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Customer Data Example

Mass Spectrometry Results

Below is a detailed summary of what your mass spectrometry results might look like in general. If you’re considering sending samples to us, or would like to better understand the results we return to you, you’ve come to the right place.

You can also watch this helpful video for a step-by-step guide to navigating ProMass results.

Accessing Your Data

When you request a mass spectral analysis from us, your data will always be provided to you via our secure data server. Once your results are available, we’ll email you with a link to your results, as well as login credentials for your company to use.

Once you follow the link we send you, you’ll see a page like this. Simply enter the username and password we provided to you to gain access to your company’s data.

Sample Report Page

You’ll typically receive a direct link to your most recent data, so once you log in, you’ll see a top-level summary screen that looks more or less like this one. This will include your company’s logo, our Q.C. standard, and a summary table giving you the highlights from your analysis. You’ll see important things like the target mass, the observed mass, a purity estimate, and a colored result code to quickly identify how successful your sample was.

Notice there is a lot of blue-colored text in the table. All of these values are hyperlinks. Clicking on any of the hyperlinks in the table will take you to that particular piece of data for the specific sample you clicked on. In the below pictures, you’ll see what the report looks like for “Your_Sample.”

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, or 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 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’s 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 your sample, which also gives you a rough visual estimate of sample purity.

Below the deconvoluted mass spectrum is a zoomed view of the same spectrum, just focused on the base peak in the spectrum. You’ll notice this peak is centered, and you can see (in most cases) a window of 700 Da (350 on either side). This just allows you to see finer detail around the largest 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.

These are the basic and main components of the sample report. For an even more detailed view of the sample, we can explore the hyperlinks.

Deconvolution Peak Report

We’ll start with the “[Deconvolution Peak Report]” hyperlink. Clicking this will send you to a new page with a very detailed table of the mass spectral peak you’re looking at. 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. In the below table for example, you can see the 920.2 Da peak is presumed to be 1212.6 minus a cytosine (minus c). Similarly, 1256.3 is 1212 plus an acetyl group. This identities are not 100% guaranteed, but they are often helpful to consider.

Using the “View Data” Tool

The last hyperlink we’ll look at is “[View Data]”. This can be a very useful tool to get a detailed visual look at both the deconvoluted mass spectrum and the raw ESI data. You’ll see both of these spectra on the page, as well as a miniature version of each. You can think of the large spectra as the viewing windows and the miniature spectra as the zoom controls.

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.

That pretty much covers the essentials (and some non-essentials) of the ProMass report you’ll receive as a Novatia customer. There are some differences you’ll see if you get LC separation data or analyze other types of molecules, but this is a good general summary. As always, for any questions, email