Introduction

msPicture is a tool that produces pseudo2d gels from mass spectra data. There are many options available for manipulating layout, color scheme, and markup of the resulting image. Being part of the proteowizard suite, msPicture can read a wide variety of MS data formats. Marking peptide locations is done easily by giving the location of pepXML, msInspect, or even a flat file.

At the Command Line

The default options allows the user to create colored images with intensity legend, TIC and total m/z graphs from any MS data format supported by the installation. The output can be customized either by the commandline options or by use of commands.

In addition to choosing visual schemes, the window of displayed data on the x-axis can be chosen to focus in on interesting bands of features. The lower m/z bound can be set by --mzLow, and the upper by --mzHigh. In addition, the y-axis can be scaled to be linear with time or scans (-t or -s, respectively).

The list of available options and commands can be listed by typing in mspicture without any arguments.:

$ mspicture
Usage: mspicture [options] [input_filenames]
Mass Spec Picture - command line access to mass spec data files with optional peptide annotation

Returns:
0 on success, or the number of input files that generated processing errors.

Options:

  -o [ --outdir ] arg (=.) : output directory
  -c [ --config ] arg      : configuration file (optionName=value) (ignored)
  -l [ --label ] arg       : set filename label to xxx
  --mzLow arg              : set low m/z cutoff
  --mzHigh arg             : set high m/z cutoff
  --timeScale arg          : set scale of time axis
  -b [ --binCount ] arg    : set histogram bin count
  -t [ --time ]            : render linearly to time
  -s [ --scan ]            : render linearly to scans
  -z [ --zRadius ] arg     : set intensity function z-score radius [=2]
  --bry                    : use blue-red-yellow gradient
  --grey                   : use grey-scale gradient
  --binSum                 : sum intensity in bins [default = max intensity]
  -m [ --ms2locs ]         : indicate masses selected for ms2
  --shape arg              : shape of the pseudo2d gel markup 
                           [circle(default)|square].
  -p [ --pepxml ] arg      : pepxml file location
  -i [ --msi ] arg         : msInspect output file location
  -f [ --flat ] arg        : peptide file location (nativeID rt mz score seq)
  -w [--width] arg         : set image width in pixels [default is calculated]
  -h [--height] arg        : set image height in pixels [default is calculated]
  -v [ --verbose ]         : prints extra information.
  -h [ --help ]            : print this helpful message.

Commands:
      label=xxxx (set filename label to xxxx)
      mzLow=N (set low m/z cutoff)
      mzHigh=N (set high m/z cutoff)
      timeScale=N (set scaling factor for time axis)
      binCount=N (set histogram bin count)
      zRadius=N (set intensity function z-score radius [=2])
      scan (render y-axis linear with scans)
      time (render y-axis linear with time)
      bry (use blue-red-yellow gradient)
      grey (use grey-scale gradient)
      binSum (sum intensity in bins [default = max intensity])
      ms2locs (indicate masses selected for ms2)
      pepxml=xxx (set ms2 id's from pepxml file xxx)
      msi=xxx (set ms2 id's from msinspect output file xxx)
      flat=xxx (set ms2 id's from tab delim file xxx)

Questions, comments, and bug reports:
https:/github.com/ProteoWizard/pwiz/issues
support@proteowizard.org

The verbose option (-v or --verbose) may be used to get more information about how msPicture is processing the input files.

Creating a Pseudo2d Gel

To create an image of an entire ms data file with the default parameters, add the data filename to the end of the command line.

$ mspicture example1.mzML

(image 1 ftms)

A new file called example1.mzML.image..ftms.png will be created in your current directory. If the MS data file contains multiple types of MS1 scan events, then one picture for each type will be generated.

$ mspicture example2.mzML

This will result in two files. example2.mzXML.image.

(image 2 ftms)

(image 3 itms)

Choosing an Output Directory

To have msPicture write the images to a different directory, use the -o option to set the output directory. If omitted, all output will be created in the current directory.

Input File

File Formats

The input into msPicture is a single MS data file in a format that's supported by the Proteowizard suite. These are mzML, mzXML, MGF, MSn, and BTDX. File type detection is done automaticly by Proteowizard, so there's no need to specify input type to the program.

Options

Common Options

Coloring and cropping are available by the command line options as well as through the command system discussed later.

There are two choices when it comes to coloring a pseaudo2d gel: heat map and grey scale. By default, msPicture will color intensity using the heat map scheme, chosen by the --bry option, or the command bry from a config file. A grey scale pseudo2d gel can be created using the --grey option, or grey command from a config file. Note that although the MS data will be grey scaled, the decorations and graphs attached to the page will not. This is a very useful way of making the identification markups from pepXML or MS2's stand out above the image clutter.

