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ProMass for the Web – FAQ

Should I use ProMass for the Web or buy my own copy of ProMass?

This depends on your needs. If you have a lot of samples or are running samples by LC/MS, you should get your own copy of ProMass. The automated batch processing pays for itself by saving you time and headaches.

If you only need to occasionally deconvolute individual ESI spectra, you ProMass for the Web is probably more valuable to you. ProMass for the Web is ideal for a group (e.g. a University research group) to share an account. There is no limit to the number of computers or users that can use a ProMass for the Web account at a time. The low-cost, easy-to-cancel subscription model provides a much lower financial barrier than buying a copy of ProMass software outright.

Do I need to download or purchase anything to use ProMass for the Web?

You do not need to download anything or make a physical software purchase to use ProMass for the Web. All it requires is an internet connection and the purchase of a subscription plan. You can try 10 free deconvolutions without requiring payment.

Can ProMass for the Web deconvolute high resolution data?

Unlike the desktop version of ProMass HR, ProMass for the web does not have the ability to deconvolute high resolution data. If you need to deconvolute high res data, you should purchase ProMass HR from our website.

How do I convert my raw data to text to use with ProMass for the Web?

There are a few ways to do this depending on the platform you’re using. One way is to right-click your raw file and choose “Open With” and select a text editor program, such as Notepad. This will automatically open your spectrum as text which can be saved or copied. Another option using Qual Browser for Xcalibur is to open your raw files, select the region of interest, pin and right-click the mass spectrum and choose “Export Clipboard (exact or nominal mass)”. The spectrum is now on your clipboard and can be pasted as text.

Can ProMass for the Web deconvolute LC/MS data sets?

ProMass for the Web is not automated, so you will have to deconvolute each LC peak individually to accomplish this. Alternatively, the desktop version of ProMass will automatically deconvolute entire LC/MS data sets.

What does “Clone Project” do?

This creates a new project with the exact same parameters as the original project. This is useful for trying slightly different parameters on the same spectrum, or for trying different spectra using the same parameters.

What is the difference between the Parameter Sets?

Each parameter set is designed to be a good general guide for molecules of that type (e.g. “Oligos” should effectively deconvolute most oligonucleotides quite well). These serve as a good starting point for deconvolution if you know what type of molecule you have but aren’t sure what other settings you may need.

What is Input M/Z Range?

This is an option to limit the x-axis of your raw ESI data, the m/z ratio. For example, you may have a large instrument noise peak at 615 m/z, and the remainder of your data has a greater m/z. You might try setting the lower number to 630 or 650. The same logic applies for the upper end of the range.

What is Output Mass Range?

This controls the mass window you’ll see in your deconvoluted output. If you want to narrow your window of mass data, you can set an upper and/or lower limit to these values. Conversely, you can extend the upper limit if you feel your mass of interest is larger than what the mass range is allowing.

What is Input Polarity?

This refers to the polarity of the instrument when your data was collected, either positive ion mode or negative ion mode.

Should I Use the Advanced Parameters?

The advanced parameters are set to be in a good range for most data. However if you are feeling adventurous, confident, curious, frustrated, or otherwise enticed, you are more than welcome to tweak the advanced parameters to fit your needs.

Should I use Comprehensive Deconvolution?

The Comprehensive Deconvolution mode should be used in the majority of applications, particularly when the input spectra are complex and could have multiple overlapping components. For simple data sets, you can turn off the Comprehensive Deconvolution if you desire faster algorithm speed. With Comprehensive Deconvolution turned off, ZNova will remove peaks of found components as the deconvolution proceeds, which results in faster execution.

Why would I check “Use 0.1 Da Mass Step size”?

The 0.1 Da step size should be used whenever the peaks in the output spectrum are expected to be narrow, e.g., peptides and other molecules under 5 kD. With this option checked, ProMass will plot output data in the deconvoluted spectrum at 0.1 Da intervals.  If this option is unchecked, 1 Da intervals are used. Checking this box will cause your deconvolution to take longer, as more processing is required.

What is Peak Width?

This is the typical peak width at the base in the raw data.

What is Merge Width?

This is the +/- m/z width in the raw data used for centroiding.

What is Minimum Score?

This is the minimum score (determined by ZNova) required for deconvolution.