PXD001819

PXD001819 is an original dataset announced via ProteomeXchange.

Title	yeast-UPS1 standard LC-MS/MS dataset
Description	Proteomic workflows based on nanoLC-MS/MS data-dependent-acquisition analysis have progressed tremendously in recent years due to the technical improvement of mass spectrometers, and now allow to extensively characterize complex protein mixtures. High-resolution and fast sequencing instruments have enabled the use of label-free quantitative methods, which appear as an attractive way to analyze differential protein expression in complex biological samples. Classical label-free quantitative workflows are based either on spectral counting of MS/MS sequencing scans for each protein, or on the extraction of peptide ion peak area values in the LC-MS map composed of all the survey MS scans acquired during the chromatographic gradient. However, the computational processing of the data for label-free quantification still remains a challenge. Here, we provide a dual proteomic standard composed of an equimolar mixture of 48 human proteins (Sigma UPS1) spiked at different concentrations into a background of yeast cell lysate, that was used to benchmark several label-free quantitative workflows, involving different software packages developed in recent years. This experimental design allowed to finely assess their performances in terms of sensitivity and false discovery rate, by measuring the number of true and false-positive (respectively UPS1 or yeast background proteins found as differential). This dataset can also be used to benchmark other label-free workflows, adjust software parameter settings, improve algorithms for extraction of the quantitative metrics from raw MS data, or evaluate downstream statistical methods
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:23:34.619.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Emmanuelle Mouton Barbosa
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-02-16 05:34:15	ID requested
1	2015-12-01 14:43:00	announced
2	2016-03-22 03:58:32	announced	Updated publication reference for PubMed record(s): 26862574.
⏵ 3	2024-10-22 04:23:42	announced	2024-10-22: Updated project metadata.

Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssi, é D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianf, é, rani S, Ferro M, Dorssaeler AV, Burlet-Schiltz O, Schaeffer C, Cout, é Y, Gonzalez de Peredo A, Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods. Data Brief, 6():286-94(2016) [pubmed]

10.1016/j.dib.2015.11.063;

curator keyword: Technical

submitter keyword: yesat, UPS1, label-free quantification, LC-MS/MS

Anne Gonzalez de Peredo
contact affiliation	CNRS, Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse
contact email	gonzalez@ipbs.fr
lab head
Emmanuelle Mouton Barbosa
contact affiliation	IPBS CNRS
contact email	emmanuelle.mouton@ipbs.fr
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD001819
     1. Label: PRIDE project
     2. Name: yeast-UPS1 standard LC-MS/MS dataset