PXD023921

PXD023921 is an original dataset announced via ProteomeXchange.

Title	Multi-protease approach for the improved identification and molecular characterization of small proteins and short open reading frame-encoded peptides
Description	The identification of proteins below 70 amino acids in bottom-up proteomics is still a challenging task due to the limited number of peptides generated by proteolytic digestion. This includes the short open reading frame-encoded peptides (SEP), which are a subset of the small proteins that were not previously annotated or that are alternatively encoded. Here, we systematically investigated the use of multiple proteases (trypsin, chymotrypsin, LysC, LysArgiNase and GluC) in GeLC-MS/MS analysis to improve the sequence coverage and the number of identified peptides for small proteins (<70 amino acids), with a focus on SEP, in the archaeon Methanosarcina mazei. Combining the data of all proteases, we identified 63 small proteins and additional 28 SEP with at least two unique peptides, while only 55 small proteins and 22 SEP could be identified using trypsin only. For 27 small proteins and 12 SEP, a 100 % sequence coverage could be achieved. Moreover, for five SEP, incorrectly predicted translation start points were identified, confirming the data of a previous top-down proteomics study of this organism. The results show clearly that a multi-protease approach can improve the identification and molecular characterization of small proteins and SEP.
HostingRepository	PRIDE
AnnounceDate	2021-04-01
AnnouncementXML	Submission_2021-04-01_02:48:37.189.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	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-01 06:50:00	ID requested
⏵ 1	2021-04-01 02:48:37	announced

Kaulich PT, Cassidy L, Bartel J, Schmitz RA, Tholey A, Multi-protease Approach for the Improved Identification and Molecular Characterization of Small Proteins and Short Open Reading Frame-Encoded Peptides. J Proteome Res, 20(5):2895-2903(2021) [pubmed]

submitter keyword: SEP, sORF, Peptidomics, LC-MSMS

Andreas Tholey
contact affiliation	Systematische Proteomics & Bioanalytik, Institut für Experimentelle Medizin Christian-Albrechts-Universität zu Kiel 24105 Kiel, Germany
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. PXD023921
     1. Label: PRIDE project
     2. Name: Multi-protease approach for the improved identification and molecular characterization of small proteins and short open reading frame-encoded peptides