Proteomics Software Downloads (by Category)
Software Categories
- Featured Tools
- Fasta File / Protein Sequence / Protein Database Related
- MS/MS Analysis Tools
- MS Analysis Tools
- Data Analysis & Data Presentation
- MS Data File Utilities
- Mass Spectrometry Auxiliary Tools
System Requirements
Most of these applications require Microsoft Windows 9x/2000/XP or newer, and the Microsoft.NET Framework 1.1. If the installer informs you that the .NET framework is not present on your computer, you can download the installer from Microsoft via this link.
Featured Tools
DAnTE
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Used to perform various downstream data analysis, data reduction, and data comparison steps including normalization, hypothesis testing and clustering. | Download Software | Download Source Code |
| Decon2LS | Used to de-isotope MS spectra and to detect features from MS data using isotopic signatures of expected components. | Download Software | Download Source Code |
| DeconMSn | Used to create .Dta files or .MGF files from tandem MS/MS data (Thermo Finnigan or mzXML format) with accurate parent monoisotopic mass and charge determined using the isotopic signatures of the parent ions. | Download Software | Download Source Code |
| MultiAlign | Aligns multiple LC-MS datasets to one another, afterwhich LC-MS features can be matched to a database of peptides (e.g. an AMT tag database) | Download Software | |
| VIPER | Used to visualize and characterize the features detected during LC-MS analyses. | Download Software | Download Source Code |
Fasta File / Protein Sequence / Protein Database Related tools
| Fasta File Comparer | Compares protein sequences from two different Fasta files and outputs the matching proteins and sequences to a text file. | Download Software | Download Source Code |
| Normalized Elution Time Prediction Utility | Used to to compute the predicted normalized elution time (NET) value for a list of peptide sequences | Download Software | Download Source Code |
| Strong Cation Exchange Elution Time Prediction Utility | Used to to compute the predicted strong cation exchange (SCX) elution time for a list of peptide sequences | Download Software | Download Source Code |
| PepAligner | Align a list of peptide sequences to a file of protein sequences (.Fasta or delimited text) using Smith-Waterman alignment. | Download Software | Download Source Code |
| Protein Digestion Simulator | Used to read a text file containing protein or peptide sequences (Fasta format or delimited text) and output the data to a tab-delimited file. | Download Software | Download Source Code |
| SVM Technique for Evaluating Proteotypic Peptides (STEPP) | Uses a trained SVM to compute a score representing how "proteotypic" a peptide is by LC-MS. | Download Software | |
| Uniprot DAT File Parser | Used to read a Uniprot (IPI) .Dat file and parse out the information for each entry, creating a tab delimited text file. | Download Software | Download Source Code |
MS/MS Analysis Tools
| DeconMSn | Used to create .Dta files or .MGF files from tandem MS/MS data (Thermo Finnigan or mzXML format) with accurate parent monoisotopic mass and charge determined using the isotopic signatures of the parent ions. | Download Software | Download Source Code |
| DtaRefinery | Improves mass measurement errors for parent ions of tandem MS/MS data by modeling systematic errors based on putative peptide identifications. This information is used to subtract out errors from parent ion protonated masses. | Download Software | Download Source Code |
| MASIC | Generates selected ion chromatograms (SICs) for all of the parent ions chosen for fragmentation in an LC-MS/MS analysis. | Download Software | Download Source Code |
| MASIC Results Merger | Reads the contents of a tab-delimited peptide hit results file (e.g. from Sequest, XTandem, or Inspect) and merges that information with the corresponding MASIC results files | Download Software | Download Source Code |
| MSMS Spectra Preprocessor | Can be used to generate or process .dta, _dta.txt and .mgf files and test spectra against one of four filters: spectral quality, amino acid spacing, intensity threshold, and phosporylation neutral loss. | Download Software | Download Source Code |
| PE-MMR | Used to refine the parent mass and charge in DTA files, which can lead to more accurate search results from MS/MS spectra | Download Software | Download User Guide |
| Peptide File Extractor | Processes SEQUEST .Out or _out.txt files to create Synopsis and First Hits files, which are tab-delimited files summarizing the peptide identifications in the SEQUEST .Out files. | Download Software | Download Source Code |
| Peptide Fragmentation Modeller | Simple program that uses the .NET Molecular Weight Calculator DLL (MwtWinDll.NET) to compute the theoretical fragmentation pattern (b and y ions) for a list of peptides. | Download Software | Download Source Code |
| Peptide Hit Results Processor | Converts an X!Tandem results file (XML format) or a SEQUEST Synopsis/First Hits file to a series of tab-delimited text files summarizing the results. | Download Software | Download Source Code |
| Phosphopeptide FDR Estimator | Linear discriminant analysis-based estimation of false discovery rates for phosphopeptide identifications. | Coming soon | |
| SpectrumLook | Allows users to visually browse the MS/MS spectra that led to the peptide identifications, including viewing annotations for the identified b and y ions, plus neutral loss ions where appropriate. | Download Software | Download Source Code |
MS Analysis Tools
| Decon2LS | Used to de-isotope MS spectra and to detect features from MS data using isotopic signatures of expected components. | Download Software | Download Source Code |
| ICR-2LS | Finds peaks in raw mass spectra. Capable of full waveform generation, automated mass spectra interpretation and databas searching integration of FASTA or GenBank files. | Download Software | |
