Mass Spectrometry Databases

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