PXD027589

PXD027589 is an original dataset announced via ProteomeXchange.

Title	Prochlorococcus marinus MED4 shotgun proteome dataset from “Protein cycling in the eastern tropical North Pacific oxygen deficient zone: a de novo-discovery peptidomic approach”
Description	For this manuscript, the Prochlorococcus MED4 strain shotgun proteome dataset was used for benchmarking a de novo-directed sequencing approach. De novo peptide sequencing, where the sequence of amino acids is determined directly from mass spectra rather than by comparison (or peptide spectrum matching) to a selected database. We perform a benchmarking experiment using Prochlorococcus culture data, demonstrating de novo peptides are sufficiently accurate and taxonomically specific to be useful in environmental studies. The MED4 dataset herein represents the output from peptide spectrum matching using COMET within the transproteomic pipeline (TPP). Additional MED4 data outside this manuscript are included for both trypsin and Glu-C protease digestions as well as TPP output for post-translational modification searches. De novo output data derived from Peaks Studio can be found by referencing the manuscript publication.
HostingRepository	PRIDE
AnnounceDate	2022-01-06
AnnouncementXML	Submission_2022-01-06_11:25:02.603.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rachel Lundeen
SpeciesList	scientific name: Prochlorococcus marinus subsp. pastoris str. CCMP1986; NCBI TaxID: 59919;
ModificationList	deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-27 07:26:52	ID requested
⏵ 1	2022-01-06 11:25:02	announced

Dataset with its publication pending

submitter keyword: Prochlorococcus, MED4, marine cyanobacteria, shotgun proteomics, de novo

Anitra Ingalls
contact affiliation	University of Washington
contact email	aingalls@uw.edu
lab head
Rachel Lundeen
contact affiliation	University of Washington
contact email	ralundeen@gmail.com
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/2022/01/PXD027589

PRIDE project URI

• PRIDE
  1. PXD027589
     1. Label: PRIDE project
     2. Name: Prochlorococcus marinus MED4 shotgun proteome dataset from “Protein cycling in the eastern tropical North Pacific oxygen deficient zone: a de novo-discovery peptidomic approach”