PXD004325

PXD004325 is an original dataset announced via ProteomeXchange.

Title	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
Description	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.
HostingRepository	PRIDE
AnnounceDate	2017-10-24
AnnouncementXML	Submission_2017-10-24_05:52:47.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andreas Tholey
SpeciesList	scientific name: Methanosarcina mazei Go1; NCBI TaxID: 192952;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-06-14 07:40:04	ID requested
1	2016-09-26 06:42:05	announced
⏵ 2	2017-10-24 05:52:48	announced	Updated project metadata.

Cassidy L, Prasse D, Linke D, Schmitz RA, Tholey A, 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. J Proteome Res, 15(10):3773-3783(2016) [pubmed]

curator keyword: Technical, Biological

submitter keyword: Methanosarcina mazei, Gelfree, High pH, 2D-LC, high pH LC, top-down

Andreas Tholey
contact affiliation	Systematic Proteome Research & Bioanalytics, University of Kiel
contact email	a.tholey@iem.uni-kiel.de
lab head
Andreas Tholey
contact affiliation	Systematic Proteome Research & Bioanalytics, University of Kiel
contact email	a.tholey@iem.uni-kiel.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD004325
     1. Label: PRIDE project
     2. Name: 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