The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses.
J Proteome Res
; 7(11): 4756-65, 2008 Nov.
Article
en En
| MEDLINE
| ID: mdl-18798661
ABSTRACT
Recently, mass spectrometry has been employed in many studies to provide unbiased, reproducible, and quantitative protein abundance information on a proteome-wide scale. However, how instruments' limited dynamic ranges impact the accuracy of such measurements has remained largely unexplored, especially in the context of complex mixtures. Here, we examined the distribution of peptide signal versus background noise (S/N) and its correlation with quantitative accuracy. With the use of metabolically labeled Jurkat cell lysate, over half of all confidently identified peptides had S/N ratios less than 10 when examined using both hybrid linear ion trap-Fourier transform ion cyclotron resonance and Orbitrap mass spectrometers. Quantification accuracy was also highly correlated with S/N. We developed a mass precision algorithm that significantly reduced measurement variance at low S/N beyond the use of highly accurate mass information alone and expanded it into a new software suite, Vista. We also evaluated the interplay between mass measurement accuracy and S/N; finding a balance between both parameters produced the greatest identification and quantification rates. Finally, we demonstrate that S/N can be a useful surrogate for relative abundance ratios when only a single species is detected.
Texto completo:
1
Bases de datos:
MEDLINE
Asunto principal:
Péptidos
/
Espectrometría de Masas
/
Proteoma
/
Proteómica
Tipo de estudio:
Prognostic_studies
Límite:
Humans
Idioma:
En
Revista:
J Proteome Res
Asunto de la revista:
BIOQUIMICA
Año:
2008
Tipo del documento:
Article
País de afiliación:
Estados Unidos