deNovo score distribution parameters:

File name (DTA, MGF, PKL or mzXML):
File with list of peptides (\n - separator):
Molecular weight (Da):
Scoring function:		RAId_DbS Weighted peak count Hyperscore XCorr Kscore
Length deconvolution:		On Off
Choose enzyme type:		No enzyme Trypsin (K,R) Lys-C (K) Arg-C (R) GluC-Phosphate (E,D) GluC-Bicarbonate (E) Pepsin (L,F) Chymotrypsin (F,Y,W)
Terminal group molecular weight (Da):
N-terminal:		C-terminal:
Mass tolerance (Da), allowed range (0,1]:
Parent ion:		Daughter ion:
Retention time parameters:
Deconvolution:	nothing to do 300A Pore Column 100A Pore Column	Error:
Slope:		Interception:
Amino acids:	Ala Cys Asp Glu Phe Gly His Ile Lys Leu Met Asn Pro Gln Arg Ser Thr Val Trp Tyr
PTMs:	AA Name Da Ala GPI-anchor amidated alanine 53.02655 Ala N,N-dimethylalanine 99.068415 Ala N,N,N-trimethylalanine 113.084065 Ala Alanine amide 70.053099 Ala Pentaglycyl murein peptidoglycan amidated alanine 51.0109 Ala N-acetylalanine 113.04768 Ala N-methylalanine 85.052765 Cys Cysteine persulfide 134.981257 Cys 3-oxoalanine Cys 85.01638 Cys S-nitrosocysteine 131.99935 Cys Cysteine sulfenic acid -SOH 119.004101 Cys N-pyruvate 2-iminyl-cysteine 173.014665 Cys N-palmitoyl cysteine 341.238852 Cys S-methylcysteine 117.024836 Cys S-geranylgeranyl cysteine 375.259587 Cys S-palmitoyl cysteine 341.238852 Cys S-farnesyl cysteine 307.196987 Cys Cysteine sulfinic acid -SO2H 134.999015 Cys S-diacylglycerol cysteine 679.520947 Cys S-selanylcysteine 182.925708 Cys S-archaeol cysteine 737.671968 Cys S-8alpha-FAD cysteine 886.15067 Cys Pyruvic acid Cys 70.005481 Cys Cysteine amide 102.02517 Cys Cysteine methyl disulfide 148.996907 Cys Cysteine methyl ester 117.024836 Cys N-acetylcysteine 145.019751 Cys S-stearoyl cysteine 369.270152 Cys S-12-hydroxyfarnesyl cysteine 323.191901 Cys S-4a-FMN cysteine 559.113801 Cys ADP-ribosylcysteine 644.070295 Cys Phosphocysteine 182.975516 Cys S-6-FMN cysteine 559.113801 Cys Farmesylation 307.196986 Cys Glutathionylation 408.07727 Cys S-Nitrosylation 131.999356 Cys Hex-Glycosylation 265.062015 Cys Carboxymethylation 161.0146499 Cys Carbamidomethylation 160.0306469 Cys Pyridylethylation 208.0664215 Asp Cis-14-hydroxy-10,13-dioxo-7-heptadecenoic acid aspartate ester 409.210054 Asp Aspartic acid 1-amide 114.042929 Asp Aspartyl aldehyde 99.03203 Asp N-acetylaspartate 157.03751 Asp 4-aspartylphosphate 194.993275 Asp 3-hydroxyaspartate 131.02186 Asp 3-methylthioaspartic acid 161.014666 Glu Glutamic acid 1-amide 128.058579 Glu Glutamate methyl ester Glu 143.058245 Glu Pyrrolidone carboxylic acid Glu 111.03203 Glu 4-carboxyglutamate 173.032424 Glu N-acetylglutamate 171.05316 Phe Phenylalanine amide 146.084401 Phe 3-phenyllactic acid 148.052433 Phe N-methylphenylalanine 161.084067 Gly Cholesterol glycine ester 425.365766 Gly N-formylglycine 85.01638 Gly 1-thioglycine 72.998621 Gly