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: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: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: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:Selecting a sample preparation strategy for mass spectrometry-based proteomics is critical to the success of quantitative workflows. Here we present a universal, solid-phase protein preparation (USP3) method which is rapid, robust and scalable, facilitating high-throughput protein sample preparation for bottom-up and top-down mass spectrometry (MS) analysis.
Project description:Desalting and concentrating peptides using reverse phase chromatography prior LC-MS/MS analysis is a critical step to improve the sensitivity of peptide detection. However, hydrophilic peptides are not easy to retain on the conventional solid phase extraction (SPE) StageTip using C18 as materials during the desalting step. In this study, graphite carbon was utilized as a SPE StageTip with strong hydrophobic adsorbent, which doubled the identification number of multiply phosphopeptides compared to the number using C18 SPE StageTip. In addition, (phospho)peptides with lower GRAVY value and shorter peptides length were enriched using the graphite SPE StageTip. Finally, a total of 7,617 phosphopeptides were identified, which covers both hydrophilic and hydrophobic properties. The complementary affinity of different desalting materials including C18, SDB-XC, and graphite was further demonstrated to deepen the coverage of proteome and phosphoproteome.
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