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Copy pathBatch.txt
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Batch.txt
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; Set weight mode
WEIGHTMODE=AVERAGE
; Set Standard Deviation mode
STDDEVMODE=OFF
; Return capitalized (formatted) formulas
CAPITALIZED=ON
fecl3-6h2o
; Expand abbreviations
EXPANDABBREVIATIONS=ON
etoac
; Don't display the source formula
MWSHOWSOURCEFORMULA=OFF
etoac
; Don't display the weight
SHOWWEIGHT=OFF
etoac
; Convert to empirical formula
; Note: no need to use EXPANDABBREVIATIONS=OFF
EMPIRICAL=ON
fecl3-6h2o
etoac
; Re-enable display of the source formula
MWSHOWSOURCEFORMULA=ON
UreaC4(NH2)4Ca
; Convert amino acid sequence from 1 letter to 3 letter sequence
AACONVERT3TO1=ON
GluGlaPheLeu
Val-Ile-Arg
AASPACEEVERY10=ON
; For really long sequences, can disable display of the source sequence
AASHOWSEQUENCEBEINGCONVERTED=OFF
GluGlaPheLeuVAlIleArgPheTyrMetCysValGluGlaGluGlaPheLeuVAlIleArgPheTyrMetCysValGluGla
AACONVERT1TO3=ON
FLEELYR
MLTSCDEEF
AASHOWSEQUENCEBEINGCONVERTED=ON
AA1TO3USEDASH=ON
FLEELYR
; To re-enable plain molecular weight computation, use MW=
; Note: this will also disable EMPIRICAL= and EXPANDABBREVIATIONS=
; Further, it will automatically re-enable SHOWWEIGHT
MW=
C4N8OH2
; Compute the mass of peptides given in 1-letter notation
ONELETTERPEPTIDEWEIGHTMODE=ON
FLEELYR
MLTSCDEEF
; Don't show the source formula when computing the peptide's mass
MWSHOWSOURCEFORMULA=OFF
MLTSCDEEF
; Enable formula finder mode using FF=, specifying the elements to use in searching
; Can also specify weight mode, maximum number of hits, and tolerance
FF=C,H,N,O,Cl,Bpy
WEIGHTMODE=ISOTOPIC
MAXHITS=5
TOLERANCE=0.05
403.84
300.58
; The tolerance can be changed
TOLERANCE=0.02
403.885
; The maximum number of hits can be changed
MAXHITS=10
632.43
; The search elements can be changed
FF=N,Br,H,Li
MAXHITS=2
389.32
; Can disable verbose output
VERBOSEMODE=OFF
; Additionally, could enable echo of comments
ECHOCOMMENTS=ON
; Switching back (this comment is in the source file)
MW=
MWSHOWSOURCEFORMULA=ON
NH2
C6H5Cl
^13C6H5Cl
WEIGHTMODE=AVERAGE
FeCl3-6H2O
; So is this one, along with the 3 blank lines above
MWSHOWSOURCEFORMULA=OFF
NH2
C6H5Cl
^13C6H5Cl
FeCl3-6H2O
VERBOSEMODE=ON
DELIMETER=<SPACE>
CAPITALIZED=on
c6h5cl
DELIMETER=,
c6h5cl
ECHOCOMMENTS=OFF
; Enable Isotopic Distribution Mode
ISOTOPICDISTRIBUTION=ON
; Simply enter a formula to obtain the isotopic distribution
CH2(CH2)7CH2Br
; Change the charge state with the following command
ISOTOPICDISTRIBUTIONCHARGE=2
CH2(CH2)7CH2Br
; Disable adding a proton when computing m/z
ISOTOPICDISTRIBUTIONADDPROTON=False
CH2(CH2)7CH2Br