View source for Data Format of Peak List Files

Peak list files combine multiple peak lists in one single file. These files are stored in a Matlab&trade; specific data format and contain the peak lists as well as the respective metadata. In Matlab peak list files can be loaded by entering the following command at the Matlab command prompt:

 >> load('ecoli-peaklist-oct16.pkf','-mat')

This command will open ''ecoli-peaklist-oct16.pkf'', an example peak list file consisting of 16 individual peak lists from spectra of five different strains of ''E. coli''. The file ''ecoli-peaklist-oct16.pkf'' can be downloaded [http://wiki.microbe-ms.com/upload/ecoli-peaklist-oct16.pkf: '''here''']. If loading was successful, you will have access to a new Matlab variable ''C'' (structure array). Details of the structure of ''C'' are described next.<br> &nbsp;<br>


'''Fields of the structure array ''C''''':

{| class="wikitable" width=1100
!width=100| Fields
!width=600| Description
!width=100| Data type
!width=300|
|-
| nam
| spectra id
| string
| rowspan="33" style="background: #ffffff;" valign="top" | [[File:Peaklist-format-C-struc.jpg|250px|thumb|center|Matlab screenshot - format of a peak list file (*.pkf) demonstrating the general structure of the structure array 'C'. In this example the metadata of peak list #1 are shown.]]
|-
| gen
| genus information
| string
|-
| spe
| species info
| string
|-
| str
| strain info
| string
|-
| typ
| type
| string
|-
| uid
| taxonomy identification number for species as used by the NCBI (see [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi])
| integer
|-
| uie
| taxonomy identification number for strains used by the NCBI (see [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi])
| integer
|-
| gti
| cultivation conditions: growth time
| string
|-
| tem
| cultivation conditions: cultivation temperature
| string
|-
| air
| cultivation conditions: cultivation under aerobic or anaerobic conditions
| string
|-
| med
| cultivation conditions: cultivation medium
| string
|-
| spo
| spore formers (YES or NO)
| string
|-
| con
| sample concentration
| string
|-
| trt 
| sample treatment
| string
|-
| ext 
| extra information
| string
|-
| las 
| laser parameters (power, diameter, frequency, etc.)
| string
|-
| cal 
| calibration info
| string
|-
| met
| measurement method
| string
|-
| cus 
| customer info
| string
|-
| tim 
| date and time of measurement
| string
|-
| pth
| path to spectrum
| string
|-
| pik
| [[#peak table format|peak table]], an array of the dimension [4 x npeaks] npeaks: number of peaks 
| float32 
|-
| cls
| class assignment (valid values are 0,1,2,3 and 4)
| float32
|-
| lms
| MALDI-TOF or LC-MS spectrum? (valid values are 0 [MALDI] and 1 [LC-MS])
| float32
|-
| lst
| formatted text containing the peak table
| char array
|-
| seq
| sequence of preprocessing steps
| string
|-
| smo
| the number of smoothing points (Savitzky-Golay smoothing)
| float32
|-
| bas
| number of intervals used for baseline correction
| float32
|-
| nrm
| normalization parameter (Yes:1, No:0)
| float32
|-
| clb
| calibration paarmeters (see below for details)
| float32
|-
| red
| data reduction factor (spectral binning)
| string
|-
| cut
| cut in the spectral domain
| string
|-
| mod
| original data modified by cut or red (Yes:1, No:0)
| float32
|-
| prm
| parameters of peak detection
| string
|-
| ccl
| [[#structure array ccl|calibration information]] (see below)
| structure array
|-
| dbs
| [[#structure array dbs|data base spectrum]] (Yes:1, No:0)
| structure array
|-
| avr
| [[#structure array avr|average spectrum]] (Yes:1, No:0)
| structure array
|}


<span class="mw-headline" id="peak table format">'''Format of peak tables''' (C.pik):</span>


