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Configuring ProMass to Search for Target Masses
 As of the release of ZNova 1.1, ProMass Xcali can now automatically report the existence of target masses and produces a top-level HTML summary page. ProMass produces a summary page in the results directory summarizing all of the files processed within this directory. When you incorporate a BioSequence into your Xcalibur sequence and process your data, ProMass will assume a target mass from the calculated mass of the peptide or oligonucleotide sequence. A status color is reported on the summary page which gives a quick indication of whether the target mass was found in your data.
Specifying target masses:
- Put a sequence (nucleotide or peptide) in the BioSequence field of the Xcalibur Sequence Setup window. Follow these instructions on how to do this.
- Additional target masses can be defined by specifying them in the Target Info field of the Xcalibur Sequence Setup window.
- You can use "offset masses" (+ or -) applied to the nucleotide or peptide sequence.
- You can explicitly specify masses as target masses.
- You don't have to specify a BioSequence and can use explicit masses instead.
- There is currently no defined limit to the number of masses and offset masses that you can define, although this is ultimately limited by the 255 character field length in the Xcalibur Sequence Setup window.
- The syntax for specifying target masses in the Target Info sequence setup field is:
+m, -n, x, y, z...
where +m and -n are offset masses applied to the calculated mass from a BioSequence, and x, y, z are explicitly defined target masses.
Example target mass list:
- I pasted the "ever popular and often overused" sequence of myoglobin into the BioSequence field, as described previously.
- I also specified in the Target Info field of the Xcalibur Sequence Setup:
+616, -57, 3493, 5985
This will instruct ProMass to look for the calculated myoglobin sequence mass (16951.5), and additionally a mass of 16951.5 + 616, 16951.5 -57, and explicit masses of 3493, and 5985. Therefore, the final target mass list will consist of masses: 16951.5, 17567.5, 16894.5, 3493, and 5985. Note that any number in the targets list preceded by a + or - will be added or subtracted, respectively, from the calculated mass of the BioSequence. This makes it very easy for you to search for proteolysis products (e.g., -131 for minus N-terminal Met), oligonucleotide failure sequences, or covalent modifications to known proteins or oligos. Make sure to use the syntax shown above with parentheses surrounding the target masses and offsets, or the target mass features will not work. Also, don't forget to specify either sequence = peptide or sequence = nucleotide in the Target Info field in the sequence setup if you have specifed a BioSequence string.
Example target mass list in the Xcalibur Sequence Setup:
Example top-level summary report:
What does all of this mean? In this case it means that ProMass Xcali has found the target mass 16951.5 as the major peak in the chromatogram but has not found any of the other targets that we were looking for. Clicking on any of the hyperlinks on this page will take you to the chromatogram summary that offers more detail. Clicking on the target masses will take you directly to the deconvoluted mass spectrum of that target if it exists. More information about the top-level summary report is available here.
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