PXD027791

PXD027791 is an original dataset announced via ProteomeXchange.

Title	MS1Connect: a mass spectrometry run similarity measure
Description	Researchers may be interested in finding proteomics runs, which have been deposited into online repositories, that are similar to their own data. However, it is difficult to measure the similarity of a pair of proteomics runs. Here, we present a new method, MS1Connect, that only uses intact peptide scans to calculate the similarity between a pair of runs. We show evidence that the MS1Connect score accurately measures the similarity between two proteomics runs. Specifically, we show that MS1Connect outperforms baseline methods for predicting the species a sample originated. In addition, we show that MS1Connect scores are highly correlated with similarities based o peptide fragment scans by observing a high correlation between MS1Connect scores and the Jaccard index between the sets of confidently detected peptides for a pair of runs.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:17:47.342.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD027791
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Andy Lin
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Bacillus cereus; NCBI TaxID: 1396; scientific name: Bacillus thuringiensis; NCBI TaxID: 1428; scientific name: Nicotiana benthamiana; NCBI TaxID: 4100; scientific name: Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028; NCBI TaxID: 1299114; scientific name: Porphyrobacter sp. WLSH-3; NCBI TaxID: 1009408; scientific name: Bacillus thuringiensis str. Al Hakam; NCBI TaxID: 412694;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF; LTQ Orbitrap XL

Revision	Datetime	Status	ChangeLog Entry
0	2021-08-06 03:46:13	ID requested
1	2023-01-05 07:24:51	announced
2	2023-02-06 05:56:02	announced	2023-02-06: Updated project metadata.
⏵ 3	2023-11-14 08:17:48	announced	2023-11-14: Updated project metadata.

10.6019/PXD027791;

Lin A, Deatherage Kaiser BL, Hutchison JR, Bilmes JA, Noble WS, MS1Connect: a mass spectrometry run similarity measure. Bioinformatics, 39(2):(2023) [pubmed]

submitter keyword: bacteria, similarity

William Noble
contact affiliation	Department of Genome Sciences, University of Washington, USA
contact email	william-noble@uw.edu
lab head
Andy Lin
contact affiliation	University of Washington
contact email	linandy@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/2023/01/PXD027791

PRIDE project URI

• PRIDE
  1. PXD027791
     1. Label: PRIDE project
     2. Name: MS1Connect: a mass spectrometry run similarity measure