format-version: 1.2
data-version: 0.1.0
date: 20:11:2013 11:03
saved-by: Mathias Walzer
remark: creator: Mathias Walzer <walzer <-at-> informatik.uni-tuebingen.de>
import: http://unit-ontology.googlecode.com/svn/trunk/unit.obo
import: http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo
default-namespace: QC
remark: namespace: QC
remark: version: 0.1.0
ontology: uo
ontology: ms

[Typedef]
id: has_regexp
name: has regexp

[Typedef]
id: has_units
name: has_units

[Typedef]
id: part_of
name: part_of
is_transitive: true

[Typedef]
id: has_order
name: has_order

[Term]
 id: QC:0000001
 name: quality parameter
 def: "A quality parameter of some sort." [PXS:QC]
 

[Term]
 id: QC:0000002
 name: run quality parameter
 def: "A run quality parameter of some sort." [PXS:QC]
 is_a: QC:0000001 ! quality parameter
 

[Term]
 id: QC:0000003
 name: set quality parameter
 def: "A set quality parameter of some sort." [PXS:QC]
 is_a: QC:0000001 ! quality parameter
 

[Term]
 id: QC:0000004
 name: MS aquisition result details
 def: "The results (e.g. counts) of the MS aquisition step of a MS experiment." [PXS:QC]
 is_a: QC:0000001 ! quality parameter

remark: run name is MS:1000577 as raw data file in [PSI:MS]
 
[Term]
 id: QC:0000005
 name: set name
 def: "The set name describing the set grouping." [PXS:QC]
 is_a: QC:0000001 ! quality parameter


[Term]
 id: QC:0000006
 name: MS1 spectra count
 def: "Contains the number of MS1 spectra recorded." [PXS:QC]
 is_a: QC:0000004 ! MS aquisition result details
 

[Term]
 id: QC:0000007
 name: MS2 spectra count
 def: "Contains the number of MS2 spectra recorded." [PXS:QC]
 is_a: QC:0000004 ! MS aquisition result details
 

[Term]
 id: QC:0000008
 name: Chromatogram count
 def: "Contains the number of chromatograms recorded." [PXS:QC]
 is_a: QC:0000004 ! MS aquisition result details


[Term]
 id: QC:0000009
 name: MS MZ aquisition ranges
 def: "Contains the min/max MZ range boundaries observed during MS aquisition." [PXS:QC]
 is_a: QC:0000004 ! MS aquisition result details
 is_a: QC:0000048 ! value table
 
 
[Term]
 id: QC:0000010
 name: MS min MZ
 def: "Contains the actual min MZ occurrence in MS aquisition." [PXS:QC]
 is_a: QC:0000009 ! MS MZ aquisition ranges
remark: supposed as table col


[Term]
 id: QC:0000011
 name: MS max MZ
 def: "Contains the actual max MZ occurrence in MS aquisition." [PXS:QC]
 is_a: QC:0000009 ! MS MZ aquisition ranges
remark: supposed as table col

 
[Term]
 id: QC:0000012
 name: MS RT aquisition ranges
 def: "Contains the min/max RT range boundaries observed during MS aquisition." [PXS:QC]
 is_a: QC:0000004 ! MS aquisition result details
 is_a: QC:0000048 ! value table


[Term]
 id: QC:0000013
 name: MS min RT
 def: "Contains the actual min RT occurrence in MS aquisition." [PXS:QC]
 is_a: QC:0000012 ! MS RT aquisition ranges
 is_a: QC:0000048 ! value table


[Term]
 id: QC:0000014
 name: MS max RT
 def: "Contains the actual max RT occurrence in MS aquisition." [PXS:QC]
 is_a: QC:0000012 ! MS RT aquisition ranges
remark: supposed as table col


[Term]
 id: QC:0000015
 name: MS gradient settings
 def: "Contains the min/max RT range boundaries used in machine settings during MS aquisition." [PXS:QC]
 is_a: QC:0000012 ! MS RT aquisition ranges
 is_a: QC:0000048 ! value table


[Term]
 id: QC:0000016
 name: MS MZ detection settings
 def: "Contains the min/max MZ range boundaries used in machine settings during MS aquisition." [PXS:QC]
 is_a: QC:0000009 ! MS MZ aquisition ranges


[Term]
 id: QC:0000017
 name: MS1 injection time
 def: "Contains the accumulation time in the ion trap device used in machine settings during MS aquisition." [PXS:QC]
 is_a: QC:0000004 ! MS aquisition result details
 

[Term]
 id: QC:0000018
 name: MS2 injection time
 def: "Contains the accumulation time in the ion trap device used in machine settings during MS aquisition." [PXS:QC]
 is_a: QC:0000004 ! MS aquisition result details
 

