Validated MALDI-TOF/TOF mass spectra for protein standards

Falkner, Jayson A.; Kachman, Maureen; Veine, Donna M.; Walker, Angela K.; Strahler, John R.; Andrews, Philip C.

doi:10.1016/j.jasms.2007.01.010

Cited by 58 publications

(58 citation statements)

References 21 publications

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“…Hence the commercially purified standard proteins from bovine, chicken, rabbit, horse, Bacillus lichenformis, yeast and Escherichia coli (Keller et al, 2002b) might each contain more than 0.01% of hundreds of copurifying proteins and this would explain that upon analysis by LC-MS/MS, the small minority of spectra showed high scores that correlated to the 18 purified proteins, but the vast majority of spectra did not match the purified targets (Keller et al, 2002b). In this regard, a set of cloned human proteins expressed in E. coli and highly purified by affinity chromatography showed that half the tandem spectra collected were correctly assigned to the specific set of recombinant proteins with the remainder presumably from the E. coli host (Falkner et al, 2007). Furthermore a more accurate estimate of instrument reliability might be obtained by analyzing a well-defined mixture of very high purity, such as purified viral proteins (Chelius et al, 2002).…”

Section: Specificity Of Lc-ms/ms Of Bloodmentioning

confidence: 99%

Mass spectrometry of peptides and proteins from human blood

Zhu

Bowden

Zhang

et al. 2010

Mass Spectrometry Reviews

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It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.

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Section: Specificity Of Lc-ms/ms Of Bloodmentioning

confidence: 99%

Mass spectrometry of peptides and proteins from human blood

Zhu

Bowden

Zhang

et al. 2010

Mass Spectrometry Reviews

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“…4E). Purified NicA was analyzed further by matrix-assisted laser desorption ionization-time of flight mass spectrometry using peptide mass fingerprinting techniques for an array of peptide masses resulting from enzymatic digestion of the protein isolated from an SDS-PAGE gel (8). The two digested peptides were both identical to the translation products of nicA gene fragments (for DAEKSFTR the MASCOT ion score was 41.4191; for LLSMSP YLTR, the Mascot ion score was 43.3286) (see Fig.…”

Section: Vol 75 2009mentioning

confidence: 99%

Novel Nicotine Oxidoreductase-Encoding Gene Involved in Nicotine Degradation by Pseudomonas putida Strain S16

Tang

Wang

Meng

et al. 2009

Appl Environ Microbiol

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There are quite a few ongoing biochemical investigations of nicotine degradation in different organisms. In this work, we identified and sequenced a gene (designated nicA) involved in nicotine degradation by Pseudomonas putida strain S16. The gene product, NicA, was heterologously expressed and characterized as a nicotine oxidoreductase catalyzing the initial steps of nicotine metabolism. Biochemical analyses using resting cells and the purified enzyme suggested that nicA encodes an oxidoreductase, which converts nicotine to 3-succinoylpyridine through pseudooxynicotine. Based on enzymatic reactions and direct evidence obtained using H 2 18 O labeling, the process may consist of enzyme-catalyzed dehydrogenation, followed by spontaneous hydrolysis and then repetition of the dehydrogenation and hydrolysis steps. Sequence comparisons revealed that the gene showed 40% similarity to genes encoding NADH dehydrogenase subunit I and cytochrome c oxidase subunit I in eukaryotes. Our findings demonstrate that the molecular mechanism for nicotine degradation in strain S16 involves the pyrrolidine pathway and is similar to the mechanism in mammals, in which pseudooxynicotine, the direct precursor of a potent tobacco-specific lung carcinogen, is produced.

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“…In such a case, no gas was added to the collision cell; only variation of the laser fluence in the ion source was employed to trigger the dissociation processes according to metastable fragmentation in a field free region [52]. Given the availability of both LID and LID/ CID high energy dissociation regimes, MALDI-TOF/TOF constitutes a major versatile analytical tool in proteomics [53,54] and more generally in any field requiring high throughput analyses [55]. The same results were obtained under all dissociation conditions as depicted in Table 1.…”

Section: Influence Of Precursor Ion Activation Methods On C-terminal Rmentioning

confidence: 99%

Occurrence of C-Terminal Residue Exclusion in Peptide Fragmentation by ESI and MALDI Tandem Mass Spectrometry

Dupré

Cantel

Martinez

et al. 2011

J. Am. Soc. Mass Spectrom.

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By screening a data set of 392 synthetic peptides MS/MS spectra, we found that a known C-terminal rearrangement was unexpectedly frequently occurring from monoprotonated molecular ions in both ESI and MALDI tandem mass spectrometry upon low and high energy collision activated dissociations with QqTOF and TOF/TOF mass analyzer configuration, respectively. Any residue localized at the C-terminal carboxylic acid end, even a basic one, was lost, provided that a basic amino acid such arginine and to a lesser extent histidine and lysine was present in the sequence leading to a fragment ion, usually depicted as (b n-1 +H 2 O) ion, corresponding to a shortened nonscrambled peptide chain. Far from being an epiphenomenon, such a residue exclusion from the peptide chain C-terminal extremity gave a fragment ion that was the base peak of the MS/MS spectrum in certain cases. Within the frame of the mobile proton model, the ionizing proton being sequestered onto the basic amino acid side chain, it is known that the charge directed fragmentation mechanism involved the C-terminal carboxylic acid function forming an anhydride intermediate structure.The same mechanism was also demonstrated from cationized peptides. To confirm such assessment, we have prepared some of the peptides that displayed such C-terminal residue exclusion as a C-terminal backbone amide. As expected in this peptide amide series, the production of truncated chains was completely suppressed. Besides, multiply charged molecular ions of all peptides recorded in ESI mass spectrometry did not undergo such fragmentation validating that any mobile ionizing proton will prevent such a competitive C-terminal backbone rearrangement. Among all well-known nondirect sequence fragment ions issued from non specific loss of neutral molecules (mainly H 2 O and NH 3 ) and multiple backbone amide ruptures (b-type internal ions), the described Cterminal residue exclusion is highly identifiable giving raise to a single fragment ion in the high mass range of the MS/MS spectra. The mass difference between this signal and the protonated molecular ion corresponds to the mass of the C-terminal residue. It allowed a straightforward identification of the amino acid positioned at this extremity. It must be emphasized that a neutral residue loss can be misattributed to the formation of a y m-1 ion, i.e., to the loss of the N-terminal residue following the a 1 -y m-1 fragmentation channel. Extreme caution must be adopted when reading the direct sequence ion on the positive ion MS/MS spectra of singly charged peptides not to mix up the attribution of the N-and C-terminal amino acids. Although such peculiar fragmentation behavior is of obvious interest for de novo peptide sequencing, it can also be exploited in proteomics, especially for studies involving digestion protocols carried out with proteolytic enzymes other than trypsin (Lys-N, Glu-C, and Asp-N) that produce arginine-containing peptides.

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Validated MALDI-TOF/TOF mass spectra for protein standards

Cited by 58 publications

References 21 publications

Mass spectrometry of peptides and proteins from human blood

Mass spectrometry of peptides and proteins from human blood

Novel Nicotine Oxidoreductase-Encoding Gene Involved in Nicotine Degradation by Pseudomonas putida Strain S16

Occurrence of C-Terminal Residue Exclusion in Peptide Fragmentation by ESI and MALDI Tandem Mass Spectrometry

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