Tandem Mass Spectrometry Research Papers (original) (raw)

Protein identification by tandem mass spectrometry (MS/MS) is key to most proteomics projects and has been widely explored in bioinformatics research. Obtaining good and trustful identification results has important implications for... more

Protein identification by tandem mass spectrometry (MS/MS) is key to most proteomics projects and has been widely explored in bioinformatics research. Obtaining good and trustful identification results has important implications for biological and clinical work. Although well matured, automated software identification of proteins from MS/MS data still faces a number of obstacles due to the complexity of the proteome or procedural issues of mass spectrometry data acquisition. Expected or unexpected modifications of the peptide sequences, polymorphisms, errors in databases, missed or non-specific cleavages, unusual fragmentation patterns, and single MS/MS spectra of multiple peptides of the same m/z are so many pitfalls for identification algorithms. A lot of research work has been carried out in recent years that yielded new strategies to handle a number of these issues. Multiple MS/MS identification algorithms are now available or have been theoretically described. The difficulty resides in choosing the most adapted method for each type of spectra being identified. This review presents an overview of the state-of-the-art bioinformatics approaches to the identification of proteins by MS/MS to help the reader doing the spadework of finding the right tools among the many possibilities offered. © 2005 Wiley Periodicals, Inc. Mass Spec Rev 25:235–254, 2006

This work reports a method for extraction and analysis of thiosultap sodium, thiocyclam, and nereistoxin in pepper. Different extraction methods were tested to attain the best recoveries. The final extraction method combines acetonitrile... more

This work reports a method for extraction and analysis of thiosultap sodium, thiocyclam, and nereistoxin in pepper. Different extraction methods were tested to attain the best recoveries. The final extraction method combines acetonitrile extraction in an acidic medium with ultrasonic extraction followed by a cleanup step with anhydrous MgSO(4). The analyses were performed on a Linear Ion Trap Quadrupole LC-MS/MS in negative mode for thiosultap sodium and in positive mode for thiocyclam and nereistoxin. Recovery studies carried out on peppers spiked at different fortification levels (20 and 200 μg∙kg(-1)) yielded average recoveries in the range 58-87% with RSD (%) values below 20%. Calibration curves covering two orders of magnitude were performed and they were linear over the concentration range studied (0.001-0.5 mg∙l(-1)). Instrumental detection limits were in the low μg∙kg(-1) range. Stability studies of thiosultap sodium in water were performed by evaluating a 100-μg∙l(-1) solution of this compound in water. It was analyzed over 7 days, after which more than 80% degradation of thiosultap sodium could be observed.

Resveratrol (Resv), a natural occurring phytolexin present in grapes and other foods, possesses chemopreventive effects revealed by its striking modulation of diverse cellular events associated with tumor initiation, promotion and... more

Resveratrol (Resv), a natural occurring phytolexin present in grapes and other foods, possesses chemopreventive effects revealed by its striking modulation of diverse cellular events associated with tumor initiation, promotion and progression. Catechol estrogens generated in the metabolism of estrogens are oxidized to catechol quinones that react with DNA to form predominantly depurinating estrogen-DNA adducts. This event can generate the mutations responsible for cancer initiation. In this regard, Resv acts as both an antioxidant and an inducer of the phase II enzyme NAD(P)H:quinone oxidoreductase 1 (NQO1). In this report, we present the effects of Resv on the metabolism of estrogens in normal breast epithelial cells (MCF-10F) treated with 4-hydroxyestradiol (4-OHE2) or estradiol-3,4-quinone (E2-3,4-Q). Resv induced NQO1 in a dose- and time-dependent manner, but did not affect the expression of catechol-O-methyltransferase. Ultraperformance liquid chromatography/tandem mass spectrometry was used to determine the effects of Resv on estrogen metabolism. Preincubation of the cells with Resv for 48 h decreased the formation of depurinating estrogen-DNA adducts from 4-OHE2 or E2-3,4-Q and increased formation of methoxycatechol estrogens. When Resv was also present with the 4-OHE2 or E2-3,4-Q, even greater increases in methoxycatechol estrogens were observed, and the DNA adducts were undetectable. We conclude that Resv can protect breast cells from carcinogenic estrogen metabolites, suggesting that it could be used in breast cancer prevention.

