Interpreting SpectConnect's Results

Condition MSL files:

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.

Metabolite matrix files:

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.