Modification Analysis

Introduction

The Modifications tab is dedicated to peptide-level post-translational modifications (PTM) analysis. The modification of interest is selected in the top left corner and the modified peptides present in the dataset will be displayed.
The modification location displayed here is also displayed in the Overview tab and the 3D Structure tab. For example, it is possible to verify here the correctness of the phosphorylation status of a peptide and to visualize it on the sequence in the tables in the Overview tab or on the 3D structure in the 3D Structure tab. Finally, you can confront your results with data in UniProt using the Annotation tab.


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Modification Selection

The modification of choice can be selected. Note that for the sake of simplicity only variable modifications are displayed in PeptideShaker. Modifications are color coded and the colors can be edited in this table or in the Search Parameters accessible from the Edit menu.


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Modified Peptides

All peptides found in the dataset with the selected variable modification are listed in the Modified Peptides table. The peptide inference status is displayed like in the Overview tab. Then, the sequence is displayed with the selected modification location confidence color coded. Note that the peptide modification status is deduced from the PSMs' modification status.
The confidence in the modification site assignment is color coded based on the modification location scores:

When both scores confidently agree on the modification site, the modification is labeled as "Very Confident"; if the A-score is confident but disagrees with the search engine's best assumption, the modification is labeled as "Confident"; if the A-score is not confident and the delta score is, the location is labeled as "Doubtful"; finally if no score is confident, the modification is labeled as "Random".

The scores are annotated on the sequence on the right of the table, the delta score on the top of the selected amino acid and the A-score below.

The confidence and validation status of the selected peptide is diplayed as in the Overview tab.


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Related Peptides

Whenever a peptide sequence contains or is contained by the selected peptide sequence, this peptide is displayed in the Related Peptides table. For instance, non-modified peptides or miscleaved peptides will be displayed and may help to validate the identification and modification status of the selected peptide.

The structure of the Related Peptides table is similar to the Modified Peptides table.


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Peptide to Spectrum Matches (PSMs)

The Peptide to Spectrum Matches (PSMs) linking to the selected peptide are displayed in the PSM table. The modification location score of these PSMs will make the peptide score. If you select a row in the PSM table, the corresponding spectrum will be displayed.


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Related Peptide to Spectrum Matches

The Peptide to Spectrum Matches (PSMs) linking to the selected related peptide are displayed in the related PSM table. The spectrum of the PSM is displayed when clicking on the row of interest.


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Spectrum and Fragment Ions

The spectrum of the selected PSM will be displayed with the peaks annotated according to the ion annotation settings. Note that the peak annotation has a dramatic effect on the A-score. It is important to carefully tune the annotation settings when inspecting a doubtful peptide.

For more information on how to interact with the spectrum see the help option in the menu below the spectrum.


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Modification Table

(to be added...)


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