pFind Studio is a computational solution for mass spectrometry-based proteomics. pFind Studio includes pFind, pBuild, pLabel, pXtract, pParse and pScan
pXtract creates .DTA .MGF and .MS2 input files directly from Thermo Scientific .raw LC-MS/MS data files.
pParse is a software dedicated to recalibrate the monoisotopic of precursors in MS/MS spectra datasets assigned by mass spectrometry
pFind is a search engine for peptide and protein identification via tandem mass spectrometry.
pNovo+ is a de novo peptide sequencing algorithm using complementary HCD and ETD tandem mass spectra.
pBuild is a tool that can compare several search engines’ results and combine them together. The latest version, pBuild v2.0, can process the search results of pFind, SEQUEST and Mascot.
pQuant is the software for quantitative proteomics, evaluates the accuracy of caluculated peptide and protein ratios.
pLabel is a spectra labeling tool that can visualize the global- and local-view peptide-spectrum matches, given the results of pFind or any other search engines. pLabel can label both CID and ETD spectra, and implement the manual de novo sequencing.
pLink is a software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry.
pScan is a flexible tool that helps biologists to preprocess protein sequence databases in proteomics research.
pCluster is a software tool aiming at detecting protein modifications independent of sequence databases by tandem mass spectral clustering.
pMatch is a spectral library search tool, which is deliberately designed for the open search mode.
DiagnoProt is a tool that finds discriminative mass spectra among different biological conditions and ultimately performs spectral profiling classification of unknown conditions by comparing sets of tandem mass spectra (MS/MS).
MET-IDEA is compatible with a diversity of chromatographically coupled mass spectrometry systems, generates an output similar to traditional quantification methods, utilizes the sensitivity and selectivity associated with selected ion quantification, and greatly reduces the time and effort necessary to obtain large-scale organized datasets by several orders of magnitude. The functionality of MET-IDEA is illustrated using metabolomics data obtained for elicited cell culture exudates from the model legume, Medicago truncatula. The results indicate that MET-IDEA is capable of rapidly extracting semi-quantitative data from raw data files, which allows for more rapid biological insight.
Cromwell is an implementation of our algorithms for low-level processing of mass spectrometry proteomics data. Cromwell represents our third attempt (at least) to find a method to process spectra that both works quickly and achieves reasonably good results.
MSFragger is an ultrafast database search tool that uses a fragment ion indexing method to rapidly perform spectra similarity comparisons.
FragPipe is a Java Graphical User Interface (GUI) for a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data. It is powered by MSFragger – an ultrafast proteomic search engine suitable for both conventional and “open” (wide precursor mass tolerance) peptide identification.
IDEAL-Q is an automated analysis tool for label-free quantitative proteomics. It accepts mzXML raw data format and Mascot xml and ProtXML/PepXML for identification result. IDEAL-Q uses an elution time prediction and peak alignment algorithms to quantify peptides across different LC-MS runs and increase quantitation coverage. Furthermore, the tool adopts an stringent validation step on Signal-to-noise ratio, Charge state, Isotopic distribution (SCI validation) to ensure quantitation accuracy. IDEAL-Q provides variously optional normalization tools for flexible workflow design such as addition of fractionation strategies and multiple spiked internal standards