PXD024423

PXD024423 is an original dataset announced via ProteomeXchange.

Title	Histone Sample Preparation for Bottom-Up Mass spectrometry: A Roadmap to Informed Decisions
Description	we aimed to provide an objective roadmap for histone sample preparation wherein the most notable findings and most important metrics were highlighted. This roadmap included a Histone Coverage Tool that allows researchers to make a snapshot of public or in-house data in search of a protocol that suits their specific needs. However, despite the fact that the coverage provided by a sample preparation workflow is pivotal to answer specific research questions, it should be noted that other metrics such as enzyme specificity and workflow variability can be equally important. Moreover, when it comes to histone sample preparation there are multiple additional challenges and pitfalls compared to regular bottom-up proteomics workflows. First there is the abundance and unequal distribution of arginine and lysine cleavage sites, which makes it virtually impossible to cover the entire histone code with a single bottom-up workflow. The most widely spread workaround for the abundance of cleavage sites is derivatization of lysine residues used to block tryptic digest and create longer peptides. However, this also introduces chemical noise, which obscures biological PTMs, while lowering sensitivity due to diluted signal. The most obvious alternative is an arginine specific digest. However, on the one hand, derivatization of lysine residues not only increases peptide length but also increases retention on the LC-system, while decreasing charge state distribution of the precursor ions. The latter presumably reduces instrumental variation of the workflow, which is remarkable since this source of variation is generally assumed to be constant in the field of LC-MS/MS based proteomics. On the other hand, lysine derivatization also increases the singly charged precursor fraction, which is usually not fragmented in regular data dependent acquisitions, thus increasing the risk of losing annotations. It is clear that not one histone sample preparation workflow will fit all research questions. However, we hope that this manuscript will guide researchers in making informed decisions about the many pitfalls and trade-offs involved in optimizing or assessing histone sample preparation workflows.
HostingRepository	PRIDE
AnnounceDate	2021-04-28
AnnouncementXML	Submission_2021-04-28_01:16:28.578.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD024423
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Maarten Dhaenens
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913;
ModificationList	monomethylated residue; ubiquitinylated lysine; crotonylated L-lysine; trimethylated residue; phosphorylated residue; acetylated residue; dimethylated residue; deamidated residue
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2021-03-01 02:32:33	ID requested
⏵ 1	2021-04-28 01:16:28	announced

Dataset with its publication pending

submitter keyword: Histone code

Coverage

Epigenetics

Mass spectrometry

Sample preparation

Work-flow optimization

GingisREX

Maarten Dhaenens
contact affiliation	Laboratory of Pharmaceutical Biotechnology/ProGenTomics, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
contact email	maarten.dhaenens@ugent.be
lab head
Maarten Dhaenens
contact affiliation	Faculity of Pharmaceutical Biotechnology
contact email	maarten.dhaenens@ugent.be
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/2021/04/PXD024423

PRIDE project URI

• PRIDE
  1. PXD024423
     1. Label: PRIDE project
     2. Name: Histone Sample Preparation for Bottom-Up Mass spectrometry: A Roadmap to Informed Decisions