MS²PIP: a tool for MS/MS peak intensity prediction

Motivation: Tandem mass spectrometry provides the means tomatch mass spectrometry signal observations with the chemical entities that generated them. The technology produces signal spectra that contain information about the chemical dissociation pattern of a peptide that was forced to fragment using methods like collision-induced dissociation. The ability to predict these MS 2 signals and to understand this fragmentation process is important for sensitive high-throughput proteomics research. Results: We present a new tool called (MSPIP)-P-2 for predicting the intensity of the most important fragment ion signal peaks from a peptide sequence. (MSPIP)-P-2 pre-processes a large dataset with confident peptide-to-spectrum matches to facilitate data-driven model induction using a random forest regression learning algorithm. The intensity predictions of (MSPIP)-P-2 were evaluated on several independent evaluation sets and found to correlate significantly better with the observed fragment-ion intensities as compared with the current state-of-the-art PeptideART tool

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis.

Data-independent acquisition (DIA) in liquid chromatography (LC) coupled to tandem mass spectrometry (MS/MS) provides comprehensive untargeted acquisition of molecular data. We provide an open-source software pipeline, which we call MS-DIAL, for DIA-based identification and quantification of small molecules by mass spectral deconvolution. For a reversed-phase LC-MS/MS analysis of nine algal strains, MS-DIAL using an enriched LipidBlast library identified 1,023 lipid compounds, highlighting the chemotaxonomic relationships between the algal strains

An optimal subgradient algorithm for large-scale convex optimization in simple domains

This paper shows that the optimal subgradient algorithm, OSGA, proposed in \cite{NeuO} can be used for solving structured large-scale convex constrained optimization problems. Only first-order information is required, and the optimal complexity bounds for both smooth and nonsmooth problems are attained. More specifically, we consider two classes of problems: (i) a convex objective with a simple closed convex domain, where the orthogonal projection on this feasible domain is efficiently available; (ii) a convex objective with a simple convex functional constraint. If we equip OSGA with an appropriate prox-function, the OSGA subproblem can be solved either in a closed form or by a simple iterative scheme, which is especially important for large-scale problems. We report numerical results for some applications to show the efficiency of the proposed scheme. A software package implementing OSGA for above domains is available

Performance of the Roche Total Mycophenolic Acid® assay on the Cobas Integra 400®, Cobas 6000® and comparison to LC-MS/MS in liver transplant patients

Background: Mycophenolic acid (MPA) is an immunosuppressant for which therapeutic drug monitoring (TDM) is performed for optimal prophylaxis and avoidance of toxicity in transplant patients. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is ideally suited for TDM of MPA. There have been several method comparisons of the Roche Total MPA assay, but none have been performed with respect to liver transplant patients. Methods: We validated the Roche Total MPA assay on the Cobas Integra 400 and Cobas 6000 and compared it to a validated LC-MS/MS (API 2000 (TM)) method. Fifty-five EDTA plasma samples from liver transplant patients were measured with the Roche assay on these platforms and compared to the LC-MS/MS results. Results: Validation of the LC-MS/MS, Cobas Integra 400 and 6000 was performed with good results. The LC-MS/MS/Integra 400/Cobas 6000 were linear up to 30, 15 and 17 mg/L, respectively. Imprecision was <10% for LC-MS/MS and <7% for the Roche assay on both platforms. The samples showed good agreement with LC-MS/MS. Passing-Bablok regression analysis showed Cobas Integra (mg/L) = 1.02 x LC-MS/MS (mg/L)-0.50 and Cobas 6000 (mg/L) = 0.98 x LC-MS/MS-0.47. Conclusions: The Roche Total Mycophenolic Acid-assay is suitable for measuring total MPA in plasma from liver transplant patients and is a good alternative for LC-MS/MS

Preclinical evaluation of local prolonged release of paclitaxel from gelatin microspheres for the prevention of recurrence of peritoneal carcinomatosis in advanced ovarian cancer

