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1 | | -#Parent mass tolerance |
| 1 | +# Parent mass tolerance |
2 | 2 | # Examples: 2.5Da or 30ppm |
3 | 3 | # Use comma to set asymmetric values, for example "0.5Da,2.5Da" will set 0.5Da to the left (expMass<theoMass) and 2.5Da to the right (expMass>theoMass) |
4 | 4 | PrecursorMassTolerance=20ppm |
5 | 5 |
|
6 | | -#Max Number of Modifications per peptide |
| 6 | +# Max Number of Modifications per peptide |
7 | 7 | # If this value is large, the search will be slow |
8 | 8 | NumMods=3 |
9 | 9 |
|
10 | | -#Modifications (see below for examples) |
| 10 | +# Modifications (see below for examples) |
11 | 11 | StaticMod=229.1629, *, fix, N-term, TMT6plex |
12 | 12 | StaticMod=229.1629, K, fix, any, TMT6plex |
13 | 13 | StaticMod=C2H3N1O1, C, fix, any, Carbamidomethyl # Fixed Carbamidomethyl C (alkylation, +57.0215) |
14 | 14 |
|
15 | 15 | DynamicMod=O1, MP, opt, any, Oxidation # Oxidized methionine and proline |
16 | 16 |
|
17 | | -#Fragmentation Method |
| 17 | +# Fragmentation Method |
18 | 18 | # 0 means as written in the spectrum or CID if no info (Default) |
19 | 19 | # 1 means CID |
20 | 20 | # 2 means ETD |
21 | 21 | # 3 means HCD |
22 | 22 | # 4 means Merge spectra from the same precursor (e.g. CID/ETD pairs, CID/HCD/ETD triplets) |
23 | 23 | FragmentationMethodID=0 |
24 | 24 |
|
25 | | -#Instrument ID |
| 25 | +# Instrument ID |
26 | 26 | # 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra |
27 | 27 | # 1 means High-res LTQ (Default for HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap, Lumos, and QEHFX instruments |
28 | 28 | # 2 means TOF |
29 | 29 | # 3 means Q-Exactive |
30 | 30 | InstrumentID=1 |
31 | 31 |
|
32 | | -#Enzyme ID |
33 | | -# 0 means No enzyme used |
34 | | -# 1 means Trypsin (Default); use this along with NTT=0 for a no-enzyme search of a tryptically digested sample |
35 | | -# 2: Chymotrypsin, 3: Lys-C, 4: Lys-N, 5: Glu-C, 6: Arg-C, 7: Asp-N, 8: alphaLP, 9: No Enzyme (for peptidomics) |
| 32 | +# Enzyme ID |
| 33 | +# 0 means unspecific cleavage (cleave after any residue) |
| 34 | +# 1 means Trypsin (Default); optionally use this along with NTT=0 for a no-enzyme-specificity search of a tryptically digested sample |
| 35 | +# 2: Chymotrypsin, 3: Lys-C, 4: Lys-N, 5: Glu-C, 6: Arg-C, 7: Asp-N, 8: alphaLP, 9: No Cleavage (for peptidomics) |
36 | 36 | EnzymeID=1 |
37 | 37 |
|
38 | | -#Isotope error range |
| 38 | +# Isotope error range |
39 | 39 | # Takes into account of the error introduced by choosing non-monoisotopic peak for fragmentation. |
40 | 40 | # Useful for accurate precursor ion masses |
41 | 41 | # Ignored if the parent mass tolerance is > 0.5Da or 500ppm |
42 | 42 | # The combination of -t and -ti determins the precursor mass tolerance. |
43 | 43 | # e.g. "-t 20ppm -ti -1,2" tests abs(exp-calc-n*1.00335Da)<20ppm for n=-1, 0, 1, 2. |
44 | 44 | IsotopeErrorRange=-1,1 |
45 | 45 |
|
46 | | -#Number of tolerable termini |
| 46 | +# Number of tolerable termini |
47 | 47 | # The number of peptide termini that must have been cleaved by the enzyme (default 1) |
48 | 48 | # For trypsin, 2 means fully tryptic only, 1 means partially tryptic, and 0 means no-enzyme search |