To crop the image in the m/z direction, use the --mzLow and --msHigh options. You can also control the coarseness of the image setting the bin count using the option. By default, msPicture will use a bin count of 640. You can create finer grain pictures with a larger bin count.

Here we use the --mzLow cutoff to remove everything below 400 m/z on the image

$ mspicture --mzLow=400 example1.mzML

And here, we combine --mzLow and --mzHigh to select a strip in the middle of the image.

$ mspicture --mzLow=800 --mzHigh=1400 example1.mzML

To expand or contract the image in the y-axis, use the --timeScale with a argument to expand or contract the height.

Here we shrink the image height to half:

$ mspicture --timeScale=0.5 example1.mzML

Here we double the height:

$ mspicture --timeScale=2 example1.mzML

Marking MS2 Locations

A very useful tool with pseudo2d gels is marking the location of events. In this tutorial, they are referred to as "markups." The locations of MS2 can be marked on the image by using the -ms2locs option. Here we use the shorthand -m 

$ mspicture -m example1.mzML

(image 4 ms2locs)

As you see, the location of the MS2's is difficult to see ini the clutter of a heat mapped image. It's often useful to use the grey scale option to help markups stand out.

$ mspicture --grey -m example1.mzML

(image 5 grey_ms2locs)

Now the locations of MS2 events is clearly visible against the monochromatic background.

Using a pepXML, msInspect, and flat files

The location of identified peptide can be marked by telling msPicture the location of the pepXML, msInspect, or flat file containing the locations and scores.

Choosing the Shape of Your Markup

The shape used for markups can be selected with the --shape argument. Currently, mspicture can draw circle or square markups.

msPicture Commands

Concepts

Command offer the same choices available on the command line, but kept in a configuration file that can be reused.

Using a Config File

A configuration file is given as a value to the command line argument --config

Reference

Options & Commands

outdir

  • Option: -o [ --outdir ] arg
  • Command: (none)

Sets the output directory. By default, this is the current directory.

config

  • Option: -c [ --config ] arg
  • Command: (none)

configuration file (optionName=value)

label

  • Option: -l [ --label ] arg
  • Command: label=xxxx (set filename label to xxxx)

set filename label to xxx

mzLow

  • Option: --mzLow arg
  • Command: mzLow=N (set low m/z cutoff)

Set low m/z cutoff

mzHigh

  • Option: --mzHigh arg
  • Command: mzHigh=N (set high m/z cutoff)

set high m/z cutoff

timeScale

  • Option: --timeScale arg
  • Command: timeScale=N (set scaling factor for time axis)

set scale of time axis

binCount

  • Option: -b [ --binCount ] arg
  • Command: binCount=N (set histogram bin count)

set histogram bin count

time

  • Option: -t [ --time ]
  • Command: time (render y-axis linear with time)

render linearly to time

scan

  • Option: -s [ --scan ]
  • Command: scan (render y-axis linear with scans)

render linearly to scans

zRadius

  • Option: -z [ --zRadius ] arg
  • Command: zRadius=N (set intensity function z-score radius [=2])

set intensity function z-score radius. By default, this value is 2.

bry

  • Option: --bry
  • Command: bry (use blue-red-yellow gradient)

Use blue-red-yellow gradient. This is the default color scheme.

grey

  • Option: --grey
  • Command: grey (use grey-scale gradient)

Use grey-scale gradient. This is useful when adding markups to an image.

binSum

  • Option: --binSum
  • Command: binSum (sum intensity in bins [default = max intensity])

Sum intensity in bins [default = max intensity]

ms2locs

  • Option: -m [ --ms2locs ]
  • Command: ms2locs (indicate masses selected for ms2)

Indicate masses selected for ms2 by adding a markup at each location.

shape

  • Option: --shape arg
  • Command:

Selects the shape of the pseudo2d gel markups. By default, this is a circle. The other option is square.

pepxml

  • Option: -p [ --pepxml ] arg
  • Command: pepxml=xxx (set ms2 id's from pepxml file xxx)

Gives the location of a pepxml file, and creates markups at all peptides locations.

msi

  • Option: -i [ --msi ] arg
  • Command: msi=xxx (set ms2 id's from msinspect output file xxx)

Gives the location of an msInspect output file, and creates markups at all peptide locations.

flat

  • Option: -f [ --flat ] arg
  • Command: flat=xxx (set ms2 id's from tab delim file xxx)

Gives the location of a flat peptide file with the fields: nativeID, rt, mz, score, sequence

verbose

  • Option: -v [ --verbose ]
  • Command: (none)

Prints extra information.

help

  • Option: -h [ --help ]
  • Command: (none)

Print this helpful message.

Last modified: Mon Feb 4 10:55:42 PDT 2013