Tools Alphabetically
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.
Optional Registration
If you would like to register as a user of our software to receive notification of changes, you are more than welcome to do so here.
| 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 |
| Concatenated Text File Splitter | Splits the concatenated tandem mass spectral data (.dta) files and the cocatenated SEQUEST output files into separate files. | 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 |
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 from the OMICS distribution center | |
| 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 |
| 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 | |
| ListPOR | Used to read a file containing columns of grouped values and remove outlier values using Grubb's test. | 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 from the OMICS distribution center | |
| MGF 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 |
Molecular Weight Calculator  |
Calculates the molecular weight and percent composition of chemical formulas and amino acids. | 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 | |
| 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 |
| 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. | Download from the OMICS distribution center | |
| 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 from the OMICS distribution center | |
| 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 |
| Peak Finder | Used to compute the peak capacity of chromatographic separations. | 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 |
| 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 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 from the OMICS distribution center | |
| Phosphopeptide FDR Estimator | Linear discriminant analysis-based estimation of false discovery rates for phosphopeptide identifications. | Coming soon | |
| Protein Coverage Summarizer | Used to determine the percent of the residues in each protein sequence that have been identified. | Download Software | Download Source Code |
| Protein Digestion Simulator
Basic |
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 |
| 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 | |
| Spectrum Look | 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 |
| 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 |
| Time-Course Analysis | MATLAB scripts to perform the analysis outlined in the manuscript "A Computational Strategy to Analyze Label-Free Temporal Bottom-up Proteomics Data". X Du et.al. submitted to J. Proteome Res.. | Download Source Code | |
| 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 |
| 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 |
| VIPER |
Used to visualize and characterize the features detected during LC-MS analyses. | Download Software | 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 |
Acknowledgment
All publications that result from the use of this software should include the acknowledgment statement specified in the Readme.txt file for the given application. If a specific application does not have a Readme.txt file or an explicitly defined Acknowledgment, then please use this statement:
Portions of this research were supported by the NIH National Center for Research Resources (Grant RR018522), and the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at PNNL). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830.
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.
