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Topic: Read peaks list in text format directly to XCMS (Read 5227 times) previous topic - next topic

Read peaks list in text format directly to XCMS

Hi,
I wonder if there is a way to read my centroid peaks list files directly for XCMS analysis. My peaks list format (.txt) is described at the end. I think it contains all info that XCMS needs for analysis purpose.

Another way is to compile these lists into mzXML format. Is there a convenient parser already there? My google search didn't turn out good solution to this.

Any suggestion in either way is greatly appreciated.

Xiyan


###The format of my peaks list in .txt#############
............
Scan#: 8
Ret.Time: 0.103439
IonInjectionTime(ms): 250
TotalIonCurrent: 288848
BasePeakMass: 104.1073965
BasePeakIntensity: 108806
83.06096   652.943
84.04497   1627.873
84.05624   275.127
.............
Scan#: 9
Ret.Time: 0.117677
IonInjectionTime(ms): 250
TotalIonCurrent: 90145.1
BasePeakMass: 255.2325484
BasePeakIntensity: 52749.7
83.02424   98.579
101.24509   105.154
103.97359   103.052
107.27591   106.289
107.41876   98.873
111.60914   120.939
119.03371   1083.924
............

Re: Read peaks list in text format directly to XCMS

Reply #1 –
Which instrument/vendor are you using ?

If the direct export to cdf/mzXML/mzData is not possible for some reason, you might try using OpenMS' FileConverter (see below) or writing your own.

Code: [Select]
FileConverter -- Converts between different MS file formats.
Version: 1.8.0 Jun 21 2011, 16:52:13

Usage:
  FileConverter <options>

Options (mandatory options marked with '*'):
All conversions are possible, but you might lose information!

  -in <file>*        Input file  (valid formats: 'mzData', 'mzXML', 'mzML', 'DTA', 'DTA2D', 'mgf', 'featureXML', 'consensusXML', 'ms2', 'fid', 'tsv', 'peplist', 'kroenik', 'edta')
  -in_type <type>    Input file type -- default: determined from file extension or content
                     (valid: 'mzData', 'mzXML', 'mzML', 'DTA', 'DTA2D', 'mgf', 'featureXML', 'consensusXML', 'ms2', 'fid', 'tsv', 'peplist', 'kroenik', 'edta')
  -out <file>*       Output file  (valid formats: 'mzData', 'mzXML', 'mzML', 'DTA2D', 'mgf', 'featureXML', 'consensusXML')
  -out_type <type>   Output file type -- default: determined from file extension or content
                     (valid: 'mzData', 'mzXML', 'mzML', 'DTA2D', 'mgf', 'featureXML', 'consensusXML')
                     
Common TOPP options:
  -ini <file>        Use the given TOPP INI file
  -threads <n>       Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini <file>  Writes the default configuration file
  --help             Shows options
  --helphelp         Shows all options (including advanced)

Re: Read peaks list in text format directly to XCMS

Reply #2 –
Ralf,
Thanks for the reply, that's quick!

I am using Thermo Exactive. The thing is that I am using a home-made program to do centroiding which only produces peaks list in text file.

I'll try Fileconverter and post my experience out of it.

Xiyan