Path to all the ancestor files (up to the native acquisition file) used to generate the current XML instance document.
Name of the parent file
Was the parent file a native acquisition file? Or was it processed data?
sha-1 sum of the parent file
General information about the MS instrument.
Any additional property of the instrument not included elsewhere in the instrument element.
Additional comments.
Description of any manipulation (from the first conversion to mzXML format until the creation of the current mzXML instance document) applied to the data.
Software used to convert the data. If data has been processed (e.g. profile > centroid) by any additional progs these should be added too.
Any additional manipulation not included elsewhere in the dataProcessing element.
Additional comments
Intensity threshold for including a peak in the XML output
Is the data centroided
Is the data deisotoped
Has the charge state been deconvoluted
Information about the separation technique, if any, used right before the acquisition.
Acquisition independent properties of a MALDI experiment.
Information about a MALDI plate.
Defines the orientation of the spotting pattern, with the IDs of the fist two consecutive spotted spots.
ID of the first spot spotted using "spottingPattern". This ID must have been defined also in the spot element.
ID of the second spot spotted using "spottingPattern". This ID must have been defined also in the spot element.
Information about individual spots.
Unique identifier for the spot.
X cartesian position of the spot.
Y cartesian position of the spot.
Unique identifier for the plate.
Information about the robot, if any, used to spot the plates.
Dead volume in ul of the spotting robot.
sha-1 sum for this file (from the beginning of the file up to (and including) the opening tag of sha1
Total number of scans contained in the XML instance document. This number should be equal to the total number of scans in the original RAW data, unless some were not converted (e.g.: signal below threshold)..
The time at which the run was started.
The time at which the run was ended.
Contact information for the person responsible for the instrument.
First name
Last name
Phone number
email address
Uniform Resource Identifier
Software identifier
acquisition: acquisition software running the MS (instrument section)
conversion: RAW data to XML converter utility (dataProcessing section)
processing: any form of data processing software not included by the two previous definitions (dataProcessing section)
Name of the acquisition software
Version of the acquisition software. Legal patterns are n.m(a or b)
Time of completion of the dataProcessing operation
The actual MS data is here
Information about the precursor ion.
This is a unique identifier in case more than one precusor were selected to generate the MS/MS spectra
This is the Intensity of the parent Ion. It is required in case of future exporting to pkl format. This should be the intensity as measured by the instrument prior to any data elaboration
If the charge state of the precursor is know, than it should be stored here.
If the exact charge state of the precursor is not known but the guessed charge states can be emunmerated, they may be recorded here as a comma-separated string of integers (for example: 2,3,4)
This is the total wideness of the precursor mass selection window.
Activation or fragmentation method: ETD, ECD, CID, etc
Acquisition dependent properties of a MALDI experiment.
Unique plate ID. This ID must have been defined also in the plate element.
Unique spot ID. This ID must have been defined also in the spot element.
Number of times the laser was fired to generate this scan.
Frequency of the laser.
Intensity of laser.
This is the actual data encoded using base64. Byte order must be network. The order of the pairs must be m/z – intensity.
nr of bits used by each component
Byte order of the encoded binary information (must be network).
Order of the m/z intensity pairs (must be m/z-int).
This is reserved for describing properties of the scan not elsewhere included in the schema
Additional comments
Scan number
1: MS
2: MS/MS
...
Total number of m/z-intensity pairs in the scan
+: positive
-: negative
any
For Thermo instruments, a space to record the "filter line" string for the scan.
This only maters if centroided attribute of dataProcessing element is 0 or absent.
This attribute should be used only if some scans were processed and others not. If all scans were processed, than the corresponding attribute form the dataProcessing element should be used instead.
This only maters if deisotoped attribute of dataProcessing element is 0 or absent.
This attribute should be used only if some scans were processed and others not. If all scans were processed, than the corresponding attribute form the dataProcessing element should be used instead.
This only maters if chargeDeconvoluted attribute of dataProcessing element is 0 or absent.
This attribute should be used only if some scans were processed and others not. If all scans were processed, than the corresponding attribute form the dataProcessing element should be used instead.
Retention time of the scan
Collision energy used to fragment the parent ion.
Setted low m/z boundary (this is the instrumetal setting)
Setted high m/z boundary (this is the instrumetal setting)
Observed low m/z (this is what the actual data looks like)
Observed high m/z (this is what the actual data looks like)
m/z of the base peak (most intense peak)
Intensity of the base peak (most intense peak)
Total ion current (total intensity in the scan)