Dataset Information

Comparative analysis of MS sample preparation methods

ABSTRACT: We compare the most commonly used proteomic sample preparation strategies such as classical in solution digest protocols, SPEED, FASP, STrap, SP3, as well as the commercially available kits iST (PreOmics) and EasyPep (Thermo Scientific) in their efficacy to extract proteomes from HeLa cells. We find a remarkably good performance of the majority of the protocols with high reproducibility, little method dependencies and low levels of artifact formation. Despite these similarities we observe significant differences in the recovery of specific sets of proteins in a k-means cluster analysis.

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hela Cell

SUBMITTER: Wolfgang Reiter

LAB HEAD: Markus Hartl

PROVIDER: PXD030406 | Pride | 2022-09-06

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20200520_QExHFX1_RSLC1_Anrather_Hartl_MFPL_01_LYS-UREA_iRT_500ng.mzML	Mzml
	20200520_QExHFX1_RSLC1_Anrather_Hartl_MFPL_01_LYS-UREA_iRT_500ng.pepXML	Pepxml
	20200520_QExHFX1_RSLC1_Anrather_Hartl_MFPL_01_LYS-UREA_iRT_500ng.raw	Raw
	20200520_QExHFX1_RSLC1_Anrather_Hartl_MFPL_02_LYS-GH_iRT_500ng.mzML	Mzml
	20200520_QExHFX1_RSLC1_Anrather_Hartl_MFPL_02_LYS-GH_iRT_500ng.pepXML	Pepxml

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Publications

In Search of a Universal Method: A Comparative Survey of Bottom-Up Proteomics Sample Preparation Methods.

Varnavides Gina G Madern Moritz M Anrather Dorothea D Hartl Natascha N Reiter Wolfgang W Hartl Markus M

Journal of proteome research 20220825 10

Robust, efficient, and reproducible protein extraction and sample processing is a key step for bottom-up proteomics analyses. While many sample preparation protocols for mass spectrometry have been described, selecting an appropriate method remains challenging since some protein classes may require specialized solubilization, precipitation, and digestion procedures. Here, we present a comprehensive comparison of the 16 most widely used sample preparation methods, covering in-solution digests, de ...[more]

PMID: 36006919

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