ProteomicsTools Software Suite
ProteomicsTools software suite contains a bunch of tools used in proteomics research, from identification result parsing to quantification, modification, et. al.
Currently, there are few major softwares with full documents, please cite corresponding paper if you use ProteomicsTools in your project:- **BuildSummary** [[Full documents](https://github.com/shengqh/RCPA.Tools/wiki/BuildSummary)] : The target-decoy database search strategy is widely accepted as a standard method for estimating the false discovery rate (FDR) of peptide identification, based on which peptide-spectrum matches (PSMs) from the target database are filtered. To improve the sensitivity of protein identification given a fixed accuracy (frequently defined by a protein FDR threshold), a post-processing procedure is often used that integrates results from different peptide search engines that had assayed the same dataset. In this work, we show that PSMs that are grouped by the precursor charge, the number of missed internal cleavage sites, the modification state, the numbers of protease termini and the proteins grouped by their unique peptide count should be filtered separately according to the given FDR. We also develop an iterative procedure to filter the PSMs and proteins simultaneously, according to the given FDR. Finally, we present a general framework to integrate the results from different peptide search engines using the same FDR threshold. Our method was tested with several shotgun proteomics datasets that were acquired by multiple LC/MS instruments from two different biological samples. The results showed a satisfactory performance. - **SRMBuilder** [[Full documents](https://github.com/shengqh/RCPA.Tools/wiki/SRMBuilder)] : With high sensitivity and reproducibility, selected reaction monitoring (SRM) has become increasingly popular in proteome research for targeted quantification of low abundance proteins and post translational modification. SRM is also well accepted in other mass-spectrometry based research areas such as lipidomics and metabolomics, which necessitates the development of easy-to-use software for both post-acquisition SRM data analysis and quantification result validation. Here, we introduce a software tool SRMBuilder, which can automatically parse SRM data in multiple file formats, assign transitions to compounds, match light/heavy transition/compound pairs and provide a user-friendly graphic interface to manually validate the quantification result at transition/compound/sample level. SRMBuilder will greatly facilitate processing of the post-acquisition data files and validation of quantification result for SRM. - **O18Quant** [[Full documents](https://github.com/shengqh/RCPA.Tools/wiki/O18Quant)] : Proteolytic 18O-labeling has been widely used in quantitative proteomics since it can uniformly label all peptides from different kind of proteins. There have been multiple algorithms and tools developed over the last few years to analyze high-resolution proteolytic 16O/18O labeled mass spectraanalyze high-resolution proteolytic 18O-labeled mass spectra. We have developed a software tool: O18Quant, which addresses two major issues in the previous developed tools. First, O18Quant uses robust linear model (RLM) for peptide-to-protein ratio estimation. RLM can minimize the effect of outliers instead of iteratively removing them which is a common practice in other approaches. Second, the existing approaches lack applicable implementation which O18Quant is implemented using C# under Microsoft .net framework and R. It automatically calculates the peptide/protein relative ratio and provides a friendly graphic user interface (GUI) which allows the user to manually validate the quantification result at scan, peptide and protein levels. The intuitive GUI O18Quant can greatly enhance the user’s visualization and understanding of the data analysis. - **TurboRaw2MGF** [[Full documents](https://github.com/shengqh/RCPA.Tools/wiki/TurboRaw2MGF)] : Isobaric labelling technique coupled with high resolution mass spectrometry has been widely employed in proteomic workflows requiring relative quantification. For each high resolution tandem mass spectrum (MS/MS), it can be used not only to quantify the peptide from different samples by reporter ions，but also to identify the peptide it derived from. Since the ions related to isobaric labeling may act as noise in database searching, the MS/MS spectrum should be preprocessed before peptide/protein identification. In this paper, we demonstrate that there are a lot of high frequency, high abundance isobaric related ions in MS/MS spectrum, and combining removing isobaric related ions with deisotoping and deconvolution in MS/MS preprocessing procedure improves the peptide/protein identification sensitivity significantly. - **DeuteriumCalculator** [[Full documents](https://github.com/shengqh/RCPA.Tools/wiki/DeuteriumCalculator)] : A promising strategy that is available for quantifying rates of protein synthesis is the administration of heavy water (deuterium oxide, D2O) to living organisms. In this strategy, mass spectrometry is used to monitor the kinetics of deuterium incorporation into the newly synthesized protein molecules, and the kinetics of deuterium enrichment are calculated over a time-course experiment. Currently, however, there are few freely available software for deuterium enrichment analysis based on high resolution mass spectrometry data. We have developed a user friendly software, DeuteriumCalculator, that efficiently extracts the chromatograph information of identified peptides from high resolution mass spectrometry data and calculates the extent of deuterium enrichment based on isotopomer distribution. A real data example is given to demonstrate the effectiveness and output format of the software. DeuteriumCalculator is designed to facilitate D2O-based protein turnover research by automating the most time-consuming step in the data analysis: calculation of the extent of deuterium enrichment from the mass spectrometry data. DeuteriumCalculator is expected to substantially expedite the process of deuterium enrichment analysis. #Prerequisites Two libraries are required for executing the software: - [MSFileReader library](http://sjsupport.thermofinnigan.com/public/detail.asp?id=703) - [dotNET Platform 4.0] (http://www.microsoft.com/download/en/details.aspx?displaylang=en&id=17718) #Installation ###Binary File Both 64bit version and 32bit version are provided in [github](https://github.com/shengqh/RCPA.Tools/releases). Download the file and decompress it to any folder you want, run ProteomicsTools.exe and have fun.
###Source The c# source code is also provided at following repositories. Visual Studio 2015 is recommended for compilation.
- SQH.Lib : Third part C# libraries required by other modules.
- RCPA.Core : Core library of GUI and utilities.
- RCPA.Proteomics : Proteomics library including a lot of proteomics related utilities and tools.
- RCPA.Tools : Proteomics Tool Suite interface.