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Comparability of differential proteomics data generated from paired archival fresh-frozen and formalin-fixed samples by GeLC–MS/MS and spectral counting

Tanca, Alessandro and Pagnozzi, Daniela and Burrai, Giovanni P. and Polinas, Marta and Uzzau, Sergio and Antuofermo, Elisabetta and Addis, Maria Filippa (2012) Comparability of differential proteomics data generated from paired archival fresh-frozen and formalin-fixed samples by GeLC–MS/MS and spectral counting. Journal of Proteomics, Vol. 77 , p. 561-576. ISSN 1874-3919. Article.

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DOI: 10.1016/j.jprot.2012.09.033

Abstract

In this study, a Veterinary Department repository composed by paired formalin-fixed paraffinembedded (FFPE) and fresh-frozen (FrFr) sets of the same tissues, routinely archived in the typical conditions of a clinical setting, was exploited to perform a comparative evaluation of the results generated by GeLC–MS/MS (1-DE followed by in-gel digestion and LC–MS/MS) and spectral counting with the two types of archival samples. Therefore, two parallel differential proteomic studies were performed using 3 canine mammary carcinomas and 3 normal controls in a paired fashion (6 FrFr and 6 FFPE in total). As a result, the FrFr and FFPE differential proteomic datasets exhibited fair consistency in differential expression trends, according to protein molecular function, cellular localization, networks, and pathways. However, FFPE samples were globally slightly less informative, especially concerning the high-MW subproteome. As a further investigation, new insights into the molecular aspects of protein fixation and retrieval were obtained. In conclusion, archival FFPE samples can be reliably used for differential proteomics studies employing a spectral counting GeLC–MS/MS approach, although some typical biases need to be taken into account, and FrFr specimens (when available) should still be considered as the gold standard for clinical proteomics.

Item Type:Article
ID Code:8217
Status:Published
Refereed:Yes
Uncontrolled Keywords:Archival samples, biorepository, FFPE, GeLC–MS/MS, spectral counting
Subjects:Area 06 - Scienze mediche > MED/07 Microbiologia e microbiologia clinica
Area 07 - Scienze agrarie e veterinarie > VET/03 Patologia generale e anatomia patologica veterinaria
Divisions:002 Altri enti e centri di ricerca del Nord Sardegna > Porto Conte Ricerche, Alghero
001 Università di Sassari > 01-a Nuovi Dipartimenti dal 2012 > Scienze Biomediche
001 Università di Sassari > 01-a Nuovi Dipartimenti dal 2012 > Medicina Veterinaria
Publisher:Elsevier
ISSN:1874-3919
Deposited On:26 Nov 2012 10:58

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