You can use "offset masses" (+ or -) applied to the nucleotide or peptide BioSequence.
ProMass automatically reports the existence of specified target masses and reports them on a top-level HTML summary page. When you incorporate a BioSequence string 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:
Target masses can be specified by either specifying a BioSequence string or file in the Xcalibur sample list and/or by explicitly declaring target masses as described below.
Target masses are specified in the Target Info field of the Xcalibur Sequence Setup window as described below:
You can use "offset masses" (+ or -) applied to the nucleotide or peptide BioSequence.
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
simply to use a list of comma separated values, for example:
+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:
The sequence of myoglobin was inserted in the BioSequence field of the Xcalibur Sequence Setup, as described previously. Additional masses were also specified in the Target Info field of the Xcalibur Sequence Setup, using the following syntax:
+616, -57, 3493, 5985
This instructed 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 consisted of: 16951.5, 17567.5, 16894.5, 3493, and 5985. Note that any number in the targets list preceded by a + or - is 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. Also, don't forget to specify either sequence = protein or sequence = oligo in the Target Info field in the sequence setup if you have specified a BioSequence string.
The example target mass list and its entry in the Xcalibur Sequence Setup is shown below. An example Xcalibur sample list with the myoglobin sequence specified as either a file or string can also be found in the TestData directory (e.g., C:\Program Files\ProMassXcali\TestData\myoglobin_with_sequence.sld).
After processing this example, the following ProMass Browser summary report was obtained:
T he report indicates that ProMass found the target mass 16951.5 as the major peak in the chromatogram but did not find any of the other targets that we were looking for. Clicking on any of the hyperlinks on the summary 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 was found. More information about the ProMass Browser summary report is available here.
Hot Tip! If you leave the output mass range fields blank in your ZNova parameter file, ProMass will automatically scan a +/- 25% mass range around your target masses.