Project description:Metadata and .raw files of LC-MS/MS files for analysis of phosphoribosylated (formerly ADP-ribosylated) peptides enriched from H2O2 induced HeLa cell proteomes solid phase extracted with TFA or TEAA
Project description:gen107_ptgs - gene profiling in silencing suppressor plants or in mirna mutants - What are the genes that are differentially regulated in various tissues derived from silencing suppressor plants or miRNA mutants? - HcPro, P15, P19, CHS-RNAi (control), were grown on MS solid medium, and tissues were harvested at different developmental stages. dcl1-9, hen1-1 and La-er (control) were grown on MS solid medium, and tissues harvested at different developmental stages. Keywords: gene knock in (transgenic),gene knock out 40 dye-swap - Chromochip Arabidopsis thaliana 21.7K CHROMO4_1
Project description:The success of bottom-up proteomic analysis frequently depends on the efficient removal of contaminants from protein or peptide samples before LC-MS/MS. For a peptide clean-up workflow, the single-pot solid-phase-enhanced peptide sample preparation on carboxylate-modified paramagnetic beads (termed SP2) was evaluated for sodium dodecyl sulfate or polyethylene glycol removal from Arabidopsis thaliana tryptic peptides. The robust and efficient 40-min SP2 protocol, tested for a 10 ng, 250ng and 10µg peptide sample, was proposed and benchmarked thoroughly against the ethyl acetate extraction protocol. The SP2 protocol on carboxylated magnetic beads proved to be the robust approach even for simultaneous removal of massive sodium dodecyl sulfate (SDS) and polyethylene glycol (PEG) contaminations from AT peptide samples in respect of the LC-MS/MS data outperforming ethyl acetate extraction.
Project description:Optimization of Solid Phase Extraction Columns (C18, HBL, PPL) for non-targeted LC-MS/MS analysis of river dissolved organic matter.
Project description:A novel chemoenzymatic method termed solid phase extraction of N-linked Glycans And Glycosite-containing peptides (NGAG) for the simultaneous analysis of N-glycans, glycosite-containing peptides, and intact N-glycopeptides with site-specific glycosylation information.
Project description:Here, we describe an approach to enrich newly transcribed RNAs from primary mouse neurons using 4-thiouridine (s4U) metabolic labeling and solid phase chemistry. This one-step enrichment procedure captures s4U-RNA by using highly efficient methane thiosulfonate (MTS) chemistry in an immobilized format. Like solution-based methods, this solid-phase enrichment can distinguish mature RNAs (mRNA) with differential stability, and can be used to reveal transient RNAs such as enhancer RNAs (eRNAs) and primary microRNAs (pri-miRNAs) from short metabolic labeling. Most importantly, the efficiency of this solid-phase chemistry made possible the first large scale measurements of RNA polymerase II (RNAPII) elongation rates in mouse cortical neurons. Thus, our approach provides the means to study regulation of RNA metabolism in specific tissue contexts as a means to better understand gene expression in vivo.
Project description:In this study, several chromatographic sorbents: porous graphitic carbon (PGC), aminopropyl-hydrophilic interaction (aminopropyl-HILIC) and phenylboronic acid (PBA) were assessed for the analysis of glycopeptides by on-line solid-phase extraction capillary electrophoresis-mass spectrometry (SPE-CE-MS). As PBA sorbent provided the most promising results, a PBA-SPE-CE-MS method was developed for the selective and sensitive preconcentration of glycopeptides from enzymatic digests of glycoproteins. Recombinant human erythropoietin (rhEPO) was selected as model glycoprotein and subjected to enzymatic digestion with several proteases. The tryptic O126 and N83 glycopeptides from rhEPO were targeted to optimize the methodology. Under the optimized conditions, repeatabilityintraday precision, linearity, limits of detection (LODs) and microcartridge lifetime were evaluated, obtaining improved results compared to a previously reported TiO2-SPE-CE-MS method, especially for LODs of N-glycopeptides (up to 500 times lower than by CE-MS and up to 200 times lower than by TiO2-SPE-CE-MS). Moreover, rhEPO Glu-C digests were also analyzed by Finally, the PBA-SPE-CE-MS method was applied to the analysis of rhEPO glycopeptides from Glu-C digests to better characterize N24 and N38 glycopeptidessites. Finally, the established method was used to analyze two rhEPO biosimilars (EPOCIM and NeuroEPO plus), demonstrating its applicability in biopharmaceutical analysis. The sensitivity of the proposed PBA-SPE-CE-MS method improves the existing CE-MS methodologies for glycopeptide analysis and shows a great potential in glycoprotein analysis to deeply characterize protein glycosites even at low concentrations of protein digest.
Project description:The ability to predict tissue type and donor’s age from molecular profiles of crime scene samples has practical implications in forensics. In order to identify body fluid- and age-associated DNA methylation changes, genome-wide DNA methylation profiling was carried out for body fluids including blood, saliva, semen, menstrual blood, and vaginal fluid obtained from individuals aged 20 to 59. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in bisulfite converted DNA. Samples included 12 of each blood, saliva and semen samples from 18 male donors aged 20 to 59, and 3 of each vaginal fluid and menstrual blood samples from 4 female donors in their twenties. Genome-wide DNA methylation profiling of body fluids obtained from individuals aged 29 to 41. The Illumina Infinium 450K Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450K CpGs from human body fluids including blood, saliva and semen. Bisulfite converted DNA from the 6 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip