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 webcite

LCMS-2D [20]

-

B5

P1, P2

http://www.bioc.aecom.yu.edu/labs/angellab/ webcite

LIMPIC [21]

S4

B2

P1, P3

http://www.biomedcentral.com/1471-2105/8/101/additional/ webcite

LMS [22]

S3

B2

P1, P4

http://bioinformatics.ust.hk/LMS.zip webcite

MapQuant [16]

S1,S2,S3

-

P7

http://arep.med.harvard.edu/MapQuant/download.html webcite

CWT [10]

S5

B4

P1, P6

http://www.bioconductor.org/packages/devel/bioc/html/MassSpecWavelet.html webcite

msInspect [23]

S6

B2

P5

http://proteomics.fhcrc.org/CPL/msinspect.html webcite

mzMine [24]

S1, S2

-

P1, P2, P8

http://mzmine.sourceforge.net/download.shtml webcite

OpenMS [15]

S5

B4

P7

http://open-ms.sourceforge.net/index.php webcite

PROcess [13]

S1

B2, B3

P1, P2, P5

http://www.bioconductor.org/packages/devel/bioc/html/PROcess.html webcite

PreMS [25]

S7

B1

P1, P4

http://sourceforge.net/projects/prepms webcite

XCMS [8]

S3

-

P1, P4

http://www.bioconductor.org/packages/1.8/bioc/html/xcms.html webcite

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.

Yang et al. BMC Bioinformatics 2009 10:4   doi:10.1186/1471-2105-10-4