XML Output File

ProMass automatically writes an XML summary file during automatic processing.  The file is called promass_results.xml and is written to the results directory.  The XML file contains all the relevant information about each sample processed from the Xcalibur sample list.  The XML file represents a convenient way to import ProMass results into a database.  An example annotated XML file is included with the installation in the ProMass install directory so that you can see what a typical ProMass XML output file would look like.  See the file called promass_annotated.xml.  The file is reproduced below, with the comments about each XML element or node shown in green text.

<?xml version='1.0' standalone='yes'?>
<!--PROMASS_RESULTS is the root node of document
The following elements are not optional and should always be present:
DATA_FILE - one or more
    CHROM_PEAK - one or more, including all CHROM_PEAK children
    COLOR_CODE
    DATA_PATH
    DETECTOR_TYPE
    MS_CHROM_GRAPHIC
    PROC_METHOD
    RESULTS_PATH
    RESULT_CODE
PROCESSING_COMPUTER_NAME
PROCESSING_DATE_TIME
VERSION

All other elements are optional, depending on the how the sample list was configured during processing.
The following optional DATA_FILE children can appear more than once:
    TARGET_MASS - one or more target masses with all TARGET_MASS children
    SEQ_LADDER - one or more found sub-sequence masses with all SEQ_LADDER children
-->
<PROMASS_RESULTS>
    <!--Information about each sample is accessed from its DATA_FILE element.
    The NAME attribute is the data file name from the sample list (does not include
    path, see DATA_PATH). The ID attribute is the vial or well position, but does not include
    tray information.  There may be multiple DATA_FILE elements, depending on how many files
    were processed.-->
    <DATA_FILE ID="1" NAME="oligo01">
        <!--Acquisition date, the date the .raw file was acquired on the MS system-->
     <ACQ_DATE>1/10/2008</ACQ_DATE>
        <!--AD_CHROM_GRAPHIC is an element of DATA_FILE, which is the name of the graphic file for the Analog Device chromatogram
        This element may only be present if the UV signal is acquired thru an ADC such as the SS420X-->
        <AD_CHROM_GRAPHIC>oligo01_ad.png</AD_CHROM_GRAPHIC>
        <!--BIOSEQUENCE element is the BioSequence string from the sample list-->
        <BIOSEQUENCE>CCGGGGTGACCACACAGC</BIOSEQUENCE>
        <!--CHROM_PEAK elements represent information from each chromatographic peak and associated spectrum.
        The RT attribute represents the retention time of each chromatographic peak.
        Multiple CHROM_PEAK children are possible-->
        <CHROM_PEAK RT="0.29">
            <!--AREA_PERCENT of the chromatographic peak, 0-100-->
            <AREA_PERCENT>100.00</AREA_PERCENT>
            <!--BASE_PEAK_INTENSITY, MS intensity of the highest peak in the deconvoluted spectrum-->
            <BASE_PEAK_INTENSITY>2.45E+005</BASE_PEAK_INTENSITY>
            <!--BASE_PEAK_MASS, The deconvoluted mass with the highest intensity in the deconvoluted spectrum-->
            <BASE_PEAK_MASS>5494.3</BASE_PEAK_MASS>
            <!--DECON_DATA, name of the raw deconvolution mass-intensity data file-->
            <DECON_DATA>oligo01_0_29.dec</DECON_DATA>
            <!--DECON_PEAK_REPORT, name of the centroids peak list file-->
            <DECON_PEAK_REPORT>oligo01_0_29.cent.txt</DECON_PEAK_REPORT>
            <!--DEC_GRAPHIC, name of the deconvoluted spectrum graphic file-->
            <DEC_GRAPHIC>oligo01_0_29.dec.png</DEC_GRAPHIC>
            <!--ESI_GRAPHIC, name of the ESI spectrum graphic file-->
            <ESI_GRAPHIC>oligo01_0_29.png</ESI_GRAPHIC>            
            <!--LOG_FILE, name of the deconvolution log file-->
            <LOG_FILE>oligo01_0_29.log.txt</LOG_FILE>
            <!--PEAK_AREA, the integrated area of the chromatogrphic peak-->
            <PEAK_AREA>2.08E+007</PEAK_AREA>
            <!--SPECTRAL_QUALITY, a string indicating the quality of the deconvoluted spectrum-->
            <SPECTRAL_QUALITY>ok</SPECTRAL_QUALITY>
            <!--ZOOM_GRAPHIC, name of the zoom deconvoluted spectrum graphic file-->
            <ZOOM_GRAPHIC>oligo01_0_29.zdec.png</ZOOM_GRAPHIC>
        </CHROM_PEAK>
        <!--CLIENT, the client field from the sample list-->
        <CLIENT>Oligos-R-Us</CLIENT>
        <!--COLOR_CODE, overall color code for the data set - cyan, red, orange, purple, blue or green.