| MTDB Creator | Can be used to generate a Mass and Time Tag database (Microsoft Access format) from local MS/MS search engine results (currently X!Tandem) that can act as input to VIPER for matching high resolution LC-MS features to peptides. Includes example data from Salmonella typhimurium. | Download Software | |
| MultiAlign | Aligns multiple LC-MS datasets to one another, afterwhich LC-MS features can be matched to a database of peptides (e.g. an AMT tag database) | Download Software | |
| Time-Course Analysis | MATLAB scripts to perform the analysis outlined in the in the manuscript: A Computational Strategy to Analyze Label-Free Temporal Bottom-Up Proteomics Data. Xiuxia Du, et. al. J. Proteome Res., 7 (7), 2595-2604 (2008). (abstract on PubMed) |
Download Source Code | |
| VIPER | Used to visualize and characterize the features detected during LC-MS analyses. | Download Software | Download Source Code |
Data Analysis & Data Presentation Tools
| Amino Acid Residue Frequency Summarizer | Prepares statistics on the occurrence of each amino acid residue throughout a file containing peptide or protein sequences. | Download Software | Download Source Code |
| DAnTE
|
Used to perform various downstream data analysis, data reduction, and data comparison steps including normalization, hypothesis testing and clustering. | Download Software | Download Source Code |
| ListPOR | Used to read a file containing columns of grouped values and remove outlier values using Grubb's test. | Download Software | Download Source Code |
| Protein Coverage Summarizer | Used to determine the percent of the residues in each protein sequence that have been identified. | Download Software | Download Source Code |
| Proteomics Peptide Data Exploration (PQuad) | Allows a user to visually integrate genomic and proteomic data at the prokaryotic scale, display biological categorical information and view differential expression experiments. | Download Software | |
| ScalaBLAST | High-performance multiprocessor implementation of the NCBI BLAST library | Download Software | View Readme File |
| Unpivot Tool | Reads in a delimited text file that is in crosstab (aka PivotTable) format and writes out a new file where the data has been unpivotted. | Download Software | Download Source Code |
| Venn Diagram Plotter | Draws correctly proportioned and positioned two and three circle Venn diagrams whose colors can be customized and the diagrams copied to the clipboard or saved to disk. | Download Software | Download Source Code |
| Visual Integration for Bayesian Evaluation (VIBE) | A visualization tool to observe classification accuracies at the class level and evaluate classification accuracies based on the posterior probability models defined for individual and integrated data. | Download Software | Download Matlab Runtime v7.9 |
MS Data File Utilities
| Concatenated Text File Splitter | Splits the concatenated tandem mass spectral data (.dta) files and the concatenated SEQUEST output files into separate files. | Download Software | Download Source Code |
| Concatenated DTA to MGF File Converter | Reads in a concatenated Dta file (_Dta.txt) and creates the equivalent Mascot Generic Format (MGF) file | Download Software | Download Source Code |
| MGF to DTA File Converter | Reads in a Mascot Generic Format (MGF) file and creates the equivalent _dta.txt or .dta files. | Download Software | Download Source Code |
| MS Data File Reader | VB.NET DLL for reading mass spectrum data from mzXML, mzData,concatenated .dta files and Mascot Generic format files. | Download Source Code | |
| MS Data File Trimmer | Creates mzXML and mzData files containing only the spectra for specified scan numbers. | Download Software | Download Source Code |
| MS File Info Scanner | Scans a series of MS data files (or data folders) and extracts the acquisition start and end times, number of spectra, and the total size of the data, saving the values in the file DatasetTimeFile.txt. | Download Software | Download Source Code |
| MS XML File Reader | VB6 DLL for reading mass spectrum data from mzXML and mzData files. | Download Source Code | |
| X2XML | Create mzXML files from various other MS data file formats, including Xcalibur .RAW, Agilent .wiff, Micromass .DAT, Bruker .acqu, Bruker ASCII .ascii, the PNNL IMS .imf format, and Bruker FTICR S-folders. | Download Software | Download Source Code |
| Spectrum Mill Data File Condenser | Used to archive the large numbers of .pkl and .pkl.spo files created by the Spectrum Mill MS Proteomics Workbench software when processing datasets. The individual files are combined into a concatenated text file, afterwhich the individual files are deleted. | Download Software | Download Source Code |
Mass Spectrometry Auxiliary Tools
imPredict: Ion Mobility Drift Time Prediction |
imPredict is a support vector regression based computational technique that computes ion mobility drift times for peptides sequences. | Download Program | Download Java 6 Runtime |
| Isotope Pattern Calculator (IPC) | Calculates and displays the isotopic distribution and exact masses for peptides and other molecules. | Download Software | Download Source Code |
Molecular Weight Calculator
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Calculates the molecular weight and percent composition of chemical formulas and amino acids. | Download Software | Download .NET DLL version |
| Peak Finder | Used to compute the peak capacity of chromatographic separations. | Download Software | Download Source Code |
Acknowledgment
All publications that utilize this software should provide appropriate acknowledgement to PNNL and the OMICS.PNL.GOV website. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, as shown in the Readme file for the given application or on the website that more fully describes the application.
Disclaimer
These programs are designed to run on Windows 9x/2000/XP machines. Please use them at your own risk. Neither PNNL nor the U.S. Department of Energy claim any responsibility for any problems associated with this software.
We would like your feedback about the usefulness of the tools and information provided by the Resource. Your suggestions on how to increase their value to you will be appreciated. Please e-mail any comments to proteomics@pnl.gov