Dataset Information

S-Trap is an ultrafast sample preparation approach for shotgun proteomics

ABSTRACT: The success of shotgun proteomic analysis depends largely on how samples are prepared. Current approaches such as gel-, solution- or filter-based, although being extensively employed in the field, are time-consuming and less effective with respect to the repetitive sample processing, recovery, and overall yield. As an alternative, suspension trapping (S-Trap) filter is commercially available very recently in the format of single or 96-well filter plate. In contrast to conventional filter aided sample preparation (FASP) approach, which utilizes a molecular weight cutoff (MWCO) membrane as the filter and requires hours of processing before digestion-ready proteins can be obtained, S-Trap employs a three-dimensional porous material as filter media, and traps particulate protein suspension with subsequent depletion of interfering substances and in-filter digestion. Due to the large (sub-micron) pore size, each centrifugation cycle of S-Trap filter only takes around 1 minute, which significantly reduces the total processing time from approximately 3 hours by FASP to less than 15 minutes, suggesting an ultrafast sample preparation approach for shotgun proteomics. Here, for the first time, we comprehensively evaluate the performance of individual S-Trap filter and 96-well filter plate in the context of global protein identification and quantitation using whole cell lysate and clinically relevant sputum samples.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Escherichia Coli

SUBMITTER: Yanbao Yu

LAB HEAD: Yanbao Yu

PROVIDER: PXD010237 | Pride | 2019-03-28

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	1DLC051018QE_ProtifiSTrap_test1.mgf	Mgf
	1DLC051018QE_ProtifiSTrap_test1.msf	Msf
	1DLC051018QE_ProtifiSTrap_test1.raw	Raw
	1DLC051018QE_ProtifiSTrap_test2.mgf	Mgf
	1DLC051018QE_ProtifiSTrap_test2.msf	Msf

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Publications

S-Trap, an Ultrafast Sample-Preparation Approach for Shotgun Proteomics.

HaileMariam Milkessa M Eguez Rodrigo Vargas RV Singh Harinder H Bekele Shiferaw S Ameni Gobena G Pieper Rembert R Yu Yanbao Y

Journal of proteome research 20180828 9

The success of shotgun proteomic analysis depends largely on how samples are prepared. Current approaches (such as those that are gel-, solution-, or filter-based), although being extensively employed in the field, are time-consuming and less effective with respect to the repetitive sample processing, recovery, and overall yield. As an alternative, the suspension trapping (S-Trap) filter has been commercially available very recently in the format of a single or 96-well filter plate. In contrast ...[more]

PMID: 30114372

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Project description:Multi-omics integrates diverse types of biological information from genomic, proteomic, and metabolomics experiments to achieve a comprehensive understanding of complex cellular mechanisms. However, this approach is also challenging due to technical issues such as limited sample quantities, complexity of data pre-processing, and reproducibility concerns. Although conventional pre-processing methods in multi-omics research are standardized to ensure consistency; their simultaneous application can obscure specific details. Here, findings obtained from various omics approaches were profiled using various extraction methods (methanol extraction, Folch method, and Matyash methods for metabolites and lipids) and two digestion methods (Filter-aided sample preparation (FASP) and suspension traps (S-Trap)) for resuspended proteins. FASP was found to be more effective for separation of membrane-related proteins, whereas S-Trap excelled in isolating nuclear-related and RNA processing proteins. Thus, ASP may be suitable for investigating the immune response and bacterial infection pathways, whereas S-Trap may be more effective for studies focused on the mechanisms of neurodegenerative diseases. Moreover, the choice of extraction method, either single-phase MeOH or two-phase using Folch and Matyash methods, significantly influences the types of compounds identified, reflecting distinct profiles in different omics data sets. Among metabolites, the single-phase methd identified organic compounds and compounds related to fatty acids, whereas the two-phase extraction identified more hydrophilic compounds such as nucleotides. Lipids with strong hydrophobicity, such as ChE and TG, were identified in the two-phase extraction results. These findings highlight that significant differences between small molecules identified are primarily due to varying polarities of extraction solvents. To address human error and batch effects, a strategy that optimizes the balance between efficiency and the quality of the results is also proposed here. Our study reaffirms the impact of choice of pre-processing method in multi-omics, and also provides specific profiles of several protein and metabolite clusters as well as lipid classes.