PXD000438-2

PXD000438 is an original dataset announced via ProteomeXchange.

Title	Super-SILAC analysis of human lung primary tumor-derived xenografts LC-MS/MS
Description	Non-small cell lung cancer (NSCLC) accounts for 85% of lung cancers, and is subdived into 2 major histological subtypes: adenocacinoma (ADC) and squamous cell carcinoma (SCC). Super-SILAC methodology was used to facilitate the quantitative comparisons of human primary tumor-derived xenograft proteomes by high resolution MS analysis. Xeno092 and Xeno441 were ADCs. Xeno 561 and Xeno691 were SCCs. Principal component analysis and supervised t-tests revealed differentially expressed proteins responsible for the classification of the samples according to their distinctive proteomes. These results confirm known differentiators between ADC and SCC subtypes of NSCLC (e.g. a keratin signature, cell adhesion molecules, and metabolism proteins), and reveal novel candidates that may be useful to classify and treat NSCLC tumors. The raw files were analyzed by MaxQuant (version 1.3.0.5). Peaks were searched against the UniProt human database (released Jul, 2012; http://www.uniprot.org) using the Andromeda search engine included in MaxQuant. Two miscleavages were allowed and at least six amino acids per identified peptide were required. The false discovery rate for peptides and proteins was set at 0.01. 'Match between runs' option was selected within a time window of 2 min. A minimum ratio count of 2 was used for quantification of SILAC pairs. Further data analysis was performed in Perseus.
HostingRepository	PRIDE
AnnounceDate	2014-01-28
AnnouncementXML	Submission_2014-03-18_03:07:04.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Wen Zhang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	6x(13)C: 4x(15)N labeled L-arginine; 6x(13)C: 2x(15)N labeled L-lysine
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2013-09-02 01:07:43	ID requested
1	2014-01-28 04:08:58	announced
⏵ 2	2014-03-18 03:07:05	announced	Updated publication reference for PubMed record(s): 24453208.
3	2014-07-25 01:36:38	announced	Updated project metadata.
4	2024-10-22 04:17:55	announced	2024-10-22: Updated project metadata.

Zhang W, Wei Y, Ignatchenko V, Li L, Sakashita S, Pham NA, Taylor P, Tsao MS, Kislinger T, Moran MF, Proteomic profiles of human lung adeno and squamous cell carcinoma using super-SILAC and label-free quantification approaches. Proteomics, 14(6):795-803(2014) [pubmed]

submitter keyword: NSCLC, super-SILAC, proteomic profile

Wen Zhang
contact affiliation	University of Toronto
contact email	wenzhang211@gmail.com
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/2014/01/PXD000438

PRIDE project URI

• PRIDE
  1. PXD000438
     1. Label: PRIDE project
     2. Name: Super-SILAC analysis of human lung primary tumor-derived xenografts LC-MS/MS