MassIVE-KB - Documentation - Creation

MassIVE-KB Library Creation

There are three distinct steps in the creation of MassIVE-KB spectral libraries.

1. Database Searching
2. Spectra Extraction/Quality Filtering
3. Library Creation/Augmentation

Database Searching Proteomics Data for Library Creation

Users can utilize a modified MSGF+ search workflow available at the Center for Computational Mass Spectrometry available here. Users may choose any public or private data they have access to and search with appropriate parameters.

For searching synthetic data, please refer to this documentation.

Spectra Extraction/Quality Filtering

After the searches are finished, the identified spectra are extracted from the original mzXML/mzML files and quality filtered. A set of search jobs can be extracted at once using this workflow. To select searches to extract, select an appropriate search job from the jobs list. Any jobs run by the specific user may be selected.

Library Creation of a New Library

To create a library from an existing spectra extraction workflow, please click the “Create Library from Extracts” link.

This bring users to an augment library page, with all appropriate fields set. The default parameters are appropriate for human HCD proteome parameters, adjust accordingly for your data.

Library Augment of an Existing Library

To augment an existing library, on the status page of the existing spectral library, please click the “Augment This Library” link.

This brings users to a library augment workflow page. Please select a spectra extraction job from the jobs table to augment to the existing library. Only one extraction can be augmented to a library at one time.

The default parameters are appropriate for human HCD proteome parameters, adjust accordingly for your data.