Dataset Information

Combination of bottom up 2D-LC-MS and intact protein separation enhances coverage of proteome and low molecular weight short open reading frame encoded peptides of the archeon Methanosarcina mazei

ABSTRACT: The recent discovery of an increasing number of small open reading frame (sORF) creates the need for suitable analytical technologies for the comprehensive identification of the corresponding gene products. In the present study we evaluated analytical approaches which will allow for simultaneous analysis of widest parts of proteome together with the predicted sORF, as for biological investigations and functional studies the knowledge of the entire set of proteins and sORF gene products is essential. We performed a full proteome analysis of the methane producing archeae Methanosarcina mazei cytosolic proteome using a high/low pH reversed phase LC-MS bottom-up approach. The second analytical approach was based on semi-top strategy, encompassing a separation at intact protein level using a GelFree system, followed by digestion and LC-MS analysis. A high overlap in identified proteins was found for both approaches yielding the most comprehensive coverage of the cytosolic proteome of this organism achieved so far. The application of the second approach and an adjustment of the search criteria for database searches further led to a significant increase of sORF peptide identifications, finally allowing to identify 30 sORF gene products.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Methanosarcina Mazei Go1

SUBMITTER: Andreas Tholey

LAB HEAD: Andreas Tholey

PROVIDER: PXD004325 | Pride | 2016-09-26

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	91_methanosarcina_sp_crap_peptides_updated.fasta	Fasta
	Gelfree_Exp1.pep.xml	Pepxml
	Gelfree_Exp2.pep.xml	Pepxml
	Gelfree_Exp3.pep.xml	Pepxml
	Mm2DLC_Exp1.pep.xml	Pepxml

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Publications

Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei.

Cassidy Liam L Prasse Daniela D Linke Dennis D Schmitz Ruth A RA Tholey Andreas A

Journal of proteome research 20160902 10

The recent discovery of an increasing number of small open reading frames (sORF) creates the need for suitable analytical technologies for the comprehensive identification of the corresponding gene products. For biological and functional studies the knowledge of the entire set of proteins and sORF gene products is essential. Consequently in the present study we evaluated analytical approaches that will allow for simultaneous analysis of widest parts of the proteome together with the predicted sO ...[more]

PMID: 27557128

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