{| class="wikitable" width=800
!width=100| Fields
!width=700| Description
|-
| C.pik(1,:) <br> &nbsp; <br>
| m/z positions of the peaks in the peak table <br> &nbsp; <br> 
|-
| C.pik(2,:) <br> &nbsp; <br>
| absolute intensities of these peaks <br> &nbsp; <br>
|-
| C.pik(3,:) <br> &nbsp; <br>
| weighting factors (the sum of these factors equals 100) <br> &nbsp; <br>
|-
| C.pik(4,:) <br> &nbsp; <br>
| in case of single spectra, i.e. no database or average spectra: baseline-corrected absolute intensities of the peaks, in case of average or database spectra: the relative peak frequency
|}


<span class="mw-headline" id="structure array ccl">'''Calibration Information''' (C.ccl):</span>

{| class="wikitable" width=1100
!width=100| Fields
!width=600| Description
!width=100| Type
!width=300| 
|-
| cl1
| calibration constant 1
| float32
| rowspan="15" style="background: #ffffff;" valign="top" | [[File:Array-spec-ccl.jpg|250px|thumb|center|Matlab screenshot - format of structure array C.ccl containing the calibration info, such as calibration constants, delay time, number of spectra data points, etc. for spectrum #1.]]
|-
| cl2
| calibration constant 2
| float32
|-
| cl3
| calibration constant 3
| float32
|-
| del 
| delay time [ns]
| float32
|-
| npt
| number of data points
| float32
|-
| res 
| time resolution [ns]
| float32
|-
| ncl
| calibration info required to store the spectrum in a Bruker-specific data format 
| string
|-
| ncr
| calibration info required to store the spectrum in a Bruker-specific data format 
| string
|-
| bid
| hardware id of the spectrum
| string
|-
| org
| manufacturer info
| string
|-
| tfu
| manufacturer info
| string
|-
| tfu
| software info, required for compatibility issues
| string
|-
| spm
| type of instrumentation
| string
|-
| stp
| type of measurement (should be 'TOF')
| string
|-
| acq
| path to the original spectrum
| string
|}




<span class="mw-headline" id="structure array dbs">'''Data Base Spectrum''' (C.dbs):</span>

A database spectrum is usually created from many (>3) individual mass spectra. The structure array ''C.dbs'' contains information (metadata, peak tables) on the mass spectra used to produce the given database spectrum. Details of the structure of ''C.dbs'' are given in the table below.

{| class="wikitable" width=1100
!width=100| Fields
!width=600| Description
!width=100| Type
!width=300| 
|-
| mem
| string defining if the current spectrum is a data base spectrum (1) or not (0)
| string
| rowspan="5" style="background: #ffffff;" valign="top" |[[File:Array-spec-dbs.jpg|250px|thumb|center|Matlab screenshot - format of structure array C.dbs. C(1,17).dbs(1,1) contains information of mass spectrum #1 which was used with others to obtain data base spectrum #17, such as the id, taxonomic information, peak tables and the respective peak detection parameters).]]
|-
| ids
| id of the individual mass spectrum used to create the data base spectrum
| string
|-
| tax
| taxonomic info of the source spectrum 
| string
|-
| pik
| peak table of the source spectrum 
| float32
|-
| prm
| parameters of peak detection 
| string
|}


<span class="mw-headline" id="structure array avr">'''Average Spectrum''' (C.avr):</span>

An average spectrum is usually created from many (>3) individual mass spectra. The structure array ''C.avr'' contains information (metadata, peak tables) on the mass spectra used to produce the given avarage spectrum. Details of the structure of ''C.avr'' are given in the table below.

{| class="wikitable" width=1100
!width=100| Fields
!width=600| Description
!width=100| Type
!width=300| 
|-
| mem
| string defining if the current spectrum is an average spectrum (1) or not (0)
| string
| rowspan="5" style="background: #ffffff;" valign="top" |[[File:Array-spec-avr.jpg|250px|thumb|center|Matlab screenshot - format of structure array C.avr. spec(1,18).avr(1,1) contains information of mass spectrum #1 which was used with others to obtain an average spectrum #18, such as the id, taxonomic information, peak tables and the respective peak detection parameters).]]
|-
| ids
| id of the individual mass spectrum used to create the avarage spectrum
| string
|-
| tax
| taxonomic info of the source spectrum 
| string
|-
| pik
| peak table of the source spectrum 
| float32
|-
| prm
| parameters of peak detection 
| string
|}