Translation of a tissue epigenetic signature to circulating free DNA suggests BCAT1 as a potential noninvasive diagnostic biomarker for lung cancer.

Lung cancer patients are diagnosed at late stages when curative treatments are no longer possible; thus, molecular biomarkers for noninvasive detection are urgently needed. In this sense, we previously identified and validated an epigenetic 4-gene signature that yielded a high diagnostic performance in tissue and invasive pulmonary fluids. We analyzed DNA methylation levels using the ultrasensitive digital droplet PCR in noninvasive samples in a cohort of 83 patients.

LipidMS 3.0: an R-package and a web-based tool for LC-MS/MS data processing and lipid annotation.

Motivation: LipidMS was initially envisioned to use fragmentation rules and data-independent acquisition (DIA) for lipid annotation. However, data-dependent acquisition (DDA) remains the most widespread acquisition mode for untargeted LC-MS/MS-based lipidomics. Here, we present LipidMS 3.

Glutamine/glutamate metabolism rewiring in reprogrammed human hepatocyte-like cells.

Human dermal fibroblasts can be reprogrammed into hepatocyte-like (HEP-L) cells by the expression of a set of transcription factors. Yet, the metabolic rewiring suffered by reprogrammed fibroblasts remains largely unknown. Here we report, using stable isotope-resolved metabolic analysis in combination with metabolomic-lipidomic approaches that HEP-L cells mirrors glutamine/glutamate metabolism in primary cultured human hepatocytes that is very different from parental human fibroblasts.

LipidMS: An R Package for Lipid Annotation in Untargeted Liquid Chromatography-Data Independent Acquisition-Mass Spectrometry Lipidomics.

High resolution LC-MS untargeted lipidomics using data independent acquisition (DIA) has the potential to increase lipidome coverage, as it enables the continuous and unbiased acquisition of all eluting ions. However, the loss of the link between the precursor and the product ions combined with the high dimensionality of DIA data sets hinder accurate feature annotation. Here, we present LipidMS, an R package aimed to confidently identify lipid species in untargeted LC-DIA-MS.

RpeakChrom: Novel R package for the automated characterization and optimization of column efficiency in high-performance liquid chromatography analysis.

Characterization of chromatographic columns using the traditional van Deemter method is limited by the necessity of calculating extra-column variance, issue particularly relevant when modeling asymmetrical peaks eluted from monolithic columns. A novel R package that implements Parabolic Variance Modified Gaussian approach for accurate peak modeling, van Deemter equation and two alternatives approaches, based on van Deemter, has been developed to calculate the height equivalent to a theoretical plate (HETP). To assess package capabilities conventional packed reverse-phase and monolithic HPLC columns were characterized.