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Auto Neutral Losses Spectrum

The Auto Neutral Losses Spectrum module is designed to help users obtain neutral losses data, allowing better utilization of the neutral loss characteristics of compounds.

Data Sources

When generating a neutral losses spectrum, users have two options:

  • Use the in-silico MS/MS data generated in the first module.
  • Import experimentally collected compound MS/MS data in the form of a .mgf file.

Parameter Inputs

To generate the neutral losses spectrum, users need to specify the following two parameters:

1. Top N (positive integer)

  • This parameter selects the Top N fragment ions with the highest intensity to generate the neutral loss spectrum.
  • This helps to reduce noise interference in the data.
  • Typically, Top N can be set to 30.

2. Min Neutral Loss (positive number)

  • This parameter sets the minimum neutral loss mass that will be accepted in the spectrum.
  • A typical value for Min Neutral Loss is 50, as lower-mass neutral losses (such as O, H₂O, CH₂, CH₃, and C₂H₄) are less characteristic and frequently found in natural products.

Note:
Selecting appropriate values for these parameters ensures better quality results and less noise in the neutral loss spectrum.

Understanding the Generated Data

In the generated neutral losses data: - Neutral loss represents the mass difference between precursor fragment ions and product fragment ions. - Intensity is calculated as the average intensity of the precursor and product ions.

If multiple precursor-product ion pairs generate the same neutral loss, the intensity is the sum of those ion pair intensities. The final intensity is normalized to 100, with the maximum intensity set at 100.

Viewing and Downloading the Data

Once the neutral losses spectrum is generated, the following options are available:

  • The generated spectrum is displayed as hyperlinks in the results table on the right side of the screen.
  • By clicking on the Spectrum link in the table, users can:
  • View the corresponding neutral losses spectrum.
  • Explore the MS/MS spectrum for more detailed interaction with the data.

Additionally, users can download the generated neutral losses data by clicking on the Download button on the right side of the table.

Quick Tips:

  • Use higher values for Top N to include more fragments and gain a broader overview of the spectrum.
  • Ensure Min Neutral Loss is set appropriately to exclude common low-mass neutral losses, which may not provide useful insight.

This module makes it easier for users to analyze and interpret neutral losses, allowing for enhanced data filtering and exploration.