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. 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 - spec

Fields	Description	Data type
nam	spectra id	char array	Screenshot showing the content of the structure array spec that is stored in so called spectrum multi files (*.muf). Fields of spec contain spectral data (original, i.e. unmodified, and pre-processed), spectrum metadata as well as peak lists, calibration information, results of quality tests, and information collected during creation of average, or database spectra. In the example of the given screenshot, the content of one database spectrum is depicted.
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]), can be modified	char array
uie	unmodified taxonomy identification number for strains used by the NCBI (see [2])	char array
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, spot 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
cls	class assignment (valid values are 0,1,2,3 and 4)	float32
lst	formatted text containing the peak table info	char array
seq	sequence of pre-processing steps	char array
smo	the number of smoothing points (Savitzky-Golay smoothing)	char array
bas	number of intervals used for baseline correction	float32
nrm	normalization parameter (Yes:1, No:0)	float32
clb	calibration parameters (not used)	float32
red	data reduction factor (spectral binning)	char array
cut	cut in the spectral domain, m/z range	char array
tmp	temporary info (not always present)	char array
mod	original data modified by cut spectra or reduce resolution (Yes:1, No:0)	float32
lms	MALDI-TOF MS, or LC-MS1 data? (0: MALDI, 1: LC-MS1)	float32
pik	peak table, an array of the dimension [4 x npeaks] or [6 x npeaks], where npeaks denotes the number of peaks	float 32
ccl	calibration information (see below)	struc array
avr	average spectrum (Yes:1, No:0)	struc array
dbs	data base spectrum (Yes:1, No:0)	struc array
prm	parameters of peak detection	char array
qt	quality test parameter	struc array

Peak table format - 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
spec.pik(5,:)	FWHH of the given peak (requires QT)
spec.pik(6,:)	resolving power of the given peak (requires QT)

Calibration information - spec.ccl

Fields	Description	Type
cl1	calibration constant 1	float32	Screenshot showing the content of the structure array spec.ccl containing the calibration info (calibration constants, delay time, number of spectrum data points, etc.)
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 ('Bruker ID')	char array
mid	MicrobeMS id of the spectrum	char array
org	manufacturer info	char array
tfu	'ToF user'	char array
spm	not used	char array
stp	type of measurement (should be 'TOF')	char array
acq	further acquisition info	char array

Database spectra - spec.dbs

A database spectrum is usually created from many (>3) individual mass spectra. Like in regular experimental spectra, spectral data and metadata of average spectra are stored in specific fields of structure array spec. In database spectra the field spec(i).dbs is used to store relevant data from experimental source spectra from which the given database spectrum has been derived. These fields are left empty in experimental and average spectra. Details of the structure of spec.dbs are given in the table below.

Fields	Description	Type
mem	specifies whether the current spectrum is a data base spectrum (1) or not (0)	char array	Screenshot of structure array spec.dbs. This screenshot shows information like the spectrum id, taxonomic information, peak tables, respective peak detection parameters, etc of mass spectrum #1 [spec(1).dbs(1,1)] that was used with others to obtain an average spectrum
ids	id of the individual mass spectrum that contributed to the given database spectrum	char array
tax	contains taxonomical information (i.e. the genus, species, strain information)	char array
pik	peak table of the given source spectrum	float32
prm	parameters used for peak detection	char array

Average spectra - spec.avr

An average spectrum is usually created from many (>3) individual mass spectra. Like in regular experimental spectra, spectral data and metadata of average spectra are stored in specific fields of structure array spec. In average spectra the field spec(i).avr is used to store relevant data from experimental source spectra from which the given average spectrum has been derived. These fields are empty in experimental and database spectra. Details of the structure of spec.avr are given in the table below.

Fields	Description	Type
mem	specifies whether the contributing spectrum is an average spectrum (1) or not (0)	char array	Screenshot of structure array spec.avr. This screenshot shows information like the spectrum id, taxonomic information, peak tables, respective peak detection parameters, etc of mass spectrum #1 [spec(1).avr(1,1)] that was used with others to obtain an average spectrum
ids	id of the individual mass spectrum that contributed to the given average spectrum	char array
tax	contains taxonomical information (i.e. the genus, species, strain information)	char array
pik	peak table of the given source spectrum	float32
prm	parameters used for peak detection	char array

Quality test results - spec.qt

The structure array spec.qt contains the results of a Quality Test. Fields of this structure are empty if no QT has been performed. Details of the structure of spec.qt are given in the table below.

Fields	Description	Type
noise	QT data of the noise test, contains fields abs, rnk, and obj	struc array	Screenshot of structure array spec.qt that contains the results of a quality test (QT).
basln	QT data of the baseline test, contains fields abs, rnk, and obj	struc array
npiks	QT data of the test number of peaks, contains fields abs, rnk, and obj	struc array
respw	QT data of the test resolution power, contains fields abs, rnk, and obj	struc array
rnk	overall rank that the given spectrum has achieved in a QT with a number of other spectra	float32
res	overall quality test score	float32