[Term]
 id: QC:0000019
 name: MS1 scan time
 def: "Contains the	average scan time for a MS1 event used in machine settings during MS aquisition." [PXS:QC]
 is_a: QC:0000004 ! MS aquisition result details


[Term]
 id: QC:0000020
 name: MS2 scan time
 def: "Contains the	average scan time for a MS2 event used in machine settings during MS aquisition." [PXS:QC]
 is_a: QC:0000004 ! MS aquisition result details
 
 
[Term]
 id: QC:0000021
 name: lock mass percentage
 def: "Contains the	percentage of found lock masses during MS aquisition." [PXS:QC]
 is_a: QC:0000004 ! MS aquisition result details
 
 
[Term]
 id: QC:0000022
 name: TICs
 def: "The total ion currents detected in each of a series of mass spectra recorded." [PXS:QC]
 is_a: QC:0000048 ! value table

 
[Term]
 id: QC:0000023
 name: TIC slump
 def: "The percentage of tic slumps below 10k." [PXS:QC]
 is_a: QC:0000004 ! MS aquisition result details

remark: TIC plot is MS:1000235
 
[Term]
 id: QC:0000024
 name: detector-saturation
 def: "The average ion saturation of the detector in MS aquisition." [PXS:QC]
 is_a: QC:0000004 ! MS aquisition result details
 

[Term]
 id: QC:0000025
 name: MS identification result details
 def: "The results (e.g. identifications) of the MS identification step of a MS experiment." [PXS:QC]
 is_a: QC:0000001 ! quality parameter


[Term]
 id: QC:0000026
 name: MS id settings
 def: "The settings of the search engine used engine name and further parameters." [PXS:QC]
 is_a: MS:1001249 ! search input details

 
[Term]
 id: QC:0000027
 name: precursor ion tolerance 
 def: "This paramter shows the precursor tolerance that was used for MS/MS identification." [PXS:QC]
 is_a: MS:1001411 ! search tolerance specification
 

[Term]
 id: QC:0000028
 name: product ion tolerance 
 def: "This paramter shows the product ion tolerance that was used for MS/MS identification." [PXS:QC]
 is_a: MS:1001411 ! search tolerance specification
 
 
[Term]
 id: QC:0000029
 name: total number of PSMs
 def: "This number indicates the number of spectra that were given peptide annotations." [PXS:QC]
 is_a: MS:1001405 ! spectrum identification result details
 is_a: QC:0000025 ! MS identification result details


[Term]
 id: QC:0000030
 name: total number of identified peptides
 def: "This number indicates the number peptides that were identified." [PXS:QC]
 is_a: MS:1001405 ! spectrum identification result details
 is_a: QC:0000025 ! MS identification result details

[Term]
 id: QC:0000031
 name: total number of uniquely identified peptides
 def: "This number indicates the number peptides that were uniquely identified." [PXS:QC]
 is_a: MS:1001405 ! spectrum identification result details
 is_a: QC:0000025 ! MS identification result details


[Term]
 id: QC:0000032
 name: total number of identified proteins
 def: "This number indicates the number proteins that were identified." [PXS:QC]
 is_a: MS:1001405 ! spectrum identification result details
 is_a: QC:0000025 ! MS identification result details
 

[Term]
 id: QC:0000033
 name: total number of uniquely identified proteins
 def: "This number indicates the number proteins that were uniquely identified." [PXS:QC]
 is_a: MS:1001405 ! spectrum identification result details
 is_a: QC:0000025 ! MS identification result details
 

[Term]
 id: QC:0000034
 name: total number of modified peptides
 def: "This number indicates the number modified peptide sequences that were identified (after FDR)." [PXS:QC]
 is_a: MS:1001405 ! spectrum identification result details
 is_a: QC:0000025 ! MS identification result details
 

[Term]
 id: QC:0000035
 name: id ratio
 def: "This ratio indicates the number of identified peptides vs. the number of recorded ms2 spectra." [PXS:QC]
 is_a: MS:1001405 ! spectrum identification result details
 is_a: QC:0000025 ! MS identification result details
 

[Term]
 id: QC:0000036
 name: id coverage
 def: "The coverages of distinct sequences for a respective engine." [PXS:QC]
 is_a: MS:1001405 ! spectrum identification result details
 is_a: QC:0000025 ! MS identification result details


[Term]
 id: QC:0000037
 name: total number of missed cleavages
 def: "This number indicates the number missed cleavages that were identified." [PXS:QC]
 is_a: MS:1001405 ! spectrum identification result details
 is_a: QC:0000025 ! MS identification result details
 

[Term]
 id: QC:0000038
 name: mass accuracy
 def: "The values of overall mass accuracy." [PXS:QC]
 is_a: MS:1001105 ! peptide result details
 is_a: QC:0000025 ! MS identification result details
 is_a: QC:0000048 ! value table
 

