Protein Filtering

Introduction

This dialog makes it straightforward to filter the data in your project, e.g., to find proteins with a given post-translational modification, or to find all peptides with more than a certain number of spectra.

You can filter the data at three levels: (i) proteins, (ii) peptides or (iii) PSMs.


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Filtering

When editing one of the filtering fields the table at the bottom will display the proteins, peptides or PSMs matching the given filter. Note that selecting a row in this table will select the given proteins, peptides or PSMs in the currently selected PeptideShaker tab.

To save a given filter click the Save button in the lower right corner.


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Case Sensitivity

Note that Identifier field for proteins and the Protein and Sequence fields for the peptides are case sensitive, i.e., searching for 'Albumin' and 'albumin' is not the same thing.

Also note that both fields support regular expression search. For more details on regular expressions in Java see Java Regular Expressions.


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Manual Selection

You can type in match identifiers (protein accession, peptide sequence or spectrum key) to be specifically selected/excluded by the filter. For example, manually starring a match in a table will result in creating such a specific filter named "Manual selection".


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Find Feature

In some cases one just wants to locate a specific protein, peptide or spectrum. For this it is often simpler to use the Find feature found in the upper right corner of PeptideShaker.

Inserting text in this field will automatically make the selection jump to the given protein, peptide or spectrum.


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