1.  IDEAL-Q is an automated analysis tool for label-free quantitative proteomics. It accepts generic input format including mzXML raw data format and Mascot, SEQUEST, PeptideProphet/ProteinProphet for search result. IDEAL-Q uses an algorithm, called IDEAL (ID-based Elution time prediction by frAgmentaL regression), to predict the elution time based on confident peptide identification (ID) result, and thus the predicted elution time together with precursor m/z to can be used to locate the peptide signal in other LC-MS runs. In comparison with conventional identity-based label-free quantitation analysis, the quantitation coverage in terms of percentage of identified peptides and proteins can be much increased. Furthermore, the tool adopts an stringent validation stelp on Signal-to-noise ratio, Charge state, Isotopic distribution (SCI validation) and modification type using computational and statistical methods so that quantitation accuracy can be ensured even with increased quantitation coverage. IDEAL-Q provides variously optional normalization tools for flexible workflow design such as addition of fractionation strategies and multiple spiked internal standards. Furthermore, many user-friendly interfaces and statistical charts are provided in IDEAL-Q for user to conveniently inspect and validate the quantitation result and also enable to manually re-quantify data. It also provides comprehensible output reports in various formats with useful visualization diagrams and statistical analysis. IDEAL-Q can be downloaded from http://ms.iis.sinica.edu.tw/IDEAL-Q/.

 MaXIC-Q is designed as a generic tool for quantitation using differential isotope-labeling techniques, e.g., SILAC, ICAT, ICPL labelings, and user-developed labeling methods. The tool can also accommodate search results from SEQUEST and Mascot, as well as mzXML files converted from raw files produced by various mass spectrometers. MaXIC-Q contains a filtering module that allows users to filter out low-confidence search results. Statistical and computational methods are applied to construct two kinds of elution profiles for each ion, namely, PIMS (projected ion mass spectrum) and XIC (extracted ion chromatogram); the latter is used to quantify the ion ratio. To ensure that the data used for quantitation analysis is of high quality, MaXIC-Q defines validation criteria for PIMSs so that ions interfered with by co-eluting peptides or noise can be detected. MaXIC-Q can be downloaded from http://ms.iis.sinica.edu.tw/MaXIC-Q/.

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