PXD003611

PXD003611 is an original dataset announced via ProteomeXchange.

Title	FASIL-MS: An Integrated Proteomic and Bioinformatic Workflow to Universally Quantitate In vivo-acetylated Positional Isomers
Description	Dynamic changes in histone post-translational modifications (PTMs) regulate gene transcription leading to fine-tuning of biological processes such as DNA replication and cell cycle progression. Moreover, specific histone modifications constitute docking sites for recruitment of DNA damage repair proteins and mediation of subsequent cell survival. Therefore, understanding and monitoring changes in histone PTMs that alter cell proliferation that can lead to disease progression are of considerable medical interest. In this study, stable isotope labelling with N-acetoxy-D3-succinimide (D3-NAS) was utilised to efficiently derivatise unmodified lysine residues at the protein level. The sample preparation method was streamlined to facilitate buffer exchange between the multiple steps of the protocol by coupling chemical derivatisation to filter-aided sample preparation (FASP). Additionally, the mass spectrometry method was adapted to simultaneously co-isolate and concurrently fragment all differentially-H3/D3-acetylated histone peptide clusters. The combination of these multi-plexed MS2 spectra with the implementation of a data analysis algorithm enabled the quantitation of each and every in vivo-acetylated DMSO- and SAHA-treated H4(4-17) and H3(18-26) peptide. We have termed our new approach FASIL-MS for filter-aided stable isotopic labelling coupled to mass spectrometry. FASIL-MS enables the universal and site-specific quantitation of peptides with multiple in vivo-acetylated lysine residues.
HostingRepository	PRIDE
AnnounceDate	2016-06-16
AnnouncementXML	Submission_2016-06-16_04:32:00.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dijana Vitko
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; propanoylated residue; acetate labeling reagent (N-term) (heavy form: +3amu)
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2016-02-10 07:55:19	ID requested
⏵ 1	2016-06-16 04:32:01	announced

Vitko D, M, á, jek P, Schirghuber E, Kubicek S, Bennett KL, FASIL-MS: An Integrated Proteomic and Bioinformatic Workflow To Universally Quantitate In Vivo-Acetylated Positional Isomers. J Proteome Res, 15(8):2579-94(2016) [pubmed]

curator keyword: Biological, Technical

submitter keyword: FASP, histone acetylation, lysine deacetylase inhibitor, mass spectrometry, MS2-based quantitation, N-acetoxy-D3-sucinnimide, protein derivatisation

Keiryn L. Bennett
contact affiliation	CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences Bennett Laboratory Mass Spectrometry & Proteomics
contact email	kbennett@cemm.oeaw.ac.at
lab head
Dijana Vitko
contact affiliation	CeMM Research Center for Molecular Medicine
contact email	dvitko@cemm.oeaw.ac.at
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003611

PRIDE project URI

• PRIDE
  1. PXD003611
     1. Label: PRIDE project
     2. Name: FASIL-MS: An Integrated Proteomic and Bioinformatic Workflow to Universally Quantitate In vivo-acetylated Positional Isomers