effect on protein synthesis correlated with a decline in the levels of the assembled mitochondrial respiratory complexes III and IV, and also cyanide-sensitive oxygen uptake. The steady-state levels of nuclear-encoded subunits of complexes III and IV were also significantly decreased. Because the levels of the corresponding mRNAs were not affected, the observed effect was likely due to an increased turnover of these imported mitochondrial proteins. This induced protein degradation was selective for components of complexes III and IV, because little effect was observed on components of the F 1 ⅐F 0 -ATPase complex and on several other mitochondrial proteins.Gene expression in the kinetoplast-mitochondrion of trypanosomatid protists involves a unique post-transcriptional mRNA maturation process, termed RNA editing, whereby Uresidues are inserted to or deleted from a pre-edited transcript, and a translatable reading frame is thus created (1-5). 12 of the 18 protein-coding genes in the maxicircle component of the mitochondrial or kinetoplast DNA in Trypanosoma brucei or Leishmania tarentolae encode transcripts that require varying degrees of editing for translation competence (6). These include mRNAs for apocytochrome b (Cyb), 1 subunits II and III of cytochrome c oxidase (COII and COIII, respectively), subunit 6 of ATPase (6), several subunits of NADH dehydrogenase, and a few others. Some transcripts, such as the cytochrome oxidase subunit I (COI) mRNA, do not require editing for translation. The mechanism of editing includes cleavage of RNA at specific editing sites, and the addition or deletion of a defined number of U-residues followed by religation (7,8). The reactions are performed by large protein complexes which include a 3Ј terminal uridylyl transferase (TUTase), an RNA ligase, endo-and exonuclease activities, as well as several additional auxiliary factors of undefined function (9 -12). Subcomplexes exist that contain subsets of proteins and which may specialize in Uaddition or U-deletion (13). The information for selection of editing sites resides in small "guide" RNAs that are mainly encoded in the kinetoplast DNA minicircles (7, 14). These RNA molecules have 3Ј oligo-U tails (15), which are added posttranscriptionally by the RET1 TUTase (16, 17). Down-regulation of RET1 expression by RNA interference (RNAi) results in a decrease in the steady-state abundance of edited transcripts (16) because of an effect on the 3Ј oligo-U tail of the guide RNAs (37).Although editing provides translatable transcripts, inhibition of editing should affect protein synthesis and, consequently, the assembly of respiratory complexes in the kinetoplast. The de novo synthesis of COI and Cyb po...

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Matrix-assisted laser desorption/ionization-tandem mass spectrometry with high resolution and sensitivity for identification and characterization of proteins

Cited by 142 publications

References 24 publications

Oxidative Post-translational Modification of Tryptophan Residues in Cardiac Mitochondrial Proteins

Oxidative Post-translational Modification of Tryptophan Residues in Cardiac Mitochondrial Proteins

Exploiting the complementary nature of LC/MALDI/MS/MS and LC/ESI/MS/MS for increased proteome coverage

The Effect of RNA Interference Down-regulation of RNA Editing 3′-Terminal Uridylyl Transferase (TUTase) 1 on Mitochondrial de Novo Protein Synthesis and Stability of Respiratory Complexes in Trypanosoma brucei

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