Search setting Configuration

This page allows one to view, add, or delete specific mass spectrometry and analysis settings unique to a project.

Click on an existing search setting to edit it or use the "ADD SEARCH SETTING" button (top right) to add a new one.

Adding/Editing a Search Setting

Description of Fields

Project: The project associated with the search setting.

Min peptide length: The minimum peptide length. Peptides identified below this length are filtered out.

Max peptide length: The maximum peptide length. Peptides identified above this length are filtered out.

Min charge: Minimum precursor charge. Peptides identified below this charge are filtered out.

Max charge: Maximum precursor charge. Peptides identified above this charge are filtered out.

Precursor Tolerance and unit: Maximum precursor error rate and unit.

Fragment Tolerance and unit: Maximum fragment error rate and unit.

Minimum and maximum precursor isotope: Isotope range permitted for precursor.

Instrument: Instrument used in the experiment.

Fragmentation: Fragmentation method used in the experiment.

PSM, Peptide, Protein FDR: False-discovery rates at the associated levels permitted.

Multiplex: Check if the experiment is a multiplexed experiment (runs additional programs).

Run deqms: Check if the software should run PEMM and DEqMS at the end (requires R).

Use crap: Check if the CRAP (contaminants) database should be added to the FASTA.

Use human: Check if the human proteome should be added to the FASTA.

Profile type: Profiling method desired. Sample pools together fractions by sample for profiling. File treats each file independently (regardless if it has been assigned a sample) and profiles each file individually. Files without samples use this method by default. Project groups all identifications together and profiles the entire project.

Profile threshold: The top % of NSAF to include when profiling. For example, this means it sorts all the identified proteomes by NSAF and only includes those above the threshold when determining which species to include in the full-proteome FASTA. If multiple proteomes have the same NSAF value and cross the threshold, they are all included.

Profile search engines: Search engines to use when profiling.

Proteome search engines: Search engines to use in the full-proteome (second) search.

Enzyme choices: Enzymes to include in the search along with the specificity and missed-cleavages (MC) allowed for that enzyme. Multiple enzymes are allowed to be added.

Mod Choices: Modifications to include in the search and the modification type (fixed or variable). Visit the "Mod lists" page to add modifications. Multiple modifications can be added.