[Term]
 id: QC:0000039
 name: delta ppm
 def: "The deviation of the precursor ion mass and the theoretical mass of the matched identification." [PXS:QC]
 relationship: has_units UO:0000169 ! parts per million
 is_a: QC:0000025 ! MS identification result details


[Term]
 id: QC:0000040
 name: mean delta ppm
 def: "The mean deviation of the precursor ion masses and the theoretical masses of the matched identifications." [PXS:QC]
 relationship: has_units UO:0000169 ! parts per million
 is_a: QC:0000025 ! MS identification result details


[Term]
 id: QC:0000041
 name: median delta ppm
 def: "The median deviation of the precursor ion masses and the theoretical masses of the matched identifications." [PXS:QC]
 relationship: has_units UO:0000169 ! parts per million
 is_a: QC:0000025 ! MS identification result details


[Term]
 id: QC:0000042
 name: enzyme contamination
 def: "The ratio of  the sum of chymotryptic and tryptic sequences by the number of tryptic sequences." [PXS:QC]
 relationship: has_units UO:0000169 ! parts per million	ratio	 NA
 is_a: QC:0000025 ! MS identification result details


[Term]
 id: QC:0000043
 name: fractional masses plot
 def: "This plot visualizes the theoretical fractional masses (e.g. from the search DB input) vs. the measured fractional masses." [PXS:QC]
 is_a: QC:0000050 ! image plot
 

[Term]
 id: QC:0000044
 name: precursors
 def: "The table of measured precursor ions over RT/mz." [PXS:QC]
 is_a: QC:0000048 ! value table
 

[Term]
 id: QC:0000045
 name: MS quantification result details
 def: "The results (e.g. number of features) of the MS quantification step of a MS experiment." [PXS:QC]
 is_a: QC:0000001 ! quality parameter


[Term]
 id: QC:0000046
 name: number of features
 def: "The number of features reported." [PXS:QC]
 is_a: QC:0000045 ! MS quantification result details
 

[Term]
 id: QC:0000047
 name: features
 def: "The tables of features over RT/mz." [PXS:QC]
 is_a: QC:0000048 ! value table
 is_a: QC:0000045 ! MS quantification result details


[Term]
 id: QC:0000048
 name: value table
 def: "The table contains generic information." [PXS:QC]

[Term]
 id: QC:0000049
 name: generic table
 def: "The table contains generic information." [PXS:QC]
 is_a: QC:0000048 ! value table


[Term]
 id: QC:0000050
 name: image plot
 def: "The plot contains generic information." [PXS:QC]
 
 
[Term]
 id: QC:0000051
 name: generic plot
 def: "The plot contains generic information." [PXS:QC]
 is_a: QC:0000050 ! image plot


[Term]
 id: QC:0000052
 name: id ratio plot
 def: "This plot visualizes the ratio of number of identified peptides vs. the number of recorded ms2 spectra." [PXS:QC]
 is_a: MS:1001405 ! spectrum identification result details
 is_a: QC:0000050 ! image plot
 
 
[Term]
 id: QC:0000053
 name: mass accurracy plot
 def: "This plot visualizes the mass accurracy of identified ms2 spectra." [PXS:QC]
 is_a: MS:1001405 ! spectrum identification result details
 is_a: QC:0000050 ! image plot
  
 
[Term]
 id: QC:0000054
 name: mass accurracy over time plot
 def: "This plot visualizes the mass accurracy over the course of RT." [PXS:QC]
 is_a: MS:1001405 ! spectrum identification result details
 is_a: QC:0000050 ! image plot
 
 
[Term]
 id: QC:0000055
 name: MS experiment heatmap
 def: "This plot visualizes the intensities on RT vs mz." [PXS:QC]
 is_a: QC:0000050 ! image plot
 

[Term]
 id: QC:0000056
 name: RICs
 def: "The reconstructed ion currents (from MS1) detected in each of a series of mass spectra recorded." [PXS:QC]
 is_a: QC:0000048 ! value table


[Term]
 id: QC:0000057
 name: RIC slump
 def: "The percentage of ric slumps below 10k." [PXS:QC]
 is_a: QC:0000004 ! MS aquisition result details

[Term]
 id: QC:0000058
 name: number of identified features
 def: "The number of identified features reported." [PXS:QC]
 is_a: QC:0000045 ! MS quantification result details
 is_a: QC:0000025 ! MS identification result details

[Term]
 id: QC:0000059
 name: IS-1A
 def: "The number of 10fold jumps in MS1 Intensity" [PXS:QC]
 is_a: QC:0000045 ! MS quantification result details
 is_a: QC:0000025 ! MS identification result details

[Term]
 id: QC:0000060
 name: IS-1B
 def: "The number of 10fold dumps in MS1 Intensity" [PXS:QC]
 is_a: QC:0000045 ! MS quantification result details
 is_a: QC:0000025 ! MS identification result details
