About FPF

Isobaric labeling relative quantitation is one of the dominating proteomic quantitation technologies. Traditional quantitation pipelines for isobaric-labeled MS data are based on sequence database searching. We present a novel quantitation pipeline which integrates sequence database searching, spectral library searching, and a feature-based peptide-spectrum-match (PSM) filter (FPF) using various spectral features for filtering. The combined database and spectral library searching results in larger quantitation coverage, and the filter removes PSMs of larger quantitation error, retaining those of higher quantitation accuracy. The proposed pipeline is fully compatible with the Trans-Proteomic Pipeline and can be executed on Windows, Linux, and MacOS platforms. The source code of FPF is also publicly available at GitHub (link).

Software Release:

FPF for Windows (download here)

FPF for Linux (download here)

FPF for MacOS (download here)

Other Materials:

User guide (download here)

Sample dataset (download here)

System Requirements:

  1. Operating Systems:  Windows 64-bit, Linux 64-bit, MacOS 64-bit
  2. Hard disk:  depending on the raw data file size. It is recommended that the free space on the disk is several times the size of the input iProphet files and mzML files (for S2I Filter).
  3. Memory:  depending on the input file size. In general, a minimum of 8GB is suggested.