        Note this color code may be different than individual target mass color codes, because the
        overall color code represents the best color observed for all target masses-->
        <COLOR_CODE>green</COLOR_CODE>
        <!--COMMENT, comment entered in the sample list at run time-->
        <COMMENT>Oh, what a wonderful XML format</COMMENT>
        <!--DATA_PATH, the path to the original MS (.raw) data file-->
        <DATA_PATH>C:\Program Files\ProMassXcali\TestData\oligos</DATA_PATH>
        <!--DETECTOR_TYPE, the type of detector used for peak detection in the processing method
        usually LC/MS, but could also be LC/UV-->
        <DETECTOR_TYPE>LC/MS</DETECTOR_TYPE>
        <!--INJ_VOL, injection volume from the sample list-->
        <INJ_VOL>25</INJ_VOL>
        <!--INST_METHOD, the instrument method file from the sample list-->
        <INST_METHOD>C:\Xcalibur\methods\oligo_htcs</INST_METHOD>
        <!--MS_CHROM_GRAPHIC, name of the graphic file for the MS chromatogram-->
        <MS_CHROM_GRAPHIC>oligo01_ms.png</MS_CHROM_GRAPHIC>
        <!--POSITION, vial position from the sample list, does not include tray-->
        <POSITION>1</POSITION>
        <!--PROC_METHOD, processing method file including path (does not include .pmd extension)-->
        <PROC_METHOD>C:\Program Files\ProMassXcali\TestData\oligos\oligo</PROC_METHOD>
        <!--RESULTS_PATH, directory where promass results for this data file were written to-->
        <RESULTS_PATH>C:\Program Files\ProMassXcali\TestData\oligos\promass_results</RESULTS_PATH>
        <!--RESULT_CODE, overall result code index for the data file, -1=cyan, 0=red, 1=orange, 2=purple, 3=blue, 4=green-->
        <RESULT_CODE>4</RESULT_CODE>
        <!--SAMPLE_ID, Sample ID from the sample list-->
        <SAMPLE_ID>test oligo 01</SAMPLE_ID>
        <!--SAMPLE_NAME, Sample Name from the sample list-->
        <SAMPLE_NAME>A1</SAMPLE_NAME>
        <!--SEQ_LADDER, a sequence ladder is a list of all partial sequences that contain either terminus of a
        biomolecule sequence.  This feature is useful for finding oligo failure sequences, for example.