49 | 49 | NTT=1 |
50 | 50 |
|
51 | | -#Target/Decoy search mode |
| 51 | +# Control N-terminal methionine cleavage |
| 52 | +# 0 means to consider protein N-term Met cleavage (Default) |
| 53 | +# 1 means to ignore protein N-term Met cleavage |
| 54 | +IgnoreMetCleavage=0 |
| 55 | + |
| 56 | +# Target/Decoy search mode |
52 | 57 | # 0 means don't search decoy database (default) |
53 | 58 | # 1 means search decoy database to compute FDR (source FASTA file must be forward-only proteins) |
54 | 59 | TDA=1 |
55 | 60 |
|
56 | | -#Number of Threads (by default, uses all available cores) |
| 61 | +# Number of Threads (by default, uses all available cores) |
57 | 62 | NumThreads=All |
58 | 63 |
|
59 | | -#Minimum peptide length to consider |
| 64 | +# Minimum peptide length to consider |
60 | 65 | MinPepLength=6 |
61 | 66 |
|
62 | | -#Maximum peptide length to consider |
| 67 | +# Maximum peptide length to consider |
63 | 68 | MaxPepLength=50 |
64 | 69 |
|
65 | | -#Minimum precursor charge to consider (if not specified in the spectrum) |
| 70 | +# Minimum precursor charge to consider (if not specified in the spectrum) |
66 | 71 | MinCharge=2 |
67 | 72 |
|
68 | | -#Maximum precursor charge to consider (if not specified in the spectrum) |
| 73 | +# Maximum precursor charge to consider (if not specified in the spectrum) |
69 | 74 | MaxCharge=5 |
70 | 75 |
|
71 | | -#Number of matches per spectrum to be reported |
72 | | -#If this value is greater than 1 then the FDR values computed by MS-GF+ will be skewed by high-scoring 2nd and 3rd hits |
| 76 | +# Number of matches per spectrum to be reported |
| 77 | +# If this value is greater than 1, the FDR values computed by MS-GF+ will be skewed by high-scoring 2nd and 3rd hits |
73 | 78 | NumMatchesPerSpec=1 |
74 | 79 |
|
75 | | -#Amino Acid Modification Examples |
76 | | -# Specific static modifications using one or more StaticMod= entries |
77 | | -# Specific dynamic modifications using one or more DynamicMod= entries |
| 80 | +# Amino Acid Modification Examples |
| 81 | +# Specify static modifications using one or more StaticMod= entries |
| 82 | +# Specify dynamic modifications using one or more DynamicMod= entries |
78 | 83 | # Modification format is: |
79 | | -# Mass or CompositionStr, Residues, ModType, Position, Name (all the five fields are required). |
| 84 | +# Mass or CompositionString, Residues, ModType, Position, Name (all five fields are required). |
| 85 | +# CompositionString can only contain a limited set of elements, primarily C H N O S or P |
| 86 | +# |
80 | 87 | # Examples: |
81 | 88 | # C2H3N1O1, C, fix, any, Carbamidomethyl # Fixed Carbamidomethyl C (alkylation) |
82 | 89 | # O1, M, opt, any, Oxidation # Oxidation M |
83 | | -# 15.994915, M, opt, any, Oxidation # Oxidation M (mass is used instead of CompositionStr) |
| 90 | +# 15.994915, M, opt, any, Oxidation # Oxidation M (mass is used instead of CompositionString) |
84 | 91 | # H-1N-1O1, NQ, opt, any, Deamidated # Negative numbers are allowed. |
85 | 92 | # CH2, K, opt, any, Methyl # Methylation K |
86 | 93 | # C2H2O1, K, opt, any, Acetyl # Acetylation K |
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