PXD019777

PXD019777 is an original dataset announced via ProteomeXchange.

Title	Evaluating the influence of MS-acquisition parameters on DDA label-free proteomics analyses
Description	Label-free proteomics enables the unbiased quantification of thousands of proteins across large sample cohorts. Commonly used mass spectrometry-based proteomic workflows rely on data dependent acquisition (DDA). However, its stochastic selection of peptide features for fragmentation-based identification inevitably results in high rates of missing values, which prohibits the integration of larger cohorts as the number of recurrently detected peptides is a limiting factor. Peptide identity propagation (PIP) can mitigate this challenge, allowing to transfer sequencing information between samples. However, despite the promise of these approaches, current methods remain limited either in sensitivity or reliability and there is a lack of robust and widely applicable software. Here we prepared a tool spike-in data set which can be used to evaluate the influence of changing Top-N, gradient length and sample injection amounts on DDA label-free proteomics results. It also includes analysis by data-independent acquisition (DIA) which allows direct comparison of DDA and DIA for label-free proteomics analyses.
HostingRepository	PRIDE
AnnounceDate	2021-07-10
AnnouncementXML	Submission_2021-08-26_06:08:12.700.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mathias Kalxdorf
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-15 02:50:54	ID requested
1	2021-07-09 23:57:27	announced
⏵ 2	2021-08-26 06:08:13	announced	2021-08-26: Updated publication reference for PubMed record(s): 34373457.

Kalxdorf M, M, ü, ller T, Stegle O, Krijgsveld J, IceR improves proteome coverage and data completeness in global and single-cell proteomics. Nat Commun, 12(1):4787(2021) [pubmed]

submitter keyword: Quantitative proteomics, DDA, DIA, label-free, MS1-based, missing values

Jeroen Krijgsveld
contact affiliation	DKFZ Heidelberg
contact email	j.krijgsveld@dkfz.de
lab head
Mathias Kalxdorf
contact affiliation	EMBL Heidelberg
contact email	mathiaskalxdorf@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/2021/07/PXD019777

PRIDE project URI

• PRIDE
  1. PXD019777
     1. Label: PRIDE project
     2. Name: Evaluating the influence of MS-acquisition parameters on DDA label-free proteomics analyses