Quality Report Generation for MaxQuant Results

Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the MaxQuant software suite (see < http://www.maxquant.org>). Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format. Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) .

PTXQC

This package allows users of MaxQuant to generate quality control reports in Html/PDF format. - plethora of quality metrics - intensity distributions - digestion efficiency - contaminant visualizations - identification performance - Match-between-runs performance

• easy usage ([Windows OS only] drag'n'drop your txt output folder onto a batch file)
  • 10 min installation, see drag'n'drop
• Html/PDF report will be generated within your txt folder
• optional configuration file in YAML format for generation of shorter/customized reports

Target audience

• MaxQuant users (no knowledge of R required)
• bioinformaticians (who want to contribute or customize)

Latest changes / Change log

See NEWS file.

Documentation

Besides this documentation on GitHub, the package vignettes of PTXQC will give you valuable information. After the package is installed (see below), you can browse the vignettes using either of these commands within R:

help(package="PTXQC")
browseVignettes(package = 'PTXQC')

If you do not want to wait that long, have a look at the 'vignettes' subfolder. The top part contains a small table with technical gibberish, but the rest is identical to the vignettes you would see in R.

You will find documentation on

• Input and Output
• Report customization
• (for MaxQuant users) Usage of Drag'n'drop
• (for R users) code examples in R
• ...

Installation

If you want to generate QC reports without actually getting involved in R:

We offer a Batch-file based Drag'n'drop mechanism to trigger PTXQC on any MaxQuant output folder. This only works for Windows (not Linux or MacOS) at the moment -- but you have a Windows anyway to run MaxQuant, right?! See drag'n'drop for details. It takes 10 minutes and you are done!

If you just want the package to use (and maybe even modify) it:

First, install pandoc (see bottom of page). Pandoc is required in order to build the package vignettes (documentation) and PTXQC reports in HTML format. In theory you can skip vignette building (see below) and read the vignettes online from the PTXQC GitHub page. The reports can also be configured to be printed as PDF instead of HTML, but HTML just looks nicer and is interactive. If you install Pandoc later while your R session is already open, you need to close and re-open R in order to make R aware of Pandoc!

The following lines will install the PTXQC package. Direct installation from GitHub requires the 'devtools' package. Run each line separately in your R console, i.e. do not copy and paste the whole block. If an error should occur, this allows to track it down more easily. See FAQ - Installation how to resolve them.

if (!require(devtools, quietly = TRUE)) install.packages("devtools")
library("devtools")             ## this might give a warning like 'WARNING: Rtools is required ...'. Ignore it.
install_github("cbielow/PTXQC", build_vignettes = TRUE)    ## use build_vignettes = FALSE if you did not install pandoc!

To get started, see the help and/or vignettes:

help(package="PTXQC")
browseVignettes(package = 'PTXQC')

Please feel free to report bugs (see below), or issue pull requests!

Platform support

• Windows (recommended for convenience to make use of the drag'n'drop batch file provided)
• Linux
• MacOSX

Bug reporting / Feature requests

If you encounter a bug, e.g. error message, wrong figures, missing axis annotation or anything which looks suspicious, please use the GitHub issue tracker and file a report.

You should include

• stage you encounter the bug, e.g. during installation, report creation, or after report creation (i.e. a bug in the report itself).
• PDF/Html report itself (if one was generated).
• version of PTXQC, e.g. see the report_XXX.pdf/html (where XXX will be the version) or see the DESCRIPTION file of the PTXQC package or call help(package="PTXQC") within R
• error message (very important!). Either copy it or provide a screen shot.

Please be as precise as possible when providing the bug report - just imagine what kind of information you would like to have in order to track down the issue. In certain situations, the whole txt-folder or a single MaxQuant file might be helpful to solve the problem.

If you want to see a new metric, or have ideas how to improve the existing ones, just open an issue ticket and leave a description.

Report Examples

An overview chart at the beginning of the report will give you a first impression.
Detailed plots can be found in the remainder of each report.

For example input data and full reports, see the 'inst/examples' subfolder.

Citation

PTXQC is published at JPR:

Proteomics Quality Control: Quality Control Software for MaxQuant Results Chris Bielow, Guido Mastrobuoni, and Stefan Kempa J. Proteome Res. Publication Date (Web): December 14, 2015 DOI: 10.1021/acs.jproteome.5b00780

Use PTXQC v0.69.3 if you want the version which was used in the paper, i.e. use install_github("cbielow/PTXQC", ref="v0.69.3", build_vignettes = TRUE) when following the Installation procedure.

The input data is available in the 'inst/examples' subfolder.

We recommend to use the most recent PTXQC for the best user experience.