PXD018565

PXD018565 is an original dataset announced via ProteomeXchange.

Title	Comparative proteomic profiling of unannotated microproteins and alternative proteins in human cell lines
Description	Ribosome profiling and mass spectrometry have revealed thousands of small and alternative open reading frames (sm/alt-ORFs) that are translated into polypeptides variously termed microproteins and alt-proteins in mammalian cells. Some micro-/alt-proteins exhibit stress-, cell type- and/or tissue-specific expression, and understanding this regulated expression will be critical to elucidating their functions. While differential translation has been inferred by ribosome profiling, quantitative mass spectrometry-based proteomics is needed for direct measurement of microprotein and alt-protein expression between samples and conditions. However, while label-free quantitative proteomics has been applied to detect stress-dependent expression of bacterial microproteins, this approach has not yet been demonstrated for analysis of differential expression of unannotated ORFs in the more complex human proteome. Here, we present global micro-/alt-protein quantitation in two human leukemia cell lines, K562 and MOLT4. We identify 19 unannotated proteins that are differentially expressed in these cell lines. The expression of six micro/alt-proteins was validated biochemically, and two were found to localize to the nucleus. Thus, we demonstrate that label-free comparative proteomics enables quantitation of micro-/alt-protein expression between human cell lines, and that differentially expressed micro-/alt-proteins have properties, like subcellular localization, consistent with functionality. We anticipate that this workflow will enable discovery of regulated sm/alt-ORF products across many biological conditions in human cells.
HostingRepository	PRIDE
AnnounceDate	2020-06-05
AnnouncementXML	Submission_2020-06-04_22:58:17.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD018565
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Alexandra Khitun
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-04-15 00:50:49	ID requested
⏵ 1	2020-06-04 22:58:18	announced

Cao X, Khitun A, Na Z, Dumitrescu DG, Kubica M, Olatunji E, Slavoff SA, Comparative Proteomic Profiling of Unannotated Microproteins and Alternative Proteins in Human Cell Lines. J Proteome Res, 19(8):3418-3426(2020) [pubmed]

submitter keyword: alt-protein, microprotein, smORF, proteogenomics

Sarah A. Slavoff
contact affiliation	Department of Chemistry Chemical Biology Institute (West Campus) Yale University
contact email	sarah.slavoff@yale.edu
lab head
Alexandra Khitun
contact affiliation	Harvard Medical School
contact email	Alexandra_Khitun@hms.harvard.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD018565
     1. Label: PRIDE project
     2. Name: Comparative proteomic profiling of unannotated microproteins and alternative proteins in human cell lines