LFQuant

LFQuant is a new analysis tool for label-free LC-MS/MS quantitative proteomics data. It is compatible with high-resolution mass spectrometers data in the standard mzXML or Thermo Raw format and major search engines (including MASCOT, SEQUEST, and X!Tandem). LFQuant is written in Microsoft Visual C++ 2005 with MFC and runs on any Windows system. This software and any associated documentation are provided “as is” and there is no warranty for this software. LFQuant can be run directly after the unpacking of the zip on windows system (windows 7, windows XP, windows 2003 and windows 2000). To run LFQuant click the "LFQuant.exe" file, then an user interface for LFQuant quantification is displayed. An extra tool (LFQuantViewer) was designed to visualize the peptide and protein quantitative results. LFQuantViewer can be divided into four parts (protein list part, peptide list part, peptide XIC part and statistic demonstration part). Protein list part shows the quantitative information of all identified proteins, including protein access number, ratios, number of unique peptide and estimated abundance. Peptide list part shows the quantitative information of the peptides which belong to the protein selected in the protein list part, including peptide IDs, sequence, peptide molecular mass, charge state, estimated abundance and spectral counts. For the peptide selected in the peptide list part, peptide XIC part shows its quantitative information of different experiments. In this part, the peptide XIC of the experiment selected in the "Information of Peptide" can be popped up through pushing the button "XIC Viewer". In statistic demonstration part, some statistic charts for peptide and protein , including "Abundance vs. abundance", "Ratio histogram plot", "Ratio scattered plot" and "RT vs. RT", can be viewed through pushing the button "Peptide Analysis" and "Protein Analysis".