Contents

Introduction

Requirements

General workflow

Helpful tips

Phenyx Desktop page

Navigation bar

Job report

Job menu

Submission page

Profiles

Title

Database(s)

Search engine

Acceptance parameters

Extended PTM Search

Peak lists

Extra Convert Spectra Arguments

Scaffold Extended Output

Server log

Management Console page

My defs

Define a new enzyme

Edit a user-defined enzyme

Delete a user-defined enzyme

Define a new modification

Edit a user-defined modification

Delete a user-defined modification

Group defs

Account Settings

Databanks

Jobs management

Browse files or export job results

Import Phenyx jobs or jobs from other search engines

Utilities

Status page

Parameters page

Proteins Overview page

Best-scoring protein table

Protein details

Peptide match table

Protein Match Details page

Protein information table

Peptide match table

Sequence views

Compounds Overview page

Functions

Validate peptide matches

Peptide Match Details page

Mass spectrum

Fragment ion tables

Results Comparison page

Insert jobs in comparison table

Define a new comparison

Remove jobs from a comparison table

Results comparison table

Protein detail list

Export options

Detailed Results Comparison page

Detailed results comparison table

Export options

Understanding Phenyx: the scoring system

The MS/MS scoring model

How a score is computed

How a score is normalized

How Phenyx retrieves amino acid modifications not specified by the user

Reproducibility of z-Scores and p-Values

Available scorings

Understanding Phenyx: the effect of submission parameters on result accuracy

Limit the search space size

Change the taxonomy or AC list

Change the cleavage mode

Change the number of missed cleavages

Change the number of variable modifications

Search in one round or two

One-round usage

Two-round usage

Two-round search parameters

Activate conflict resolution

How Phenyx resolves conflicts

Some points to consider