A rapid, simple and sensitive method was developed and validated using liquid chromatography-tandem mass spectrometry (LC-MS/MS) for determination of albendazole sulfoxide (ABZOX) in human plasma. The plasma samples were extracted by... more

A rapid, simple and sensitive method was developed and validated using liquid chromatography-tandem mass spectrometry (LC-MS/MS) for determination of albendazole sulfoxide (ABZOX) in human plasma. The plasma samples were extracted by protein precipitation using albendazole sulfoxide-d3 as internal standard (IS). The chromatographic separation was performed on Waters Xbridge C18Column (100×4.6mm, 3.5μm) with a mobile phase consisting of ammonia solution, water and methanol at a flow rate of 0.70mL/min. ABZOX was detected and identified by mass spectrometry with electrospray ionization (ESI) in positive ion and multiple-reaction monitoring (MRM) mode. The method was linear in the range of 3-1500ng/mL for ABZOX. This method was successfully applied to the bioequivalence study in human plasma samples.

A simple method was developed for the analysis of hyoscyamine and scopolamine in human serum and urine using liquid chromatography with tandem mass spectrometry (LC/MS/MS). Hyoscyamine and scopolamine in serum and urine were cleaned up... more

A simple method was developed for the analysis of hyoscyamine and scopolamine in human serum and urine using liquid chromatography with tandem mass spectrometry (LC/MS/MS). Hyoscyamine and scopolamine in serum and urine were cleaned up with an Oasis HLB cartridge and a PSA cartridge. The LC separation was carried out on an ODS column, using linear gradient elution with 5 mmol/L IPCC-MS3-methanol as the mobile phase. The mass spectral acquisition was done in the positive ion mode by applying selected reaction monitoring (SRM). The recoveries of hyoscyamine and scopolamine were 86.0-105% from human serum and urine fortified at 0.2 ng/mL and 10 ng/mL. The detection limits of hyoscyamine and scopolamine were 0.02 ng/mL. Four serum and three urine samples of humans poisoned by eating Datura innoxia Mill. were analyzed by this method. Hyoscyamine and scopolamine were detected at the levels of 0.45-3.5 ng/mL in all serum samples and 170-670 ng/mL in all urine samples.

This is the first study reporting the presence of endogenous caffeine, theobromine, and theophylline in all organs of poplar plants. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was used in order to evaluate the... more

This is the first study reporting the presence of endogenous caffeine, theobromine, and theophylline in all organs of poplar plants. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was used in order to evaluate the uptake, translocation, and metabolism of caffeine-(trimethyl-(13)C) in Populus alba L. Villafranca clone grown in hydroponic conditions. We investigated the remediation of caffeine since it is one of the most widely consumed drugs and it is frequently detected in wastewater treatment plant effluents, surface water, and groundwater worldwide. Our results demonstrated that poplar can absorb and degrade exogenous caffeine without negative effects on plant health. Data showed that concentrations of all endogenous compounds varied depending on caffeine-(trimethyl-(13)C) treatments. In particular, in control conditions, endogenous caffeine, theobromine, and theophylline were mainly distributed in roots. On the other hand, once caffeine-(trimethyl-(13)C) was provided, this compound and its dimethy-(13)C metabolites are mainly localized at leaf level. In conclusion, our results support the possible use of Villafranca clone in association with other water treatment systems in order to complete the process of caffeine remediation.

A method was validated for the multi-residue analysis of 82 pesticides in grapes at ≤25 ng/g level. Berry samples (10 g) mixed with sodium sulphate (10 g) were extracted with ethyl acetate (10 mL); cleaned by dispersive solid phase... more

A method was validated for the multi-residue analysis of 82 pesticides in grapes at ≤25 ng/g level. Berry samples (10 g) mixed with sodium sulphate (10 g) were extracted with ethyl acetate (10 mL); cleaned by dispersive solid phase extraction and the results were obtained by liquid chromatography–tandem mass spectrometry. Reduction in sample size and proportion of ethyl acetate for extraction did not affect accuracy or precision of analysis when compared to the reported methods and was also statistically similar to the QuEChERS technique. The method was rugged (HorRat < 0.5) with <20% measurement uncertainties. Limit of quantification was <10 ng/g with recoveries 70–120% for most pesticides. The method offers cheaper and safer alternative to typical multi-residue analysis methods for grape.