Phosphatidylethanolamine amidated glycine 756.541755 Gly N-acetylglycine 99.03203 Gly Glycine amide 56.037449 Gly N-palmitoyl glycine 295.251131 Gly N-myristoyl glycine 267.21983 His Pros-8alpha-FAD histidine 920.200398 His Tele-methylhistidine 151.074564 His Diphthamide 280.177352 His Pros-phosphohistidine 217.025244 His Histidine amide 136.074898 His Pros-methylhistidine 151.074564 His Phosphohistidine 217.025244 His Tele-8alpha-FMN histidine 591.147879 His Methylhistidine 151.074564 His Tele-8alpha-FAD histidine 920.200398 His Bromohistidine 214.969427 His Glucose 299.111743 His ADP-Ribosylation 678.119914 Ile N-methylisoleucine 127.099717 Ile Isoleucine amide 112.100051 Ile N-acetylisoleucine 155.094632 Lys Pyrrolysine 237.147731 Lys Hypusine 215.163381 Lys Lysine amide 127.110951 Lys Lysine methyl ester 142.110617 Lys 5-hydroxylysine 144.089882 Lys N6,N6,N6-trimethyl-5-hydroxylysine 186.136832 Lys N6,N6,N6-trimethyllysine 170.141917 Lys N6,N6-dimethyllysine 156.126267 Lys 4,5-dihydroxylysine 160.084796 Lys N6-1-carboxyethyl lysine 200.116096 Lys N6-acetyllysine 170.105532 Lys N6-carboxylysine 172.084796 Lys N6-formyllysine 156.089882 Lys Allysine 127.063333 Lys N6-palmitoyl lysine 366.324633 Lys N6-myristoyl lysine 338.293332 Lys N6-methylated lysine 170.141917 Lys N6-methyllysine 142.110617 Lys Glucose 290.147796 Lys Galactose 290.147796 Leu N-methylleucine 127.099717 Leu Leucine methyl ester 127.099717 Leu Leucine amide 112.100051 Met N-acetylmethionine 173.051052 Met N-methylmethionine 145.056137 Met Methionine sulfone 163.030316 Met Methionine amide 130.056471 Met N-formylmethionine 159.035402 Asn 3-hydroxyasparagine 130.037844 Asn Deamidated asparagine 115.026945 Asn N4-methylasparagine 128.058579 Asn N4,N4-dimethylasparagine 142.074229 Asn Asparagine amide 113.058913 Asn Aspartyl isopeptide Asn 115.026945 Asn ADP-ribosylasparagine 655.104038 Asn N-Acetylglucosamine 317.12231 Asn GlcNAc-GlcNAc 502.19112 Asn GlcNAc-GlcNAc-Man 664.24395 Asn GlcNAc-GlcNAc-Man-Man 826.29678 Asn GlcNAc-GlcNAc-Man-Man-Man 988.34961 Asn Glucose 276.09576 Asn Hex-Glycosylation 276.09576 Pro Proline amide 96.06875 Pro Hydroxyproline 113.047681 Pro 4-hydroxyproline 113.047681 Pro N,N-dimethylproline 125.084066 Pro 3-hydroxyproline 113.047681 Pro 3,4-dihydroxyproline 129.042595 Pro N-methylproline 111.068416 Pro N-acetylproline 139.063331 Gln Glutamine amide 127.074564 Gln Omega-hydroxyceramide glutamate ester 888.789442 Gln Glutamate methyl ester Gln 143.058246 Gln 2-methylglutamine 142.07423 Gln N5-methylglutamine 142.07423 Gln Pyrrolidone carboxylic acid 111.032031 Gln Deamidated glutamine 129.042596 Gln Glucose 290.111409 Arg ADP-ribosylarginine 697.162224 Arg 5-methylarginine 170.116765 Arg 4-hydroxyarginine 172.09603 Arg Symmetric dimethylarginine 184.132415 Arg 3,4-dihydroxyarginine 188.090944 Arg Arginine amide 155.117099 Arg Asymmetric