PXD023901

PXD023901 is an original dataset announced via ProteomeXchange.

Title	A proteomics data analysis protocol using Open-pFind
Description	High-throughput proteomics based on mass spectrometry (MS) analysis has permeated biomedical science and propelled numerous research projects. pFind 3 is a database search engine for high-speed and in-depth proteomics data analysis (Chi et al. 2018). pFind 3 features a swift open search workflow that is adept at uncovering less obvious information such as unexpected modifications or mutations that would have gone unnoticed using a conventional data analysis pipeline. In this protocol, we provide step-by-step instructions to help users mastering various types of data analysis using pFind 3 in conjunction with pParse for data preprocessing and if needed, pQuant for quantitation. This streamlined pParse-pFind-pQuant workflow offers exceptional sensitivity, precision, and speed. It can be easily implemented in any laboratory in need of identifying peptides, proteins, or post-translational modifications, or of quantitation based on 15N-labeling, SILAC-labeling, or TMT/iTRAQ labeling.
HostingRepository	iProX
AnnounceDate	2021-01-31
AnnouncementXML	Submission_2023-06-11_20:13:54.692.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Guangcan Shao
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606; scientific name: Caenorhabditis elegans; NCBI TaxID: 6239;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-31 21:17:38	ID requested
1	2021-01-31 21:18:21	announced
⏵ 2	2023-06-11 20:13:55	announced	2023-06-12: Update publication information.

Shao G, Cao Y, Chen Z, Liu C, Li S, Chi H, Dong MQ, How to use open-pFind in deep proteomics data analysis?- A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data. Biophys Rep, 7(3):207-226(2021) [pubmed]

submitter keyword: Open-pFind, protein identification, protein quantitation

Mengqiu Dong
contact affiliation	National Institute of Biological Sciences
contact email	dongmengqiu@nibs.ac.cn
lab head
Guangcan Shao
contact affiliation	National Institute of Biological Sciences
contact email	shaoguangcan@nibs.ac.cn
dataset submitter

iProX dataset URI