PXD033016

PXD033016 is an original dataset announced via ProteomeXchange.

Title	Coisolation of peptide pairs for peptide identification and MS/MS-based quantification
Description	SILAC-based metabolic labeling is a widely adopted proteomics approach that enables quantitative comparisons among a variety of experimental conditions. Despite its quantitative capacity, SILAC experiments analyzed with data dependent acquisition (DDA) do not fully leverage peptide pair information for identification and suffer from undersampling compared to label-free proteomic experiments. Herein, we developed a data dependent acquisition strategy that coisolates and fragments SILAC peptide pairs and uses y-ions for their relative quantification. To facilitate the analysis of this type of data, we adapted the Comet sequence database search engine to make use of SILAC peptide paired fragments and developed a tool to annotate and quantify MS/MS spectra of coisolated SILAC pairs. In an initial feasibility experiment, this peptide pair coisolation approach generally improved expectation scores compared to the traditional DDA approach. Fragment ion quantification performed similarly well to precursor quantification in the MS1 and achieved more quantifications. Lastly, our method enables reliable MS/MS quantification of SILAC proteome mixtures with overlapping isotopic distributions, which are difficult to deconvolute in MS1-based quantification. This study demonstrates the initial feasibility of the coisolation approach. Coupling this approach with intelligent acquisition strategies has the potential to improve SILAC peptide sampling and quantification.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_07:35:32.833.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ian Smith
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-04-06 08:27:44	ID requested
1	2022-11-03 03:31:26	announced
⏵ 2	2023-11-14 07:35:33	announced	2023-11-14: Updated project metadata.

Smith IR, Eng JK, Barente AS, Hogrebe A, Llovet A, Rodriguez-Mias RA, Vill, é, n J, Coisolation of Peptide Pairs for Peptide Identification and MS/MS-Based Quantification. Anal Chem, 94(44):15198-15206(2022) [pubmed]

submitter keyword: MS/MS, yeast,SILAC, peptide pairs, quantification, Comet

Judit Villén
contact affiliation	Department of Genome Sciences University of Washington Seattle, WA USA
contact email	jvillen@uw.edu
lab head
Ian Smith
contact affiliation	University of Washington
contact email	smithi2@uw.edu
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/2022/11/PXD033016

PRIDE project URI

• PRIDE
  1. PXD033016
     1. Label: PRIDE project
     2. Name: Coisolation of peptide pairs for peptide identification and MS/MS-based quantification