Table 1.
Selection of Software Tools for the Analysis of Mass Spectrometry Data
| Software | Use | Open source | URL | Reference |
|---|---|---|---|---|
| Processing of raw peak data | ||||
| mzMine | Peak detection, labeling, deisotoping. | Y | http://mzmine.sourceforge.net/ | (Katajamaa et al., 2006) |
| Sequence database search engines | ||||
| Mascot | Determines proteins present in a sample. Also includes emPAI for protein quantification | N | http://www.matrixscience.com/ | (Perkins et al., 1999) |
| Sequest | Determines proteins present in a sample. | N | http://fields.scripps.edu/sequest/ | (Link et al., 1999) |
| X!Tandem | Determines proteins present in a sample. | Y | http://www.thegpm.org/tandem/ | (Craig and Beavis, 2004) |
| Label-free quantification of proteins | ||||
| emPAI | Label free (included in Mascot results) | Y | http://www.matrixscience.com/help/quant_empai_help.html | (Ishihama et al., 2005) |
| PepC | Label free | Y | http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/src/Quantitation/Pepc/ | (Heinecke et al., 2010) |
| APEX | Label free, including absolute quantitation | Y | http://pfgrc.jcvi.org/index.php/bioinformatics/apex.html | (Vogel and Marcotte, 2008) |
| Feature selection/machine learning | ||||
| WEKA | Includes many methods for both feature selection and classification | Y | http://www.cs.waikato.ac.nz/ml/weka/ | (Witten et al., 2011) |
| Multiple functions | ||||
| R packages | There are many different packages available for analysis of MS data using R, including ‘xcms’ and ‘MassSpecWavelet’ for processing of mass spectral data, along with other Bioconductor packages. | Y |
http://www.r-project.org/ http://bioconductor.org/packages/release/bioc/html/xcms.html http://bioconductor.org/packages/release/bioc/vignettes/MassSpecWavelet/inst/doc/MassSpecWavelet.pdf |
(Du et al., 2007; Gentleman et al., 2004; Smith et al., 2006) |