Data Format of Peak List Files

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:

>> 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 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.
 

Fields of the structure array C:

Fields	Description	Data type
nam	spectra id	char array	File:Peaklist-format-C-struc.jpg 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	char array
spe	species info	char array
str	strain info	char array
typ	type	char array
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])	integer
gti	cultivation conditions: growth time	char array
tem	cultivation conditions: cultivation temperature	char array
air	cultivation conditions: cultivation under aerobic or anaerobic conditions	char array
med	cultivation conditions: cultivation medium	char array
spo	spore formers (YES or NO)	char array
con	sample concentration	char array
trt	sample treatment	char array
ext	extra information	char array
las	laser parameters (power, diameter, frequency, etc.)	char array
cal	calibration info	char array
met	measurement method	char array
cus	customer info	char array
tim	date and time of measurement	char array
pth	path to spectrum	char array
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 preprocessing steps	char array
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)	char array
cut	cut in the spectral domain	char array
mod	original data modified by cut or red (Yes:1, No:0)	float32
prm	parameters of peak detection	char array
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 (C.pik):

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

Fields	Description	Type
cl1	calibration constant 1	float32	File:Array-spec-ccl.jpg 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	char array
ncr	calibration info required to store the spectrum in a Bruker-specific data format	char array
bid	hardware id of the spectrum	char array
org	manufacturer info	char array
tfu	manufacturer info	char array
tfu	software info, required for compatibility issues	char array
spm	type of instrumentation	char array
stp	type of measurement (should be 'TOF')	char array
acq	path to the original spectrum	char array

Data Base Spectrum (C.dbs):

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.

Fields	Description	Type
mem	expression defining if the current spectrum is a data base spectrum (1) or not (0)	string	File:Array-spec-dbs.jpg 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	char array
tax	taxonomic info of the source spectrum	char array
pik	peak table of the source spectrum	float32
prm	parameters of peak detection	char array

Average Spectrum (C.avr):

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.

Fields	Description	Type
mem	defines whether the current spectrum is an average spectrum (1) or not (0)	char array	File:Array-spec-avr.jpg 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	char array
tax	taxonomic info of the source spectrum	char array
pik	peak table of the source spectrum	float32
prm	parameters of peak detection	char array