title: Protein phosphorylation analysis in archival clinical cancer samples by shotgun and targeted proteomics approaches.
abstract: Protein phosphorylation affects most eukaryotic cellular processes and its deregulation is considered a hallmark of cancer and other diseases. Phosphoproteomics may enable monitoring of altered signaling pathways as a means of stratifying tumors and facilitating the discovery of new drugs. Unfortunately, the development of molecular tests for clinical use is constrained by the limited availability of fresh frozen, clinically annotated samples. Here we report phosphopeptide analysis in human archival formalin-fixed, paraffin-embedded (FFPE) cancer samples based on immobilized metal affinity chromatography followed by liquid chromatography coupled with tandem mass spectrometry and selected reaction monitoring techniques. Our results indicate the equivalence of detectable phosphorylation rates in archival FFPE and fresh frozen tissues. Moreover, we demonstrate the applicability of targeted assays for phosphopeptide analysis in clinical archival FFPE samples, using an experimental workflow suitable for processing and analyzing large sample series. This work paves the way for the application of shotgun and targeted phosphoproteomics approaches in clinically relevant studies using archival clinical samples.
authors: Instituto de Investigación Sanitaria, IdIPAZ, Hospital Universitario La Paz, Madrid, Spain.
authors: Angelo
authors: A
authors: Gámez-Pozo
authors: Iker
authors: I
authors: Sánchez-Navarro
authors: Enrique
authors: E
authors: Calvo
authors: Esther
authors: E
authors: Díaz
authors: María
authors: M
authors: Miguel-Martín
authors: Rocío
authors: R
authors: López
authors: Teresa
authors: T
authors: Agulló
authors: Emilio
authors: E
authors: Camafeita
authors: Enrique
authors: E
authors: Espinosa
authors: Juan Antonio
authors: JA
authors: López
authors: Manuel
authors: M
authors: Nistal
authors: Juan Ángel Fresno
authors: JÁ
authors: Vara