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Navigating ProMass Results

Click here for a youtube tutorial guide on how to navigate your ProMass results

Sample Report Page

Opening your ProMass results (quick guide here) will take you to a sample index page. This will list all the samples run in this set of analysis (if samples were submitted to Novatia to run this will include our Q.C. standard). This page will provide you with highlights from the analysis. This includes important details such as target mass, observed mass, a relative purity estimate, and a colored result code to quickly identify the success of that sample’s analysis.

The data file and sample ID contains hyperlinks that will take you to the associated data for those samples.

Viewing a Specific Sample

There is a lot of information packed into the top of this report. Along the top left, you’ll see finer details about how your sample was analyzed: the acquisition date, the injection volume and position, the actual instrument method, and more. We’ll sometimes leave comments here as well if there’s anything extra we feel you need to know.

Center stage at the top of the report is a similar summary table to the previous page, however this contains a few more details about your sample. Here you can see a separate Target Mass Summary (which includes the mass difference between your target and observed masses, the mass intensity, and the %abundance in the mass spectrum) and a Chromatogram Summary (which includes LC information like the peak area and area percent). The chromatogram summary is much more important for analysis using LC/MS separation, as you can view each LC-separated peak separately based on its retention time and all of the mass spectral peaks within it. Once again, both of these summary tables contain blue-colored hyperlinks to take you to the designated section of the report.

Total Ion Chromatogram

Now, onto the chromatograms! Just below the summary tables is the Total Ion Chromatogram (TIC). Here you can see the mass spectral response of your sample represented as mass intensity vs. time. This is a good way to quickly tell how well and/or how much sample was ionized upon injection.

LC/UV and Raw ESI Mass Spectra

Scrolling further down the page you’ll come upon the LC/UV chromatogram. Similar to above, you can see how much sample was injected as UV absorbance vs. time.

Just below this is the raw ESI mass spectral data, shown as intensity vs. m/z. This is what the mass spectrometer picked up before any real data processing (i.e. deconvolution) occurred. Your m/z range may differ depending on the analysis you are getting. You’ll also notice that there are many more hyperlinks at the top of this spectrum. These help you quickly navigate from one spectra to the next within this sample’s report. Click on one to jump to the appropriate section.

Deconvoluted Mass Spectrum

Finally, we come to the most informative piece of the report: the deconvoluted mass spectrum. This is the result of ProMass’ efforts to deconvolute the raw ESI spectrum. In an ideal world, this spectrum would be a single, towering peak — but as scientists know, experimental conditions are rarely ideal. Using the ZNova charge deconvolution algorithm, ProMass converts the raw m/z values into the useful information we need: Mass. It is in the deconvoluted mass spectra that you can see all of the masses present in the mass spectrum.

Below the deconvoluted mass spectrum is a zoomed view of the same spectrum, just focused on the base peak in the spectrum. This allows the user to view peaks closer to the base peak.

Interpreting the Result Code

Finally, at the very bottom of the page there’s a pictorial guide to the Result Code, which is a color system to help you quickly identify good, bad, and other types of samples. I’ll let the chart speak for itself, but you’ll see there is a bit more nuance than you might expect. Check the color in the left column and you’ll see what that means by reading the right column. Match this with the Result Code at the top of your sample report and you’re in business.

Using the [View Data] Tool

At the top of each ESI or deconvoluted mass spectra there is a [View Data] hyperlink. This hyperlink will take you to an interactive version of both the deconvoluted and raw ESI mass spectra. The larger version is a viewing window while the miniature version is used as a zoom control.

You can click and drag an area in the miniature spectrum and you’ll see a gray box appear over that area. You’ll now see that the full-size spectrum has zoomed in to the exact same region of the spectra. You can then click and drag the center of the gray box to move across the spectrum, or you can click and drag its edges to resize its width.

Additionally, if you click on a peak in the deconvoluted spectrum, you’ll see the charge states for that peak appear in the ESI mass spectrum below. They’ll be labeled as blue vertical lines with the charge state listed at the top and to the left (e.g. -1, -2, -3, etc). Clicking on a different deconvoluted peak will then change the charge states you see in the ESI spectrum accordingly. This will also complete the “Mass Difference” field between the deconvoluted mass spectrum and the ESI mass spectrum. You’ll be able to see the mass difference in Daltons between two peaks that you click on in the deconvoluted spectrum. Similarly, clicking on two peaks in the ESI spectrum will show you the m/z difference between them. Overall, this interactive tool lets you manually dig in to the raw and deconvoluted data to see all of the finer details of the spectra.

Deconvolution Peak Report

For each spectra there is an associated deconvolution peak report table. To navigate to this page just click the [Deconvolution Peak Report] hyperlink above the spectra you wish to view. This will take you to a new page containing a detailed table of masses in the spectra. This is a great way to see every single species ProMass deconvoluted organized by mass and placed in reference to the base peak. This includes each peak’s mass intensity, the difference in mass between any given peak and the base peak, and the %abundance (both relative and total). There is also a helpful “Presumed Identity” column which can sometimes help label a mass’s likely identity. For example, in the table below, you can see a 7566.6 Da peak which is presumed to be the hfip adduct of the target mass. As hfip is present in the LC solvents used for analysis it is most likely to be the correct identity. However, these identities are not 100% guaranteed, but are often helpful to consider.

Wrapping up

This quick guide covers the essentials of how to navigate your ProMass data. There will be some variability in how the results look depending on the type of analysis (MW confirmation, 5 or 20-min LCMS, HRMS, etc…). As always if you have any other questions feel free to contact us by email (

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