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Indication of interferences either in MS1 or MS2 using Skyline custom annotation

Indication of interferences either in MS1 or MS2 using Skyline custom annotation. Screenshot from Skyline report. File Naming. The sample/file naming (so you know what is what) is as follows:  

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Indication of interferences either in MS1 or MS2 using Skyline custom annotation

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  1. Indication of interferences either in MS1 or MS2 using Skyline custom annotation

  2. Screenshot from Skyline report

  3. File Naming The sample/file naming (so you know what is what) is as follows:   6 samples contain the name Mito100 in the file and sample name (indicated in red below).  Those are 100 ng mitochondrial extract. 6 samples contain the name Mito300 in the file and sample name (indicated in red below). Those are 300 ng mitochondrial extract. All other numbers in the file name after Mito 100 or Mito 300 have no meaning and you can ignore that.  But here we would have 6 and 6 replicates that one can use to form a 3:1 ratio (that we know, that is the ratio all peptides should have). sample names,you can find this in the excel sheet (Skyline report) in column A-file names or also column B sample name: 120110_0005_Mito100_300_1.wiff 120110_0006_Mito100_300_2.wiff 120110_0007_Mito100_300_3.wiff 120110_0008_Mito100_3000_1.wiff 120110_0009_Mito100_3000_2.wiff 120110_0010_Mito100_3000_3.wiff 120110_0023_Mito300_300_1.wiff 120110_0024_Mito300_300_2.wiff 120110_0025_Mito300_300_3.wiff 120110_0026_Mito300_3000_1.wiff 120110_0027_Mito300_3000_2.wiff 120110_0028_Mito300_3000_3.wiff

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