Shifting unoccupied spectral space in mass spectrum of peptide fragment ions

Bajrami, Bekim; Shi, Yu; Lapierre, Pascal; Yao, Xudong

doi:10.1016/j.jasms.2009.07.005

Cited by 10 publications

(12 citation statements)

References 36 publications

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“…Absorbance of each culture was recorded at different time intervals after vortexing for 5 sec, to re-suspend the settled cells. USA); the quantization protocol was followed as published by the vendor 34,35 . Glucose concentration as a measure of polysaccharide content was quantified by the method as described elsewhere 36 .…”

Section: Planktonic Growth Studiesmentioning

confidence: 99%

Staphylococcus aureusBiofilm Removal by Targeting Biofilm-Associated Extracellular Proteins

Shukla

Rao

2017

Preprint

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Abstract:Aim: Among cell surface proteins, biofilm-associated protein promotes biofilm development in Staphylococcus aureus strains. Aim of this study was to investigate proteinase-mediated biofilm dispersion in different isolates of S. aureus. Methods and Results:Microtitre plate based biofilm assay showed that 2 µg/mL proteinase K significantly inhibited biofilm development in bap-positive S. aureus V329 as well as other S. aureus strains, i.e. SA7, SA10, SA33, SA352 and but not in bap-mutant M556 and SA392 (a weak biofilm producing strain). However, proteinase K treatment on S. aureus planktonic cells showed that there was no inhibition of planktonic growth at any concentration of proteinase K when tested up to 32 µg/mL. This observation ruled out the possibility of S. aureus biofilm inhibition by altering the cell viability. Proteinase K treatment upon 24 h old preformed biofilms showed an enhanced dispersion of bap-positive V329 and SA7, SA10, SA33 and SA352 biofilms, however, proteinase K did not affect the bap-mutant S. aureus M556 and SA392 biofilms. Biofilm compositions study before and after proteinase K treatment indicated that Bap might also be involved in eDNA retention in the biofilm matrix that aid in biofilm stability. When proteinase K was used in combination with antibiotics, a synergistic effect in antibiotic efficacy was observed against all biofilm forming S. aureus strains.. CC-BY-NC4.0 International license not peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/102384 doi: bioRxiv preprint first posted online Jan. 23, 2017; Conclusion:Proteinase K inhibited biofilms growth in S. aureus bovine mastitis isolates but did not affect their planktonic growth. An enhanced dispersion of preformed S. aureus biofilms was observed upon proteinase K treatment. Proteinase K treatment with antibiotics showed a synergistic effect against S. aureus biofilms.Significance of the study: The study suggests that dispersing S. aureus by protease can be of use while devising strategies against S. aureus biofilms. Proteinase K treatment has a wider scope for control of S. aureus biofilms.

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Section: Planktonic Growth Studiesmentioning

confidence: 99%

Staphylococcus aureusBiofilm Removal by Targeting Biofilm-Associated Extracellular Proteins

Shukla

Rao

2017

Preprint

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“…Originally introduced to provide non-overlapping (typically fluorinated) mass calibrants [ref to pfk mixtures], mass defect labeling of peptides has been used to identify protein serine (pS) and tyrosine (pY) phosphorylation. [27, 29–32]. Here, we point out that, by virtue of its large mass defect (-0.0262 Da, see Table 1), the presence of 31 P in a peptide ion can in principle be identified by sufficiently accurate mass measurement alone.…”

Section: Introductionmentioning

confidence: 82%

“…Moreover, peptide masses are discrete, so that amino acid composition can be uniquely inferred from sufficiently resolved and accurate mass measurement. [27, 28]. The introduction of another element with a large mass defect into the elemental compositions can shift a modified peptide ion into an otherwise empty mass spectral segment, for unique identification by accurate mass measurement.…”

Section: Introductionmentioning

confidence: 99%

Identification of phosphorylated human peptides by accurate mass measurement alone

Yuan

Zamdborg

Kelleher

et al. 2011

International Journal of Mass Spectrometry

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At sufficiently high mass accuracy, it is possible to distinguish phosphorylated from unmodified peptides by mass measurement alone. We examine the feasibility of that idea, tested against a library of all possible in silico tryptic digest peptides from the human proteome database. The overlaps between in silico tryptic digest phosphopeptides generated from known phosphorylated proteins (1–12 sites) and all possible unmodified human peptides are considered for assumed mass error ranges of ±10, ±50, ±100, ±1,000, and ±10,000 ppb. We find that for mass error ±50 ppb, 95% of all phosphorylated human tryptic peptides can be distinguished from nonmodified peptides by accurate mass alone through the entire nominal mass range. We discuss the prospect of on-line LC MS/MS to identify phosphopeptide precursor ions in MS1 for selected dissociation in MS2 to identify the peptide and site(s) of phosphorylation.

