Label-free, normalized quantification of complex mass spectrometry data for proteomics analysis

By N. Griffin, Jingyi Yu, F. Long, P. Oh, Sabrina Shore, Yan Li, J. Koziol, J. Schnitzer. Nature Biotechnology, 2009

412 citations recorded by the source corpus.

Replicate mass spectrometry (MS) measurements and the use of multiple analytical methods can greatly expand the comprehensiveness of shotgun proteomic profiling of biological samples. However, the inherent biases and variations in such data create computational and statistical challenges for quantitative comparative analysis. We developed and tested a normalized, label-free quantitative method termed the normalized spectral index (SIN), which combines three MS abundance features: peptide count, spectral count and fragment-ion (tandem MS or MS/MS) intensity. SIN largely eliminated variances between replicate MS measurements, permitting quantitative reproducibility and highly significant quantification of thousands of proteins detected in replicate MS measurements of the same and distinct samples. It accurately predicts protein abundance more often than the five other methods we tested. Comparative immunoblotting and densitometry further validate our method. Comparative quantification of complex data sets from multiple shotgun proteomics measurements is relevant for systems biology and biomarker discovery.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/5aed05ced445fed9cc64fa39279391152fc522b4

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

In Spectroscopy

Citations in the corpus

Less label, more free: Approaches in label‐free quantitative mass spectrometry (2011, methodology): “Peptide count (the number of unique peptides identified for the protein of interest), SpC (the number of MS/MS spectra per peptide) and fragment ion intensity from each tandem mass spectra were merged to give SIN, a normalised spectral index (SI) [50].”