PXD028840

PXD028840 is an original dataset announced via ProteomeXchange.

Title	A method for independent estimation of false localisation rate for phosphoproteomics
Description	Phosphoproteomics methods are commonly employed in labs to identify and quantify the sites of phosphorylation on proteins. In recent years, various software tools have been developed, incorporating scores or statistics related to whether a given phosphosite has been correctly identified, or to estimate the global false localisation rate (FLR) within a given data set for all sites reported. These scores have generally been calibrated using synthetic data sets, and their statistical reliability on real datasets is largely unknown. As a result, there is considerable problem in the field of reporting incorrectly localised phosphosites, due to inadequate statistical control. In this work, we develop the concept of using scoring and ranking modifications on a decoy amino acid, i.e. one that cannot be modified, to allow for independent estimation of global FLR. We test a variety of different amino acids to act as the decoy, on both synthetic and real data sets, demonstrating that the amino acid selection can make a substantial difference to the estimated global FLR. We conclude that while several different amino acids might be appropriate, the most reliable FLR results were achieved using alanine and leucine as decoys, although we have a preference for alanine due to the risk of potential confusion between leucine and isoleucine amino acids. We propose that the phosphoproteomics field should adopt the use of a decoy amino acid, so that there is better control of false reporting in the literature, and in public databases that re-distribute the data.
HostingRepository	PRIDE
AnnounceDate	2022-06-09
AnnouncementXML	Submission_2022-06-09_04:29:28.966.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD028840
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Kerry Ramsbottom
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Orbitrap Fusion ETD; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-09-29 06:13:18	ID requested
⏵ 1	2022-06-09 04:29:29	announced

Ramsbottom KA, Prakash A, Riverol YP, Camacho OM, Martin MJ, Vizca, í, no JA, Deutsch EW, Jones AR, Method for Independent Estimation of the False Localization Rate for Phosphoproteomics. J Proteome Res, 21(7):1603-1615(2022) [pubmed]

submitter keyword: Phosphorylation, false localisation

Prof. Andrew R Jones
contact affiliation	Biochemistry & Systems Biology, Universiy of Liverpool, UK
contact email	Andrew.Jones@liverpool.ac.uk
lab head
Kerry Ramsbottom
contact affiliation	University of Liverpool
contact email	kramsb@liverpool.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD028840
     1. Label: PRIDE project
     2. Name: A method for independent estimation of false localisation rate for phosphoproteomics