Data Format of Peak List Files and Data Format of Spectral Multifiles: Difference between pages

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Peak list files combine multiple peak lists in one single file. These files are stored in a Matlab™ 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:
Spectral multifiles combine multiple spectra in one single file. These files are stored in a Matlab™ specific data format and contain the spectral as well as the respective metadata. Spectral multifiles can be loaded in Matlab by entering the following command:


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




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


{| class="wikitable" width=1100
{| class="wikitable" width=1100
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!width=100| Data type
!width=100| Data type
!width=300|
!width=300|
|-
| org
| original mass spectra [2 x n array], n: number of data points
| float32
| rowspan="35" style="background: #ffffff;" valign="top" | [[File:Multifile-format-spec-struc.jpg|250px|thumb|center|Matlab screenshot - format of a spectral multifile (*.muf) demonstrating the general structure of the structure array 'spec'. In this example the metadata of spectrum #17 are shown. Spectrum #17 is a data base spectrum which has been created from 8 individual mass spectra (cf. spec(1,17).dbs)]]
|-
| pre
| pre-processed spectra [2 x n array], n: number of data points
| float32
|-
|-
| nam
| nam
| spectra id
| spectra id
| string
| 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
| gen
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|-
|-
| seq
| seq
| sequence of preprocessing steps
| sequence of pre-processing steps
| string
| string
|-
|-
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<span class="mw-headline" id="peak table format">'''Format of peak tables''' (C.pik):</span>
<span class="mw-headline" id="peak table format">'''Format of peak tables''' (spec.pik):</span>




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!width=700| Description
!width=700| Description
|-
|-
| C.pik(1,:) <br> &nbsp; <br>
| spec.pik(1,:) <br> &nbsp; <br>
| m/z positions of the peaks in the peak table <br> &nbsp; <br>  
| m/z positions of the peaks in the peak table <br> &nbsp; <br>  
|-
|-
| C.pik(2,:) <br> &nbsp; <br>
| spec.pik(2,:) <br> &nbsp; <br>
| absolute intensities of these peaks <br> &nbsp; <br>
| absolute intensities of these peaks <br> &nbsp; <br>
|-
|-
| C.pik(3,:) <br> &nbsp; <br>
| spec.pik(3,:) <br> &nbsp; <br>
| weighting factors (the sum of these factors equals 100) <br> &nbsp; <br>
| weighting factors (the sum of these factors equals 100) <br> &nbsp; <br>
|-
|-
| C.pik(4,:) <br> &nbsp; <br>
| spec.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
| 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>
<span class="mw-headline" id="structure array ccl">'''Calibration Information''' (spec.ccl):</span>


{| class="wikitable" width=1100
{| class="wikitable" width=1100
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| calibration constant 1
| calibration constant 1
| float32
| 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.]]
| rowspan="15" style="background: #ffffff;" valign="top" | [[File:Array-spec-ccl.jpg|250px|thumb|center|Matlab screenshot - format of structure array spec.ccl containing the calibration info, such as calibration constants, delay time, number of spectra data points, etc. for spectrum #1.]]
|-
|-
| cl2
| cl2
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<span class="mw-headline" id="structure array dbs">'''Data Base Spectrum''' (C.dbs):</span>
<span class="mw-headline" id="structure array dbs">'''Data Base Spectrum''' (spec.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.
A [[Create database spectra|database spectrum]] is usually created from many (>3) individual mass spectra. The structure array ''spec.dbs'' contains information (metadata, peak tables) on the mass spectra used to produce the given database spectrum. Details of the structure of ''spec.dbs'' are given in the table below.  


{| class="wikitable" width=1100
{| class="wikitable" width=1100
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| string defining if the current spectrum is a data base spectrum (1) or not (0)
| string defining if the current spectrum is a data base spectrum (1) or not (0)
| string
| 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).]]
| rowspan="5" style="background: #ffffff;" valign="top" |[[File:Array-spec-dbs.jpg|250px|thumb|center|Matlab screenshot - format of structure array spec.dbs. spec(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
| ids
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<span class="mw-headline" id="structure array avr">'''Average Spectrum''' (C.avr):</span>
<span class="mw-headline" id="structure array avr">'''Average Spectrum''' (spec.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.
An [[Averaging Mass Spectra|average spectrum]] is usually created from many (>3) individual mass spectra. The structure array ''spec.avr'' contains information (metadata, peak tables) on the mass spectra used to produce the given avarage spectrum. Details of the structure of ''spec.avr'' are given in the table below.  


{| class="wikitable" width=1100
{| class="wikitable" width=1100
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|-
|-
| mem
| mem
| string defining if the current spectrum is an average spectrum (1) or not (0)
| string defining if the current spectrum is a data base spectrum (1) or not (0)
| string
| 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).]]
| rowspan="5" style="background: #ffffff;" valign="top" |[[File:Array-spec-avr.jpg|250px|thumb|center|Matlab screenshot - format of structure array spec.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
| ids

Latest revision as of 16:32, 21 March 2023

Spectral multifiles combine multiple spectra in one single file. These files are stored in a Matlab™ specific data format and contain the spectral as well as the respective metadata. Spectral multifiles can be loaded in Matlab by entering the following command:

>> load('ecoli-filelist-oct16.muf','-mat')

This command will open ecoli-filelist-oct16.muf, an example multifile containing 16 individual MALDI-TOF mass spectra acquired from five different strains of E. coli. The file ecoli-filelist-oct16.muf can be downloaded here. If loading was successful, you will have access to a new Matlab variable spec (structure array). Details of the structure of spec are described next.
 


Fields of the structure array spec:

Fields Description Data type
org original mass spectra [2 x n array], n: number of data points float32
Matlab screenshot - format of a spectral multifile (*.muf) demonstrating the general structure of the structure array 'spec'. In this example the metadata of spectrum #17 are shown. Spectrum #17 is a data base spectrum which has been created from 8 individual mass spectra (cf. spec(1,17).dbs)
pre pre-processed spectra [2 x n array], n: number of data points float32
nam spectra id string
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 [1]) integer
uie taxonomy identification number for strains used by the NCBI (see [2]) interger
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, 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 pre-processing 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 calibration information (see below) structure array
dbs data base spectrum (Yes:1, No:0) structure array
avr average spectrum (Yes:1, No:0) structure array


Format of peak tables (spec.pik):


Fields Description
spec.pik(1,:)
 
m/z positions of the peaks in the peak table
 
spec.pik(2,:)
 
absolute intensities of these peaks
 
spec.pik(3,:)
 
weighting factors (the sum of these factors equals 100)
 
spec.pik(4,:)
 
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


Calibration Information (spec.ccl):

Fields Description Type
cl1 calibration constant 1 float32
Matlab screenshot - format of structure array spec.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



Data Base Spectrum (spec.dbs):

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

Fields Description Type
mem string defining if the current spectrum is a data base spectrum (1) or not (0) string
Matlab screenshot - format of structure array spec.dbs. spec(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


Average Spectrum (spec.avr):

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

Fields Description Type
mem string defining if the current spectrum is a data base spectrum (1) or not (0) string
Matlab screenshot - format of structure array spec.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