title: Proteome and transcriptome profiles of a Her2/Neu-driven mouse model of breast cancer.
abstract: OBJECTIVE
  We generated extensive transcriptional and proteomic profiles from a Her2-driven mouse model of breast cancer that closely recapitulates human breast cancer. This report makes these data publicly available in raw and processed forms, as a resource to the community. Importantly, we previously made biospecimens from this same mouse model freely available through a sample repository, so researchers can obtain samples to test biological hypotheses without the need of breeding animals and collecting biospecimens.
  
  
  METHODS
  Twelve datasets are available, encompassing 841 LC-MS/MS experiments (plasma and tissues) and 255 microarray analyses of multiple tissues (thymus, spleen, liver, blood cells, and breast). Cases and controls were rigorously paired to avoid bias.
  
  
  RESULTS
  In total, 18,880 unique peptides were identified (PeptideProphet peptide error rate ≤1%), with 3884 and 1659 non-redundant protein groups identified in plasma and tissue datasets, respectively. Sixty-one of these protein groups overlapped between cancer plasma and cancer tissue.
  
  
  CONCLUSIONS
  These data are of use for advancing our understanding of cancer biology, for software and quality control tool development, investigations of analytical variation in MS/MS data, and selection of proteotypic peptides for multiple reaction monitoring-MS. The availability of these datasets will contribute positively to clinical proteomics.
authors: Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
authors: Regine M
authors: RM
authors: Schoenherr
authors: Karen S
authors: KS
authors: Kelly-Spratt
authors: ChenWei
authors: C
authors: Lin
authors: Jeffrey R
authors: JR
authors: Whiteaker
authors: Tao
authors: T
authors: Liu
authors: Ted
authors: T
authors: Holzman
authors: Ilsa
authors: I
authors: Coleman
authors: Li-Chia
authors: LC
authors: Feng
authors: Travis D
authors: TD
authors: Lorentzen
authors: Alexei L
authors: AL
authors: Krasnoselsky
authors: Pei
authors: P
authors: Wang
authors: Yan
authors: Y
authors: Liu
authors: Kay E
authors: KE
authors: Gurley
authors: Lynn M
authors: LM
authors: Amon
authors: Athena A
authors: AA
authors: Schepmoes
authors: Ronald J
authors: RJ
authors: Moore
authors: David G
authors: DG
authors: Camp
authors: Lewis A
authors: LA
authors: Chodosh
authors: Richard D
authors: RD
authors: Smith
authors: Peter S
authors: PS
authors: Nelson
authors: Martin W
authors: MW
authors: McIntosh
authors: Christopher J
authors: CJ
authors: Kemp
authors: Amanda G
authors: AG
authors: Paulovich
mesh_terms: D000818:Animals; D001943:Breast Neoplasms / Q000235:genetics*; D030562:Databases, Protein; D004195:Disease Models, Animal; D020869:Gene Expression Profiling; D051379:Mice; D008822:Mice, Transgenic; D020543:Proteome / Q000032:analysis* / Q000235:genetics*; D040901:Proteomics; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000032:analysis / Q000235:genetics*; D053719:Tandem Mass Spectrometry; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D020543:Proteome; D018719:Erb-b2 Receptor Tyrosine Kinases; C524056:Erbb2 protein, mouse