Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis

BMC Bioinformatics

Table 1 Open source software packages for MS data analysis

Program	S	B	P	Web link
Cromwell [12]	S7	B1	P1, P4	http://bioinformatics.mdanderson.org/software.html
LCMS-2D [20]	-	B5	P1, P2	http://www.bioc.aecom.yu.edu/labs/angellab/
LIMPIC [21]	S4	B2	P1, P3	http://www.biomedcentral.com/1471-2105/8/101/additional/
LMS [22]	S3	B2	P1, P4	http://bioinformatics.ust.hk/LMS.zip
MapQuant [16]	S1,S2,S3	-	P7	http://arep.med.harvard.edu/MapQuant/download.html
CWT [10]	S5	B4	P1, P6	http://www.bioconductor.org/packages/devel/bioc/html/MassSpecWavelet.html
msInspect [23]	S6	B2	P5	http://proteomics.fhcrc.org/CPL/msinspect.html
mzMine [24]	S1, S2	-	P1, P2, P8	http://mzmine.sourceforge.net/download.shtml
OpenMS [15]	S5	B4	P7	http://open-ms.sourceforge.net/index.php
PROcess [13]	S1	B2, B3	P1, P2, P5	http://www.bioconductor.org/packages/devel/bioc/html/PROcess.html
PreMS [25]	S7	B1	P1, P4	http://sourceforge.net/projects/prepms
XCMS [8]	S3	-	P1, P4	http://www.bioconductor.org/packages/1.8/bioc/html/xcms.html

Here "S" denotes smoothing filter, "B" denotes baseline correction method, "P" denotes peak finding criterion and "-" means smoothing or baseline correction method is not used. Cromwell, LIMPIC, LMS, CWT, and PROcess are designed for single spectrum peak detection. LCMS-2D, MapQuant, msInspect, mzMine, OpenMS and XCMS are designed for LC-MS (Liquid Chromatography Mass Spectrometry) data analysis. PreMS is a GUI (Graphic User Interface) package based on Cromwell.

ISSN: 1471-2105