Patients with advanced ovarian cancer develop recurrence despite initial treatment response to standard treatment of surgery and intravenous/intraperitoneal (IP) chemotherapy, partly due to a limited peritoneal exposure time of chemotherapeutics. Paclitaxel-loaded genipin-crosslinked gelatin microspheres (PTX-GP-MS) are evaluated for the treatment of microscopic peritoneal carcinomatosis and prevention of recurrent disease. The highest drug load (39.2 mu g PTX/mg MS) was obtained by immersion of GP-MS in aqueous PTX nanosuspension (PTXnano-GP-MS) instead of ethanolic PTX solution (PTXEtOH-GP-MS). PTX release from PTX-GP-MS was prolonged. PTXnano-GP-MS displayed a more controlled release compared to a biphasic release from PTX-GP-MS. Anticancer efficacy of IP PTX-GP-MS (PTXEtOH-GP-MS, D = 7.5 mg PTX/kg; PTXnano-GP-MS D= 7.5 and 35 mg PTX/kg), IP nanoparticular albumin-bound PTX (D = 35 mg PTX/kg) and controls (0.9% NaCl, blank GP-MS) was evaluated in a microscopic peritoneal carcinomatosis xenograft mouse model. PTXnano-GP-MS showed superior anticancer efficacy with significant increased survival time, decreased peritoneal carcinomatosis index score and ascites incidence. However, prolonged PTX release over 14 days from PTXnano-GP-MS caused drug-related toxicity in 27% of high-dosed PTXnano-GP-MS-treated mice. Dose simulations for PTXnano-GP-MS demonstrated an optimal survival without drug-induced toxicity in a range of 7.5-15 mg PTX/kg. Low-dosed PTXnano-GP-MS can be a promising IP drug delivery system to prevent recurrent ovarian cancer

The Economic Impacts of GM Contamination Incidents on the Organic Sector

This paper examines the economic impact of GM co-existence on the global organic sector to date through GM contamination of organic food and crops. A total of 15 GM contamination incidents in the organic sector are identified, occurring either from cross-pollination from GM crops being grown in the area or due to contamination in the post-harvest supply chain. The financial losses incurred by organic farmers and food companies due to GM contamination are considerable, through lost markets, lost sales, lower prices, negative publicity, withdrawal of organic certification and product recalls. It is important that co-existence regimes address all of these impacts, with the GM sector being held accountabl

Neutral particle Mass Spectrometry with Nanomechanical Systems

Current approaches to Mass Spectrometry (MS) require ionization of the analytes of interest. For high-mass species, the resulting charge state distribution can be complex and difficult to interpret correctly. In this article, using a setup comprising both conventional time-of-flight MS (TOF-MS) and Nano-Electro-Mechanical-Systems-based MS (NEMS-MS) in situ, we show directly that NEMS-MS analysis is insensitive to charge state: the spectrum consists of a single peak whatever the species charge state, making it significantly clearer than existing MS analysis. In subsequent tests, all charged particles are electrostatically removed from the beam, and unlike TOF-MS, NEMS-MS can still measure masses. This demonstrates the possibility to measure mass spectra for neutral particles. Thus, it is possible to envisage MS-based studies of analytes that are incompatible with current ionization techniques and the way is now open for the development of cutting edge system architectures with unique analytical capability

Validation of the Patient Activation Measure in a Multiple Sclerosis Clinic Sample and Implications for Care

Purpose. Patient engagement in multiple sclerosis (MS) care can be challenging at times given the unpredictable disease course, wide range of symptoms, variable therapeutic response to treatment and high rates of patient depression. Patient activation, a model for conceptualising patients’ involvement in their health care, has been found useful for discerning patient differences in chronic illness management. The purpose of this study was to validate the patient activation measure (PAM-13) in an MS clinic sample. Methods. This was a survey study of 199 MS clinic patients. Participants completed the PAM-13 along with measures of MS medication adherence, self-efficacy, depression and quality of life. Results. Results from Rasch and correlation analyses indicate that the PAM-13 is reliable and valid for the MS population. Activation was associated with MS self-efficacy, depression and quality of life but not with self-reported medication adherence. Also, participants with relapse-remitting MS, current employment, or high levels of education were more activated than other subgroups. Conclusions. The PAM-13 is a useful tool for understanding health behaviours in MS. The findings of this study support further clinical consideration and investigation into developing interventions to increase patient activation and improve health outcomes in MS