PXD000477

PXD000477 is an original dataset announced via ProteomeXchange.

Title	Mspire-Simulator: LC-MS shotgun proteomic simulator for creating realistic gold standard data - HEK cell lysate
Description	The most important step in any quantitative proteomic pipeline is feature detection (aka peak picking). However, generating quality hand-annotated data sets to validate the algorithms, especially for lower abundance peaks, is nearly impossible. An alternative for creating gold standard data is to simulate it with features closely mimicking real data. We present Mspire-Simulator, a free, open source shotgun proteomic simulator that goes beyond previous simulation attempts by generating LC-MS features with realistic m/z and intensity variance along with other noise components. It also includes machine learned models for retention time and peak intensity prediction and a genetic algorithm to custom fit model parameters for experimental data sets. We show that these methods are applicable to data from three different mass spectrometers, including two fundamentally different types, and show visually and analytically that simulated peaks are nearly indistinguishable from actual data. Researchers can use simulated data to rigorously test quantitation software, and proteomic researchers may benefit from overlaying simulated data on actual data sets. While not directly relevant in this case, a search was conducted by Proteome-Discoverer v1.4 by both mascot and Sequest-HT. The parameters included 2 missed cleavages by Trypsin, carboamidomethylation of the Cysteines, Phosphorylations of STY residues, and Oxidations of HW residues, and at a precursor mass tolerance of 10 ppm.
HostingRepository	PRIDE
AnnounceDate	2020-01-24
AnnouncementXML	Submission_2020-01-24_05:21:16.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ryan Taylor
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-09-23 01:55:39	ID requested
⏵ 1	2020-01-24 05:21:17	announced

Noyce AB, Smith R, Dalgleish J, Taylor RM, Erb KC, Okuda N, Prince JT, Mspire-Simulator: LC-MS shotgun proteomic simulator for creating realistic gold standard data. J Proteome Res, 12(12):5742-9(2013) [pubmed]

submitter keyword: Human, HEK-293T, Ms-Simulator, FASP

John T. Prince
contact affiliation	Department of Biochemistry, Brigham Young University , 701 East University Parkway, BNSN C100, Provo, Utah 84602, United States
contact email	jtprince@gmail.com
lab head
Ryan Taylor
contact affiliation	Chemistry and Biochemistry
contact email	ryanmt@byu.net
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/2020/01/PXD000477

PRIDE project URI

• PRIDE
  1. PXD000477
     1. Label: PRIDE project
     2. Name: Mspire-Simulator: LC-MS shotgun proteomic simulator for creating realistic gold standard data - HEK cell lysate