dimethylarginine 184.132415 Arg Citrulline 157.085131 Arg Phosphoarginine 236.067445 Arg N2-acetylarginine 198.11168 Arg Omega-N-methylated arginine 184.132415 Arg Omega-N-methylarginine 170.116765 Arg N5-methylarginine 170.116765 Ser O-palmitoyl serine 325.261696 Ser Serine amide 86.048014 Ser Serine microcin E492 siderophore ester 918.229071 Ser Lactic acid 72.021131 Ser ADP-ribosylserine 628.093139 Ser Phosphoserine 166.99836 Ser O-octanoyl serine 213.136495 Ser 3-oxoalanine Ser 85.01638 Ser O-decanoyl serine 241.167795 Ser O-acetylserine 129.042595 Ser O-sn-1-glycerophosphorylserine 241.03514 Ser FMN phosphoryl serine 525.12608 Ser D-alanine Ser 71.037115 Ser Sulfoserine 166.988845 Ser Pyruvic acid Ser 70.005481 Ser N-acetylserine 129.042595 Ser 2,3-didehydroalanine Ser 69.021465 Ser N-Acetylgalactosamine 274.11649 Ser Beta-D-Gal1:3Beta-D-GalNAc 452.164243 Ser Alpha-0-SilicAcid2:3Beta-D-Gal1:3 Beta-D-GalNAc 743.259653 Ser Alpha-0-SilicAcid2:3Beta-D-Gal1:3Beta-D-GalNAc<-Alpha-0-SilicAcid2:6 1050.349986 Ser Fucose 233.08994 Ser Glucose 249.084859 Ser Xylose 221.08994 Ser Hex-Glycosylation 249.084859 Thr Threonine amide 100.063665 Thr N-acetylthreonine 143.058246 Thr 2,3-didehydrobutyrine 83.037116 Thr Sulfothreonine 181.004496 Thr 2-oxobutanoic acid 84.021132 Thr O-acetylthreonine 143.058246 Thr O-decanoyl threonine 255.183446 Thr O-octanoyl threonine 227.152146 Thr O-palmitoyl threonine 339.277347 Thr Phosphothreonine 181.014011 Thr FMN phosphoryl threonine 539.141731 Thr N-Acetylgalactosamine 304.127064 Thr Beta-D-Gal1:3Beta-D-GalNAc 466.179894 Thr Alpha-0-SilicAcid2:3Beta-D-Gal1:3 Beta-D-GalNAc 757.275304 Thr Alpha-0-SilicAcid2:3Beta-D-Gal1:3Beta-D-GalNAc<-Alpha-0-SilicAcid2:6 1064.35947 Thr Glucose 263.10051 Thr Fucose 247.105591 Thr Hex-Glycosylation 263.10051 Val N-pyruvate 2-iminyl-valine 169.073896 Val D-4-hydroxyvaline 115.063332 Val N-acetylvaline 141.078982 Val Valine amide 98.084401 Val Glucose 261.121246 Trp 3'-geranyl-2',N2-cyclotryptophan 322.204517 Trp 3-hydroxytryptophan 202.074231 Trp 6'-bromotryptophan 263.989829 Trp 6'-chlorotryptophan 220.040344 Trp N2-succinyltryptophan 286.09536 Trp Tryptophan amide 185.0953 Trp Tryptophylquinone 216.053495 Trp N-Linked Manose 348.13215 Trp C-Linked Manose 348.13215 Trp Hex-Glycosylation 348.13215 Tyr Z-2,3-didehydrotyrosine 161.047681 Tyr Thyroxine 758.676118 Tyr Triiodothyronine 632.779475 Tyr Tyrosine amide 162.079315 Tyr Sulfotyrosine 243.020146 Tyr 2,3-didehydrotyrosine 161.047681 Tyr E-2,3-didehydrotyrosine 161.047681 Tyr 2',4',5'-topaquinone 193.03751 Tyr 3',4'-dihydroxyphenylalanine 179.058246 Tyr Phosphotyrosine 243.029661 Tyr O-8alpha-FAD tyrosine 946.204815 Tyr N-methyltyrosine 177.078981 Tyr Nitrated tyrosine 208.048409 Tyr N-acetyltyrosine 205.073896 Tyr Glucose 325.11616 Tyr Hex-Glycosylation 325.11616
Series to score:	a b c b-NH3 b-H2O b2 x y z y-NH3 y-H2O y2