        ProMass reports the results of a sequence ladder search in the SEQ_LADDER element.  The SEQ_LADDER
        attribute is MASS, which is the expected (calculated) mass.  Ladder masses are ONLY reported
        for those masses that are found.-->
        <SEQ_LADDER MASS="5205.4">
            <!--INTENSITY, the deconvoluted intensity of the found mass-->
            <INTENSITY>4.60E+004</INTENSITY>
            <!--MASS_ERROR, the mass error, observed minus expected mass-->
            <MASS_ERROR>-0.5</MASS_ERROR>
            <!--OBSERVED_MASS, experimentally observed seq_ladder mass-->
            <OBSERVED_MASS>5204.9</OBSERVED_MASS>
            <!--RT, retention time of the found ladder mass-->
            <RT>0.29</RT>
            <!--SEQUENCE, putative sequence of the found ladder-->
            <SEQUENCE>C2-C18</SEQUENCE>
        </SEQ_LADDER>
        <!--STUDY, STUDY field from the sample list-->
        <STUDY>867-5309</STUDY>
        <!--TARGET_INFO, string from the Target Info field of the sample list-->
        <TARGET_INFO>sequence = oligo, ladder=5'</TARGET_INFO>
        <!--TARGET_MASS, elements present information about target masses that have been defined.
        Target masses can be explicitly defined in the target info field of the sample list or
        calculated from BioSequence strings.  Multiple target masses are possible. The MASS
        attribute represents the expected target mass.-->
        <TARGET_MASS MASS="5494.6">
            <!--COLOR_CODE, the color code for this particular target mass - cyan, red, orange, purple, blue or green.-->
            <COLOR_CODE>green</COLOR_CODE>
            <!--IDENTITY, a string representing the identity of the found species.  Usually, this will indicate "Target Mass"
            for a found component or "Not Found" if the target mass is not found.-->
            <IDENTITY>Target Mass</IDENTITY>
            <!--INTENSITY, the deconvoluted intensity of the found target mass-->
            <INTENSITY>2.45E+005</INTENSITY>
            <!--MASS_ERROR, the mass error, observed minus expected mass-->
            <MASS_ERROR>-0.3</MASS_ERROR>
            <!--OBSERVED_MASS, experimentally observed target mass-->
            <OBSERVED_MASS>5494.3</OBSERVED_MASS>
            <!--PURITY_ESTIMATE, the purity estimate is a percentage based on the TOTAL_ABUNDANCE corrected for "acceptable impurities" and
            normalized by peak area percent.  For example, if a target mass with 50% total abundance has an acceptable M+Na impurity which is 10%, and
            a CHROM_PEAK area percent of 20%, then the PURITY_ESTIMATE = (50+10)*0.2 = 12%.  The PURITY_ESTIMATE will often equal the
            TOTAL_ABUNDANCE when single chromatographic peaks are present and no acceptable impurities are detected-->
            <PURITY_ESTIMATE>59.10</PURITY_ESTIMATE>
            <!--RESULT_CODE, result code index for this target mass, -1=cyan, 0=red, 1=orange, 2=purple, 3=blue, 4=green-->
            <RESULT_CODE>4</RESULT_CODE>
            <!--RT, retention time of the found target mass-->
            <RT>0.29</RT>
            <!--TOTAL_ABUNDANCE, the %total abundance of the target mass in the spectrum where found-->
            <TOTAL_ABUNDANCE>59.1</TOTAL_ABUNDANCE>
        </TARGET_MASS>
        <!--UV_CHROM_GRAPHIC, name of the graphic file for the UV chromatogram-->
        <UV_CHROM_GRAPHIC>oligo01_uv.png</UV_CHROM_GRAPHIC>
        <!--ZNOVA_PARAMS, ZNova Params string, as entered in the sample list-->
        <ZNOVA_PARAMS>-P &quot;C:\Program Files\ProMassXcali\TestData\oligos\oligo.PARAMS&quot; </ZNOVA_PARAMS>
    </DATA_FILE>
    <!--PROCESSING_COMPUTER_NAME, the computer name where the data processing was performed-->
    <PROCESSING_COMPUTER_NAME>LTQ</PROCESSING_COMPUTER_NAME>
    <!--PROCESSING_DATE_TIME, the date and time that the last file was processed for this sample list-->
    <PROCESSING_DATE_TIME>Mon Mar 12 15:38:01 2007</PROCESSING_DATE_TIME>
    <!--VERSION, the version of the software used to process this data set-->
    <VERSION>ZNova #.#.#</VERSION>
</PROMASS_RESULTS>