These files provide the conserved, deconvoluted metabolites that are present
in the samples in a given class. By default, these metabolites are present
in at least 75% of the samples for a given class, though this can be changed
via the "Additional User Options" button.
For each conserved metabolite, a sample spectrum that is indicative of the
occurrences of the metabolite is provided in this file. Note that this
is not an averaged spectrum; it is the deconvoluted spectrum provided by
AMDIS. For a given set of metabolite occurrences, the spectrum with the
minimum pairwise difference to the other occurrences in the set is chosen,
and we refer to this as a "representative peak".
A file is provided for each condition, and the name given for the file is
the name of the condition provided by the user, appended with ".MSL". The files
contain the data for a series of metabolites in the following format:
NAME: A unique name given for each peak, based on the name of the
file from which the representative peak is taken and the relative location
of that peak within the file.
CASNO: The Chemical Abstracts number for the compound; currently not used.
RI: Currently not used.
RW: Currently not used.
RT: The retention time of the representative peak.
COMMENTS: A series of lines with relevant information.
SOURCE: The file from which the representative peak was taken.
NUM PEAKS: The number of peaks in the mass spectrum of the representative peak.
This line is followed by a series of lines containing the actual spectrum in
the following format:
(m/z intensity) (m/z intensity) (m/z intensity) (m/z intensity) (m/z intensity)
Similar to the individual condition libraries, except it contains the union of all metabolites that were detected in at least one of the conditions. It also indicates (in the comment field) which conditions a metabolite occurs in and whether the difference in relative amount between any two classes is statistically significant.
This list tells you which condition numbers in your master CumulativeLibrary.MSL file correspond with which of the conditions that you gave as input. Conditions are listed one to a line in the following format: <condition number>: <user's name for condition>
This file contains the details of the metabolites that were found using
SpectConnect. For each metabolite, retention time of the representative
peak (or "centroid") is given, and data for all occurrences of that metabolite
are listed. The data included is:
RT: retention time
RA: relative abundance
IS: integrated signal
AM: base peak
Note that only the metabolite occurrences in conditions where it was found
to be conserved are included. For instance, if a certain metabolite
occurred in all samples of condition 1 but only in 1 out of 10 in condition
2, the occurrence from condition 2 would not be included in this list.
Nonetheless, we hope this file will prove useful for further calculations
and manipulations.
These files provide a summary of all of the metabolite peaks found across
all of your sample files. Each line represents a different metabolite, and each
column represents either the name of the metabolite, its retention time, or
the data value for the metabolite in a specific sample file. The "data" values
are either RA, IS, or AM (explained above); these values are each provided in
separate files (one matrix of RA values, one matrix of IS values, and one matrix
of AM values). These files are in .csv (comma-separated values) format, and so
can easily be imported into spreadsheet and other data manipulation programs.
Note that all metabolite occurrences are included in these files. The
metabolite mentioned in the "details" explanation
that is in all samples of condition 1 and only
one sample of condition 2 will have non-zero values in the columns representing
all of the samples for condition 1 as well as the single sample in condition 2
in which it is present.