PXD030780

PXD030780 is an original dataset announced via ProteomeXchange.

Title	A multi-species spike-in sample set for performance evaluation of label-free proteomics quantification
Description	When evaluating the quantitative performance of label-free proteomics method(s), samples with known compositions are necessary to define key parameters such as reproducibility, missing data levels, accuracy, precision, as well as sensitivity/specificity for biomarker discovery. Here, we provide a carefully-designed multi-species spike-in sample set for such purposes, which was prepared by spiking small, variable amounts of E. Coli (for mimicking significant protein changes, i.e., true positives) and yeast (for balancing the variable levels of E. coli proteins) proteins into a large, constant background of human proteins (representing unchanged proteins). The sample set encompasses a total of 25 LC-MS sample runs (5 E.coli-level groups, 5 LC-MS replicate runs in each group). The proportion of human proteins is 60% across all samples, and each group contains the following percentage of E. coli and yeast proteins : A: 5%/35%, B: 7.5%/32.5%, C: 10%/30%, D: 15%/25%, E: 20%/20%. These files were used to comprehensively evaluate the quantitative performances by ultra-high-resolution (UHR)-IonStar and SWATH-MS in Result 3.2 of “Ultra-High-Resolution IonStar Strategy Enhancing Accuracy and Precision of MS1-Based Proteomics and an Extensive Comparison with State-of-the-Art SWATH-MS in Large-Cohort Quantification (DOI: 10.1021/acs.analchem.0c05002)”.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:54:15.289.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Shuo Qian
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-01-06 01:48:25	ID requested
1	2022-01-06 11:11:11	announced
⏵ 2	2023-11-14 08:54:16	announced	2023-11-14: Updated project metadata.

Wang X, Jin L, Hu C, Shen S, Qian S, Ma M, Zhu X, Li F, Wang J, Tian Y, Qu J, Ultra-High-Resolution IonStar Strategy Enhancing Accuracy and Precision of MS1-Based Proteomics and an Extensive Comparison with State-of-the-Art SWATH-MS in Large-Cohort Quantification. Anal Chem, 93(11):4884-4893(2021) [pubmed]

submitter keyword: Performance evaluation, Label-free quantification, IonStar

Jun Qu
contact affiliation	Department of Pharmaceutical Sciences, School of Pharmacy, University at Buffalo, Buffalo, New York, United States
contact email	junqu@buffalo.edu
lab head
Shuo Qian
contact affiliation	Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center
contact email	sqian@buffalo.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/2022/01/PXD030780

PRIDE project URI

• PRIDE
  1. PXD030780
     1. Label: PRIDE project
     2. Name: A multi-species spike-in sample set for performance evaluation of label-free proteomics quantification