Biomolecular Function Discovery Division

MS Cleaner Version 1.0.000
Supplement to the article
"Processing of raw protein MS/MS spectra:
Detection of multiply charged peaks, isotope clusters and background noise"

Proteomics. 2006 Oct;6(19):5117-5131

Authors:

Nedim Mujezinovic, Sarajevo School of Science and Technology
Guenther Raidl, Institute of Computer Graphics and Algorithms, TU Vienna
James R. A. Hutchins, IMP Mitocheck Group
Jan-Michael Peters, IMP Mitocheck Group
Karl Mechtler, IMP MS Group
Frank Eisenhaber, Bioinformatics Institute, A*Star Singapore

Contact coordinates:

Bioinformatics Institute 30 Biopolis Street, #07-01 Matrix Singapore 138671 Tel. (65) 6478 8298 Fax. (65) 6478 9050

List of Supplements
• Suppl. Figs. 1-12: Analysis of example tandem mass spectrum for motivating the application of signal processing procedures for background removal in protein tandem mass spectra

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  Supplementary data for the BSA example 
• MS/MS data (mgf-format) for bovine serum albumine (raw and cleaned versions)
• Peptide-wise comparison of scores of top-hit peptides before and after background removal for bovine serum albumine
• Supplement to Figure 3:
  • A)Figure3A.dta and it's view in .tif and .jpg formats.
  • B)Figure3B.dta and it's view in .tif and .jpg formats.
• Supplement to Figure 4: Exemplary case of a spectrum that was interpretable for Mascot only after background removal with MS Cleaner: dta-files with raw and with cleaned data
• Before and after background removal with MS Cleaner: detailed analysis of the exemplary real tandem mass spectrum 1.369.369.2 from the BSA set

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Supplementary data for the ADH example
• MS/MS data (mgf-format) for yeast alcohol dehydrogenase (raw and cleaned versions)
• Peptide-wise comparison of scores of top-hit peptides before and after background removal for yeast alcohol dehydrogenase

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  Supplementary data for the TRF example
• MS/MS data (mgf-format) for human transferin (raw and cleaned versions)
• Peptide-wise comparison of scores of top-hit peptides before and after background removal for human transferin
• Supplementary data to the single dta-file example from the TRF set that has been false-positively rejected by MS Cleaner

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Supplementary data for the condensin example
• Condensin sample, before and after cleaning procedure with MS Cleaner: Mascot search aginst nr-Database with taxonomy specified as Homo sapiens and Mascot search aginst nr-Database without taxonomy specified
• Supplementary data to the single dta-file example from the condensin set that has been false-positively rejected by MS Cleaner

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• MS Cleaner has been upgraded to MS Cleaner  Version 2.0