msaccess

msaccess is a command line tool for extracting data and metadata from data files.

Examples (see below for many more options, see here for details on the --filter option):

• msaccess data.mzML -x spectrum_table
  (creates data.mzML.spectrum_table.txt with summary information for all spectra as read from the scan headers)

• msaccess data.mzML -x "binary index=0,3"
  (creates files data.mzML.binary.*.txt with binary data for spectra 0 through 3)

• msaccess data.mzML -x "slice delimiter=tab index=2,6 mz=100,600"
  (creates data.mzML.slice.index_2-6.mz_100.0000-600.0000.tsv with a table of data in the selected range)

• msaccess data.mzML -x "tic mz=409,410 delimiter=comma" --filter="msLevel 2"
  (creates data.mzML.tic.409.00-410.00.csv with total ion current info for mass range 409-410 in ms2 scans)

  Note this could also be achieved as:
  msaccess data.mzML -c cfg.txt
  where cfg.txt is a file containing the lines
  exec = tic mz=409,410 delimiter=comma
filter = msLevel 2


• msaccess data.mzML -x "image width=800 height=600"
  (creates data.mzML.image* with pseudo-2D-gel image of the data file, sized at 800x600 pixels)

Run msaccess with no command line arguments to see this usage message:

Usage: msaccess [options] [filenames]
MassSpecAccess - command line access to mass spec data files
uses -x/--exec to specify analysis command.

Options:

-f [ --filelist ] arg : text file containing filenames to process
-o [ --outdir ] arg (=.) : output directory
-c [ --config ] arg : configuration file (containing settings as optionName=value)
-x [ --exec ] arg : execute command, e.g --exec "tic mz=409-412"
--filter arg : add a spectrum list filter, e.g. --filter="msLevel [2,3]"
(see a full list of supported filter types here)
-v [ --verbose ] : print progress messages

Analysis commands (used with -x/--exec):

metadata
(write file-level metadata)

run_summary [msLevels=<int_set>] [charges=<int_set>] [delimiter=<fixed|space|comma|tab>]
(print summary statistics about a run)
msLevels: if specified, summary only operates on these MS levels; default is all MS levels
charges: if specified, summary only operates on these charge states; default is all charges
delimiter: sets column separation; default is fixed width

spectrum_table [delimiter=<fixed|space|comma|tab>]
(write spectrum metadata as read from scan headers, in a table format)
delimiter: sets column separation; default is fixed width

binary index=<spectrumIndexLow>[,<spectrumIndexHigh>] | sn=<scanNumberLow>[,<scanNumberHigh>] [precision=<precision>]
(write binary data for selected spectra)
index: write data for spectra in this index range
sn: write data for spectra in this scan number range
precision: write d decimal places

slice [mz=<mzLow>[,<mzHigh>]] [rt=<rtLow>[,<rtHigh>]]] [index=<indexLow>[,<indexHigh>] | sn=<scanLow>[,<scanHigh>]] [delimiter=<fixed|space|comma|tab>]
(write data from a rectangular region)
mz: set m/z range
rt: set retention time range
index: set spectrum index range
sn: set scan number range
delimiter: sets column separation; default is fixed width

tic [mz=<mzLow>[,<mzHigh>]] [delimiter=<fixed|space|comma|tab>]
(write total ion counts for an m/z range)
mz: set mz range
delimiter: sets column separation; default is fixed width

sic mzCenter=<mz> radius=<radius> radiusUnits=<amu|ppm> [delimiter=<fixed|space|comma|tab>]
(write selected ion chromatogram for an m/z and radius)
mzCenter: set mz value
radius: set radius value
radiusUnits: set units for radius value (must be amu or ppm)
delimiter: sets column separation; default is fixed width

image [args - see list]
(create pseudo-2D-gel image)
args:
label=<xxxx> (set filename label to xxxx)
mz=<mzLow>[,<mzHigh>] (set m/z cutoff range)
timeScale=<N> (set scaling factor for time axis)
binCount=<N> (set histogram bin count)
zRadius=<N> (set intensity function z-score radius, default=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, else show 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)
width=<xxx> (set image width to xxx pixels, default is calculated)
height=<yyy> (set image height to yyy pixels, default is calculated)

Examples:

msaccess data.mzML -x "tic mz=409-410" --filter="msLevel 2"
(creates data.mzML.tic.409.00-410.00.txt with total ion current info for mass range 409-410 in ms2 scans)
This could also be achieved as "msaccess data.mzML -c mycfg.txt" where mycfg.txt is a file containing the lines
exec = tic mz=409-410
filter = msLevel 2

msaccess data.mzML -x spectrum_table
(creates data.mzML.spectrum_table.txt with summary information for all spectra as read from the scan headers)

msaccess data.mzML -x "binary index=0-3"
(creates files data.mzML.binary.*.txt with binary data for spectra 0 through 3)

msaccess data.mzML -x "slice index=2,6 mz=100,600 delimiter=tab"
(creates data.mzML.slice.index_2-6.mz_100.0000-600.0000.tsv with a table of data in the selected range)

msaccess data.mzML -x "image width=800 height=600"
(creates data.mzML.image* with pseudo-2D-gel image of the data file)

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

ProteoWizard release: 3.0.4388
Build date: Mar 14 2013 12:14:30