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One-pot method for preparing DNA, RNA, and protein for multiomics analysis II

ABSTRACT: One-pot method for preparing DNA, RNA, and protein for multiomics analysis II

PROVIDER: PRJNA1008155 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25734029_1.fastq.gz	Fastqsanger.gz
	SRR25734029_2.fastq.gz	Fastqsanger.gz
	SRR25734030_1.fastq.gz	Fastqsanger.gz
	SRR25734030_2.fastq.gz	Fastqsanger.gz
	SRR25734031_1.fastq.gz	Fastqsanger.gz

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One-pot method for preparing DNA, RNA, and protein for multiomics analysis

Project description:One-pot method for preparing DNA, RNA, and protein for multiomics analysis

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One-pot method for preparing DNA, RNA, and protein for multiomics analysis I

Project description:One-pot method for preparing DNA, RNA, and protein for multiomics analysis I

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One-pot method for preparing DNA, RNA, and protein for multiomics analysis II

Project description:Typical multiomics studies employ separate methods for DNA, RNA, and protein sample preparation, which is labor intensive, costly, and prone to sampling bias. We describe a method for preparing high-quality, sequencing-ready DNA and RNA, and either intact proteins or mass-spectrometry-ready peptides for whole proteome analysis from a single sample. This method utilizes a reversible protein tagging scheme to covalently link all proteins in a lysate to a bead-based matrix and nucleic acid precipitation and selective solubilization to yield separate pools of protein and nucleic acids. We demonstrate the utility of this method to compare the genomes, transcriptomes, and proteomes of four triple-negative breast cancer cell lines with different degrees of malignancy. These data show the involvement of both RNA and associated proteins, and protein-only dependent pathways that distinguish these cell lines. We also demonstrate the utility of this multiomics workflow for tissue analysis using mouse brain, liver, and lung tissue.

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One-pot method for preparing DNA, RNA, and protein for multiomics analysis I

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One-pot method for preparing DNA, RNA, and protein for multiomics analysis

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2024-03-08 | GSE241434 | GEO

One-Pot

Project description:Data files and supplementary data associated with the one-pot method. These files are the results of one-pot enrichment of both acetylated and succinylated peptides.

2017-12-08 | MSV000081794 | MassIVE

One-pot analysis on cyclosporine A binding

Project description:Investigate if one-pot analysis works on several energetic-based proteomics method on cyclosporine A.

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A chemoenzymatic method for simultaneous profiling N- and O-glycans on glycoproteins using one-pot format

Project description:Glycosylation, including N-glycosylation and O-glycosylation is generally characterized and controlled as a critical quality attribute for therapeutic glycoproteins because glycans can impact protein-based drug product efficacy, half-life, stability, and safety. Analytical procedures to characterize N-glycans are relatively well-established, but the characterization of O-glycans is challenging due to the complex workflows and lack of enzymatic tools. Here we present a simplified chemoenzymatic method to simultaneously profile N- and O-glycans from the same sample using a one-pot format by mass spectrometry (MS). N-glycans were first released by PNGase F, followed by O-glycopeptide generation by Proteinase K, selective N-glycan reduction, and O-glycan release by β-elimination during permethylation of both N- and O- glycans. Glycan structural assignments, and determination of N- to O-glycan ratio was obtained from the one-pot mass spectra. The streamlined, one-pot method is an accurate and reproducible approach that will facilitate advanced characterizations for quality assessments of therapeutic glycoproteins.

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Simultaneous Quantification of the Acetylome and Succinylome by One-Pot Affinity Enrichment

Project description:Protein post-translational modifications (PTMs) are of increasing interest in biomedical research, yet studies rarely examine more than one PTM. One barrier to multi-PTM studies is the time cost for both sample preparation and data acquisition, which scale linearly with the number of modifications. The most prohibitive requirement is often the need for large amounts of sample, which must be increased proportionally with the number of PTM enrichment steps. Here we describe a streamlined, quantitative label-free proteomic workflow – “one-pot” PTM enrichment – which enables comprehensive identification and quantification of peptides containing acetylated and succinylated lysine residues from a single sample containing as little as 1 mg mitochondria protein. Coupled with a label-free, data-independent acquisition (DIA), we identified and quantified 2235 acetylated and 2173 succinylated peptides with the one-pot method and show that peak areas are highly correlated between the one-pot and traditional single-PTM enrichments. The ‘one-pot’ method makes possible detection of multiple PTMs occurring on the same peptide, and we show that it can be used to make unique biological insights into PTM crosstalk. Compared to single-PTM enrichments, the one-pot workflow has equivalent reproducibility and enables direct assessment of PTM crosstalk from biological samples in less time from less tissue.

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Project description:Bacterial endospores, the transmissible forms of pathogenic bacilli and clostridia, are heterogeneous multilayered structures composed of proteins. These proteins protect the spores against variety of stresses, thus helping spore survival, and assist in germination, by interacting with the environment to form vegetative cells. Owing to the complexity, insolubility, and dynamic nature of spore proteins, it has been difficult to obtain their comprehensive protein profiles. The intact spores of Bacillus subtilis, Bacillus cereus, and Peptoclostridium difficile and their vegetative counterparts were disrupted by bead-beating in 6M urea under reductive conditions. The heterogeneous mixture was then double-digested with LysC and trypsin. Next, the peptide mixture was pre-fractionated with Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) followed by reverse phase LC-FT-MS analysis of the fractions. ‘One-pot’ method is a simple, robust method that yields identification of >1000 proteins with high confidence, across all spore layers from Bacillus subtilis, Bacillus cereus, and Peptoclostridium difficile. This method can be employed for proteome-wide analysis of non-spore-forming as well as spore-forming pathogens. Analysis of spore protein profile will help to understand the sporulation and germination processes and to distinguish immunogenic protein markers.

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