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Output examples
Every example on this page is real output from one pair of files: a PRM run on an Orbitrap Fusion from PRIDE PXD006618 (1fmol_HSP90_SILpepmix_PRM.raw, 2,103 spectra), converted twice. A, trfp.mzML, is ThermoRawFileParser's mzML; B, mzdata.mzML, is the mzdata converter's. They differ in 11 major and 14 minor classes, so every mode has something to show.
The default. Classes, most severe and most frequent first, each with its count of records and examples (--examples N, default 3). --severity major keeps the minor classes out of the way here.
$ mzdiff --severity major --examples 1 trfp.mzML mzdata.mzML
A trfp.mzML (ThermoRawFileParser)
B mzdata.mzML (thermo_xcalibur)
spectra A 2103 B 2103 paired 2103
chromatograms A 1 B 2 paired 1
result differs: 0 critical, 11 major, 14 minor difference classes
MAJOR
2103 value differs spectrum/precursor/isolationWindow MS:1000828 (isolation window lower offset)
controllerType=0 controllerNumber=1 scan=1 A: 0.7 B: 1.4000244
2103 value differs spectrum/precursor/isolationWindow MS:1000829 (isolation window upper offset)
controllerType=0 controllerNumber=1 scan=1 A: 0.7 B: 1.4000244
2103 only in B spectrum/precursor/selectedIon MS:1000042 (peak intensity)
controllerType=0 controllerNumber=1 scan=1 A: - B: 0
2103 only in B spectrum/scan/instrumentConfiguration/analyzer MS:1000081 (quadrupole)
controllerType=0 controllerNumber=1 scan=1
2014 value differs spectrum MS:1000285 (total ion current)
controllerType=0 controllerNumber=1 scan=1 A: 15869.6875 B: 15869.7529296875
1 record only in B chromatogram @id (chromatogram)
TIC A: - B: TIC
1 missing in B mzML/fileDescription/fileContent MS:1000810 (ion current chromatogram)
header
1 only in B mzML/instrumentConfiguration/analyzer MS:1000081 (quadrupole)
header
1 only in B mzML/instrumentConfiguration/analyzer MS:1000083 (radial ejection linear ion trap)
header
1 only in B mzML/instrumentConfiguration/detector MS:1000253 (electron multiplier)
header
1 missing in B run @startTimeStamp
header A: 2015-10-14T03:22:49.63Z B: -
11 of 25 classes shown (--severity, --key)
One line, the same verdict and counts, for a quick look or a script.
$ mzdiff --summary trfp.mzML mzdata.mzML
complete: differs | classes: critical 0, major 11, minor 14 | spectra: A 2103, B 2103, paired 2103 | chromatograms: A 1, B 2, paired 1
As TSV, with a header row:
$ mzdiff --summary --tsv trfp.mzML mzdata.mzML
completion status fail_on critical major minor a_spectra b_spectra paired_spectra a_chromatograms b_chromatograms paired_chromatograms
complete differs major 0 11 14 2103 2103 2103 1 2 1
As JSON, one document (schema 1):
$ mzdiff --summary --json trfp.mzML mzdata.mzML
{
"schema_version": 1,
"tool": {"name": "mzdiff", "version": "0.1.0"},
"a": {"path": "trfp.mzML", "software": "ThermoRawFileParser", "spectra": 2103, "chromatograms": 1},
"b": {"path": "mzdata.mzML", "software": "thermo_xcalibur", "spectra": 2103, "chromatograms": 2},
"paired": {"spectra": 2103, "chromatograms": 1},
"completion": "complete",
"status": "differs",
"fail_on": "major",
"totals": {"critical": 0, "major": 11, "minor": 14}
}
Every difference, in the order found, grouped under its record. --limit caps it and says how many it held back.
$ mzdiff --list --severity major --limit 8 trfp.mzML mzdata.mzML
header
MAJOR missing in B mzML/fileDescription/fileContent MS:1000810 (ion current chromatogram)
MAJOR only in B mzML/instrumentConfiguration/analyzer MS:1000081 (quadrupole)
MAJOR only in B mzML/instrumentConfiguration/analyzer MS:1000083 (radial ejection linear ion trap)
MAJOR only in B mzML/instrumentConfiguration/detector MS:1000253 (electron multiplier)
MAJOR missing in B run @startTimeStamp A: 2015-10-14T03:22:49.63Z B: -
controllerType=0 controllerNumber=1 scan=1
MAJOR value differs spectrum MS:1000285 (total ion current) A: 15869.6875 B: 15869.7529296875
MAJOR value differs spectrum/precursor/isolationWindow MS:1000828 (isolation window lower offset) A: 0.7 B: 1.4000244
MAJOR value differs spectrum/precursor/isolationWindow MS:1000829 (isolation window upper offset) A: 0.7 B: 1.4000244
10424 more differences not shown (--limit)
complete: differs | classes: critical 0, major 11, minor 14 | spectra: A 2103, B 2103, paired 2103 | chromatograms: A 1, B 2, paired 1
As JSON Lines, one difference per line and a summary line at the end:
$ mzdiff --list --json --severity major --limit 2 trfp.mzML mzdata.mzML
{"type": "difference", "record": "header", "severity": "major", "kind": "missing", "path": "mzML/fileDescription/fileContent", "key": "MS:1000810", "name": "ion current chromatogram", "a": "", "b": ""}
{"type": "difference", "record": "header", "severity": "major", "kind": "extra", "path": "mzML/instrumentConfigurationList/instrumentConfiguration/componentList/analyzer", "key": "MS:1000081", "name": "quadrupole", "a": "", "b": ""}
{"type": "summary", "schema_version": 1, "tool": {"name": "mzdiff", "version": "0.1.0"}, "a": {"path": "trfp.mzML", "software": "ThermoRawFileParser", "spectra": 2103, "chromatograms": 1}, "b": {"path": "mzdata.mzML", "software": "thermo_xcalibur", "spectra": 2103, "chromatograms": 2}, "paired": {"spectra": 2103, "chromatograms": 1}, "completion": "complete", "status": "differs", "fail_on": "major", "totals": {"critical": 0, "major": 11, "minor": 14}, "shown": 2, "not_shown": 10430}
The differing records as a diff: - for A, + for B, each pair tagged with its severity.
