Before and after background removal with MS Cleaner: detailed analysis of an examplary real tandem mass spectrum

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• dta file used for the analysis: 100fmol_BSA_run1.369.369.2.dta (dta-file before background removal)

• Mascot interpretation of the original spectrum

• Log output of MS Cleaner for this dta file

• dta file used for the analysis: 100fmol_BSA_run1.369.369.2_c.dta (dta-file after background removal)

• Mascot interpretation of the cleaned spectrum

• Case of multiply charged peaks



MS Cleaner message	expert interpretation
2-fold charged peak cluster deconvoluted: 299.40 Da --> 597.80  2-fold charged peak cluster deconvoluted: 364.20 Da --> 727.40  2-fold charged peak cluster deconvoluted: 375.10 Da --> 749.20  2-fold charged peak cluster deconvoluted: 401.65 Da --> 802.30  2-fold charged peak cluster deconvoluted: 406.70 Da --> 812.40	peak cluster among noise
2-fold charged peak cluster deconvoluted: 315.70 Da --> 630.40  2-fold charged peak cluster deconvoluted: 320.30 Da --> 639.60	removal of true doubly charged peak cluster from the sample



• Multiply charged peaks detected by Mascot but not by MS Cleaner
  
  • y++ 324.19739
    
  • y*++ 359.20013, 315.68412


• Case of latent periodic noise:  none detected


• Case of high-frequency random noise: list of 72 detected peaks that are removed by the background clearing procedure

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