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PTXQC will provide you with a report in Html/PDF format, summarizing the quality of your data.

Please refer to the publication (currently under review; link is coming soon) for details on which quality metrics are available and how they are scored.

Obtaining example data

If you want to generate a report yourself, example input data can be found on the PRIDE repository under the following accession numbers: PXD003133 (MBR), PXD003134 (Myco), and PXD000427 (TMT). This data corresponds to the MaxQuant data used in the publication.

The PTXQC-Basic_Guide_for_R_users vignette has R code snippets to automatically download the data. If you are not an R person and have Windows as operating system, just download the zip files from the PRIDE link above, and run PTXQC via drag'n'drop (as described in the PTXQC-DragNDrop vignette).

Report Layout

The first page shows an overview heatmap, representing scores for each Raw file for a set of quality metrics. The screenshots given here, a from a rather small run of just 5 files. You can easily analyse a study with more than 100 files, but the report will get bigger :)

Overview Heatmap

After that, there is a summary of MaxQuant parameters (i.e. which FASTA files were used, was Match-between-runs activated etc...).

In the remainder of the report you can follow up on each individual metric and explore the reason for failure. The Html output additionally contains a helpful description of each metric in case you have not read the publication or need a refresh on what the plot actually tells you.

For example, the alignment in MaxQuant via the Match-between-runs did not work optimal across all Raw files in this case, since MaxQuant could not normalize the LC gradients at the start and end of the run: Alignment Performance

Also, you could check how a new LC gradient influences the identifications over time: Identifications over Retention Time

Find a full report as html or pdf.

See the package vignettes for documentation on how to create and customize a report.

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