Q-Fish

Q-FISH (Quantification method based on Finding the Identical Spectral set for a Homogenous peptide) is to estimate the peptide’s abundance from its tandem mass spectrometry (MS/MS) spectra through the direct comparison of experimental spectra.

Quantification of protein expression by means of mass spectrometry (MS) has been introduced in various proteomics studies. In particular, two label-free quantification methods, namely spectral counting and spectra feature analysis, have been extensively demonstrated on a wide variety of proteomes. The cornerstone of both methods is peptide identification based on protein database search and subsequent estimation of peptide retention time. However, they may suffer from restrictive database searching and inaccurate estimation of the liquid chromatography (LC) retention time. Furthermore, conventional peptide identification method of the database searching or the spectral library searching algorithms such as SEQUEST or SpectraST can provide neither the best match nor high-scored matches, which are reliable indicators of protein targets. Lastly, peptides cannot be identified unless they have been previously generated and stored into the database or spectral libraries.
To overcome these limitations, we propose a novel method called Q-FISH to estimate the peptide’s abundance from its tandem mass spectrometry (MS/MS) spectra through the direct comparison of experimental spectra. Because our proposed Q-FISH method compares all possible pairs of experimental spectra, it is possible to identify modified as well as unknown peptides.

R code for Q-FISH : Q-FISH.R

Reference : Lee S, Kwon MS, Lee HJ, Paik YK, Tang H, Lee JK and Park T, Enhanced peptide quantification using spectral count clustering and cluster abundance, BMC Bioinformatics (2011), PMCID PMC3234305.