Dataset Information

Quick 96FASP for high throughput quantitative proteome analysis

ABSTRACT: An upgraded and quick 96FASP approach using 30k MWCO filter plates was developed for high throughput quantitative proteomics analysis.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human) Klebsiella Pneumoniae Uhkpc27

SUBMITTER: Yanbao Yu

LAB HEAD: Yanbao Yu

PROVIDER: PXD006137 | Pride | 2018-05-24

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	1DLC081216QE_q96FASP_PCR_B1.mgf	Mgf
	1DLC081216QE_q96FASP_PCR_B1.msf	Msf
	1DLC081216QE_q96FASP_PCR_B1.mzid.gz	Mzid
	1DLC081216QE_q96FASP_PCR_B1.pride.mgf.gz	Mgf
	1DLC081216QE_q96FASP_PCR_B1.pride.mztab.gz	Mztab

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Publications

Quick 96FASP for high throughput quantitative proteome analysis.

Yu Yanbao Y Bekele Shiferaw S Pieper Rembert R

Journal of proteomics 20170629

Filter aided sample preparation (FASP) is becoming a central method for proteomic sample cleanup and peptide generation prior to LC-MS analysis. We previously adapted this method to a 96-well filter plate, and applied to prepare protein digests from cell lysate and body fluid samples in a high throughput quantitative manner. While the 96FASP approach is scalable and can handle multiple samples simultaneously, two key advantages compared to single FASP, it is also time-consuming. The centrifugati ...[more]

PMID: 28669814

Similar Datasets

Project description:Filter aided sample preparation (FASP) is becoming a central method for proteomic sample cleanup and peptide generation prior to LC-MS analysis. We previously adapted this method to a 96-well filter plate, and applied to prepare protein digests from cell lysate and body fluid samples in a high throughput quantitative manner. While the 96FASP approach is scalable and can handle multiple samples simultaneously, two key advantages compared to single FASP, it is also time-consuming. The centrifugation-based liquid transfer on the filter plate takes 3-5 times longer than single filter. To address this limitation, we now present a quick 96FASP (named q96FASP) approach that, relying on the use of filter membranes with a large MWCO size (~30kDa), significantly reduces centrifugal times. We show that q96FASP allows the generation of protein digests derived from whole cell lysates and body fluids in a quality similar to that of the single FASP method. Processing a sample in multiple wells in parallel, we observed excellent experimental repeatability by label-free quantitation approach. We conclude that the q96FASP approach promises to be a promising cost- and time-effective method for shotgun proteomics and will be particularly useful in large scale biomarker discovery studies.SignificanceHigh throughput sample processing is of particular interests for quantitative proteomics. The previously developed 96FASP is high throughput and appealing, however it is time-consuming in the context of centrifugation-based liquid transfer (~1.5h per spin). This study presents a truly high throughput sample preparation method based on large cut-off 96-well filter plate, which shortens the spin time to ~20min. To our knowledge, this is the first multi-well method that is entirely comparable with conventional FASP. This study thoroughly examined two types of filter plates and performed side-by-side comparisons with single FASP. Two types of samples, whole cell lysate of a UTI (urinary tract infection)-associated Klebsiella pneumoniae cell and human urine, were tested which demonstrated its capability for quantitative proteomics. The q96FSAP approach makes the filter plate-based approach more appealing for protein biomarker discovery projects, and could be broadly applied to large scale proteomics analysis.