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“…Data Acquisition Methods That Generate Pseudo MS/MS Data-The MS E scan function was first applied to drug metabolite profiling and identification on the Waters Q-TOF platform (29,31,35), and subsequently, similar methods were employed on orbitrap instrumentation (57,61). In the MS E acquisition, full-scan MS experiments at alternating low and high collision energies are performed, resulting in collection of two data sets.…”

Section: Data Acquisition Methods Facilitating Drug Metabolite Identimentioning

confidence: 99%

“…Even more fundamental changes may be on the horizon as HR-MS instruments are developed that can fully support quantitative workflows (72,73). These instruments have the potential to simultaneously provide both qualitative and quantitative information on multiple analytes, including metabolites (61). Additionally, it should be possible to use data sets for multiple purposes, e.g.…”

Section: Future Perspectivementioning

confidence: 99%

Drug Metabolite Profiling and Identification by High-resolution Mass Spectrometry

Zhu

Zhang

Humphreys

2011

Journal of Biological Chemistry

191

110

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Mass spectrometry plays a key role in drug metabolite identification, an integral part of drug discovery and development. The development of high-resolution (HR) MS instrumentation with improved accuracy and stability, along with new data processing techniques, has improved the quality and productivity of metabolite identification processes. In this minireview, HR-MSbased targeted and non-targeted acquisition methods and data mining techniques (e.g. mass defect, product ion, and isotope pattern filters and background subtraction) that facilitate metabolite identification are examined. Methods are presented that enable multiple metabolite identification tasks with a single LC/HR-MS platform and/or analysis. Also, application of HR-MS-based strategies to key metabolite identification activities and future developments in the field are discussed. High-resolution (HR)2 MS has made a huge impact in a number of analytical fields. Most applications utilize the robust accuracy of modern instruments to do unsupervised searches or cataloging of ions present in a given sample. Examples of the impact of HR-MS on these types of applications are identification of unknown proteins (1) and protein modification (2-4), peptide mapping (5, 6), metabonomics (7), and biomarker discovery (8). Drug metabolism research is slightly different in that the ions of interest all arise from a known starting mass, the administered drug, which can be used as a starting point for searches. Although the design of specific search techniques that take advantage of properties of the drug makes finding drugrelated material easier, the fact that these components must be found in a very sensitive fashion from among a variety of very complex background matrices still presents many challenges. The application of HR-MS technology to drug metabolism shares many similarities with applications in areas such as forensic science and doping control (9 -11).Targeted searches for metabolites take advantage of the fact that the majority of drug metabolites can be categorized as predictable, i.e. those formed via common biotransformation reactions. However, there are many examples of important metabolites that arise from uncommon reactions and are thus not easily predicted a priori. Molecular masses of predicted metabolites (m/z values) can be readily calculated based on mass shifts from the parent drug (e.g. the protonated molecular mass of M2 and M5 of nefazodone is that of the parent drug plus 15.9949 Da) (Fig. 1). Detection of expected metabolites by LC/MS can be accomplished by acquisition of full-scan MS data sets using various MS instruments, followed by extracted ion chromatography (EIC) of the ions (e.g. ion at m/z 486.2272 for M2 and M5 in Fig. 1) (12, 13). The most challenging task in metabolite identification by LC/MS is the detection and structural elucidation of trace levels of unexpected metabolites in the presence of large amounts of complex interference ions from endogenous components (14 -16).Since electrospray instruments were introduced in the 1...

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Shifting unoccupied spectral space in mass spectrum of peptide fragment ions

Cited by 10 publications

References 36 publications

Staphylococcus aureusBiofilm Removal by Targeting Biofilm-Associated Extracellular Proteins

Staphylococcus aureusBiofilm Removal by Targeting Biofilm-Associated Extracellular Proteins

Identification of phosphorylated human peptides by accurate mass measurement alone

Drug Metabolite Profiling and Identification by High-resolution Mass Spectrometry

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