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Low-input proteomics using lauryl maltose neopentyl glycol

ABSTRACT: We developed a sample preparation method for low-input proteomics using lauryl maltose neopentyl glycol. Using the developed method, we performed proteome analysis of 100ng of HEK293T proteins, coIP samples, and serum extracellular vesicles, and further challenged label-free single-cell proteomics of HEK293F cells.

ORGANISM(S): Homo Sapiens (human) Bos Taurus

SUBMITTER: Yusuke Kawashima

PROVIDER: PXD044605 | JPOST Repository | Wed Mar 06 00:00:00 GMT 2024

REPOSITORIES: jPOST

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			Action	DRS
	HEK1ng_R30k-IW16-P500-740.raw	Raw
	HEK1ng_R30k-IW16-P550-790.raw	Raw
	HEK1ng_R30k-IW16-P600-840.raw	Raw
	HEK1ng_R30k-IW16-P650-890.raw	Raw
	HEK1ng_R30k-IW16-P700-940.raw	Raw

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Publications

Universal Pretreatment Development for Low-input Proteomics Using Lauryl Maltose Neopentyl Glycol.

Konno Ryo R Ishikawa Masaki M Nakajima Daisuke D Endo Yusuke Y Ohara Osamu O Kawashima Yusuke Y

Molecular & cellular proteomics : MCP 20240304 4

In recent years, there has been a growing demand for low-input proteomics, particularly in the context of single-cell proteomics (SCP). In this study, we have developed a lauryl maltose neopentyl glycol (LMNG)-assisted sample preparation (LASP) method. This method effectively reduces protein and peptide loss in samples by incorporating LMNG, a surfactant, into the digestion solution and subsequently removing the LMNG simply via reversed phase solid-phase extraction. The advantage of removing LMN ...[more]

PMID: 38447790

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Low-input proteomics using lauryl maltose neopentyl glycol

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Fully automated sample processing and analysis workflow for low-input proteome profiling

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Low-input ATAC&mRNA-Seq: a simple and robust method for simultaneous dual-omics profiling with low cell number

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High-throughput, Efficient, and Unbiased Capture of Small RNAs from Low-input Samples for Sequencing

Project description:We developed a high-throughput sequencing protocol that efficiently captures small RNAs from low input samples while minimizing inherent biases associated with library production. The protocol was builds on previously published method that adds a barcode to samples at the earliest step in preparation such that all downstream manipulations can be performed on a pool of many samples thereby greatly reducing reagent usage and workload. We optimized adapter concentrations and showed modified adapters greatly increases the efficiency of small RNA capture. This work also demonstrates that unique molecular identifiers incorporated into the adapters can be used to bioinformatically remove PCR duplication.

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Comprehensive analysis of RNA-seq kits for standard, low and ultra-low quantity samples

Project description:High-throughput RNA-sequencing has now become the gold standard method for whole-transcriptome gene expression analysis. It is widely used in a number of applications studying various transcriptomes of cells and tissues. It is also being increasingly considered for a number of clinical applications, including expression profiling for diagnostics or alternative transcripts detection. However, RNA sequencing can be challenging in some situations, for instance due to low input quantities or degraded RNA samples. Several protocols have been proposed to overcome some of these challenges, and many are available as commercial kits. Here we perform a comprehensive testing of three recent commercial technologies for RNA-seq library preparation (Truseq, Smarter and Smarter Ultra-Low) on human reference tissue preparations, for standard (1ug), low (100 and 10 ng) and ultra-low (< 1 ng) input quantities, and for mRNA and total RNA, stranded or unstranded. We analyze the results using read quality and alignments metrics, gene detection and differential gene expression metrics. Overall, we show that the Truseq kit performs well at 100 ng input quantity, while the Smarter kit shows degraded performances for 100 and 10 ng input quantities, and that the Smarter Ultra-Low kit performs quite well for input quantities < 1 ng. All the results are discussed in details, and we provide guidelines for the selection of a RNA-seq library preparation kits by biologists.

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