|Sequence-Specific Ni(II)-Dependent Peptide Bond Hydrolysis for Protein Engineering. Combinatorial Library Determination of Optimal Sequences|
The sequence-specific cleavage of the peptide bond is a crucial procedure in protein engineering and purification. The extreme stability of this bond, with half-life for spontaneous hydrolysis estimated as 350-600 years at neutral pH and room temperature, limits the range of appropriate cleavage reagents.
|An improved data processing pipe-line for comprehensive H-NMR and X/MS -omics data|
R. J. O. Torgrip, K. M. Åberg, E. Alm
In the post acqusition analysis of comprehensive -omics data the pre-processing pipe-line is crucial to extract the maximum possible amount of information from the data. Here we show a processing pipe-line for (1D)H-NMR and (2D)X/MS data comprising; feature detection, inter-sample feature alignment and internal-standard free normalization that outperforms today’s state-of-the-art processing schemes.
|LC-MS Approaches to Profiling of Non-Radiolabelled Metabolites in Response to Recent Regulatory Changes|
Richard Clayton, Caroline Anderson, Brian Morrison and Lindsay Corfield
Following publication of the FDA MIST guidelines and revision of ICH M3, there is increasing interest in obtaining metabolic profiling data at an early stage in the development of a drug. This has led to a requirement to estimate the relative abundance of metabolites in samples prior to the synthesis of the radiolabelled compound and from a wider range of studies.
|Basic amino acids profiling during hepatic tumorigenesis by hydrophilic interaction liquid chromatography tandem mass spectrometry (HILIC-MS/MS)|
O. D’Apolito (1), D. Garofalo (1), D. Paris (2), D. Melck (2), R. Calemma (3), F. Izzo (3), G. Palmieri (2), A. Motta (2) and G. Corso (1)
This study is aimed to characterize basic aminoacids profiles from liver tissues of primary hepatocarcinoma (HCC) and metastases from colorectalcarcinomas (MET), and from adjacent cirrhotic related hepatitis-C-virus (CIRR) and non-cirrhotic normal liver (NT). Arginine levels in MET are significantly higher (P<0.05) compared to NT, CIRR and HCC. Although our preliminary data should be validated, profiling of basic aminoacids could allow a better classification of liver malignancies in humans.
|A method for the quantification of sterols for a rapid screening of Smith-Lemli-Opitz Syndrome by Atmospheric Pressure Thermal Desorption Chemical Ionization -Mass Spectrometry (APTDCI -MS)|
G. Paglia (1), O. D'Apolito (1), M. Gelzo (2), D. Garofalo (1), A. Dello Russo (2), and G. Corso (1,2)
An atmospheric pressure thermal desorption chemical ionization MS/MS method to quantify cholesterol and 7- and 8-dehydrocholesterols directly in dried blood/plasma spots, is reported. Cholesterol levels from dried plasma spots of 23 unaffected subjects and 9 Smith-Lemli-Opitz patients by APTDCI-MS/MS method and by enzymatic method were correlated (y=0.9166x + 0.3811; r= 0.8831) as well as dehydrocholesterol levels obtained by APTDCI-MS/MS method and by GC-FID method (y=0.8214x + 0.7388; r= 0.828
|Alteration of urinary metabolic profile in rats treated with methylmercury|
Pierre Ayotte, Dinesh Kumar, Pierre-Yves Tremblay, Xiaolei Jin, Sevini Shahbaz, Rekha Mehta, Hing Man Chan, and Oliver Fiehn
A metabolomic approach was used to detect changes in urinary metabolic profile of rats treated orally with methylmercury (MeHg), a ubiquitous fish contaminant with well known neurotoxic properties. An aliquot of urine was collected on day 14, extracted and the extract successively methoxymated and trimethylsilylated prior to analysis by GC/TOF-MS. Results indicate that several metabolic pathways were altered by MeHg treatment, including urea cycle, glutathione metabolism and amino acid degradati
|Minor change in the structure major change in the mass spectrum in the example of an N-toluene-pyrrolidine derivative|
MS2 and further MSn spectra of SAR cannot provide sufficient information for metabolite structure elucidation because the masses of fragments in MSn correspond only to separate moieties of SAR. Nevertheless almost the exact structure of a dehydrogenated compound - has a poor MS2 spectrum - could be determined by further fragmentation in an LTQ-Orbitrap instrument and using the MSn mass spectra of an impurity of SAR.
|Capture Compounds towards a targeted reduction of proteome complexity|
Erik Duelsner, Aysel Alici, Christian Jurinke, Hubert Koester
Capture Compound Mass Spectrometry (CCMS) enables the enrichment of proteins based on their functionality. CCMS is commercialized as kits for research applications and in collaborations with pharmaceutical companies. The focus is on investigating mechanisms of drug action and avoidance of toxic effects of small molecule drugs.
|A Novel Approach to Internal Standardization in LC/MS/MS Analysis; Sensitive LC/MS/MS Analysis of Gentamicin|
Bruce Babson, Noel Henderson and Nicholas Chestara
A novel approach to internal standardization in LC/MS/MS is demonstrated. Gentamicin, a multi-component aminoglycoside, is derivatized with propyl-d7 chloroformate making the internal standard. Gentamicin components in the samples are derivatized with non-labeled propyl chloroformate making them analogous to the internal standard. Additional benefits of the derivatization are increased hydrophobicity and excellent MS/MS fragmentation.