$ mzdiff --view --severity major --record "controllerType=0 controllerNumber=1 scan=5" trfp.mzML mzdata.mzML
controllerType=0 controllerNumber=1 scan=5
spectrum
- total ion current = 17442.453125 MAJOR value differs
+ total ion current = 17442.513671875
spectrum/precursor/isolationWindow
- isolation window lower offset = 0.7 MAJOR value differs
+ isolation window lower offset = 1.4000244
- isolation window upper offset = 0.7 MAJOR value differs
+ isolation window upper offset = 1.4000244
spectrum/precursor/selectedIon
+ peak intensity = 0 MAJOR only in B
spectrum/scan/instrumentConfiguration/analyzer
+ quadrupole MAJOR only in B
complete: differs | classes: critical 0, major 11, minor 14 | spectra: A 2103, B 2103, paired 2103 | chromatograms: A 1, B 2, paired 1
Side by side, --side-by-side with --width N:
$ mzdiff --view --side-by-side --width 110 --severity major --record "controllerType=0 controllerNumber=1 scan=5" trfp.mzML mzdata.mzML
controllerType=0 controllerNumber=1 scan=5
A | B
spectrum
total ion current 17442.453125 | 17442.513671875 MAJOR value differs
spectrum/precursor/isolationWindow
isolation window lower offset 0.7 | 1.4000244 MAJOR value differs
isolation window upper offset 0.7 | 1.4000244 MAJOR value differs
spectrum/precursor/selectedIon
peak intensity - | 0 MAJOR only in B
spectrum/scan/instrumentConfiguration/analyzer
quadrupole - | (present) MAJOR only in B
complete: differs | classes: critical 0, major 11, minor 14 | spectra: A 2103, B 2103, paired 2103 | chromatograms: A 1, B 2, paired 1
When too many records differ to read, the view prints nothing and says how to narrow it:
$ mzdiff --view trfp.mzML mzdata.mzML
mzdiff: too large to view: 2106 records differ (critical 0, major 2105, minor 1); the view shows at most 40.
mzdiff: --key MS:1000081 (quadrupole) differs in 2104 records
mzdiff: --key MS:1000485 (nanospray inlet) differs in 2104 records
mzdiff: --key array:MS:1000515 (intensity array) differs in 2104 records
mzdiff: --record ID shows one record; --limit N raises the cap; --list shows everything
complete: differs | classes: critical 0, major 11, minor 14 | spectra: A 2103, B 2103, paired 2103 | chromatograms: A 1, B 2, paired 1
--view --html writes the view as one self-contained page to open in a browser, with severity filters, search, a unified or side-by-side layout, and a tooltip on every key, severity, and kind:
mzdiff --view --html --record "controllerType=0 controllerNumber=1 scan=5" --record "controllerType=0 controllerNumber=1 scan=6" trfp.mzML mzdata.mzML > diff.html
The same run converted by mzBridge differs only in intensity precision, a minor class, so the verdict is tolerated and the exit status 0:
$ mzdiff trfp.mzML mzbridge.mzML
A trfp.mzML (ThermoRawFileParser)
B mzbridge.mzML (mzBridge)
spectra A 2103 B 2103 paired 2103
chromatograms A 1 B 1 paired 1
result tolerated: 0 critical, 0 major, 1 minor difference classes
minor
2103 array precision differs spectrum array:MS:1000515 (intensity array)
controllerType=0 controllerNumber=1 scan=1 A: float64 B: float32
controllerType=0 controllerNumber=1 scan=2 A: float64 B: float32
controllerType=0 controllerNumber=1 scan=3 A: float64 B: float32
A missing or unreadable file exits 3. With --json, stdout still gets a JSON error object, and stderr the line for people:
$ mzdiff --json trfp.mzML nothere.mzML
{"type": "error", "schema_version": 1, "tool": {"name": "mzdiff", "version": "0.1.0"}, "error": "FileNotFound", "side": "b", "path": "nothere.mzML", "message": "no such file"}
mzdiff: B nothere.mzML: no such file