RAId | Quantitative Molecular Biological Physics (QMBP)

Acceptable formats are: DTA, PKL, MGF(GPM), MSP(NIST or ISB), mzXML, mzML or mzData.
Currently, no spectrum was uploaded to the server. Clear

MS/MS spectrum acquisition mode: "centroid" or "profile".

RAId scoring functions were implemented to resemble RAId DbS score, SEQUEST XCorr, X!Tandem Hyperscore and X!Tandem Kscore plug-in.

For each scoring function other than RAId_score, many heuristics are employed in the original version. Because these heuristics are neither described nor justified in the original papers, RAId does not include those unpublished heuristics while implementing these scoring functions.

Specify the protease which was used to digest the protein mixture.

RAId will use specified series to score peptides from the uploaded file. If nothing is specified, default series are used for each selected scoring function.

Cysteine modification:

[?]

Terminal group molecular weight (Da):

N-terminal:	[?]	C-terminal:	[?]
Molecular weight of the chemical group attached to the peptide N-terminal.		Molecular weight of the chemical group attached to the peptide C-terminal.

PTMs [?]	AA Name Da N-term Anywhere C-term Acetylation +42.010565 Amidation -0.984016 Methylation +14.015650 Di-Methylation +28.031300 Oxidation or Hydroxylation +15.994915 Di-Oxidation +31.989829 Phosphorylation +79.966330 Sulfation +79.956815 A01 GPI-anchor amidated alanine 53.026550 A02 N,N-dimethylalanine 99.068415 A03 N,N,N-trimethylalanine 113.084065 A04 Alanine amide 70.053099 A05 Pentaglycyl murein peptidoglycan amidated alanine 51.010900 A06 N-acetylalanine 113.047680 A07 N-methylalanine 85.052765 A08 N,N-dimethylalanine (Deuterium) 103.093521 C01 Cysteine persulfide 134.981257 C02 3-oxoalanine (Cys) 85.016380 C03 S-nitrosocysteine 131.999350 C04 Cysteine sulfenic acid (-SOH) 119.004101 C05 N-pyruvate 2-iminyl-cysteine 173.014665 C06 N-palmitoyl cysteine 341.238852 C07 S-methylcysteine 117.024836 C08 S-geranylgeranyl cysteine 375.259587 C09 S-palmitoyl cysteine 341.238852 C10 S-farnesyl cysteine 307.196987 C11 Cysteine sulfinic acid (-SO2H) 134.999015 C12 S-diacylglycerol cysteine 679.520947 C13 S-selanylcysteine 182.925708 C14 S-archaeol cysteine 737.671968 C15 S-8alpha-FAD cysteine 886.150670 C16 Pyruvic acid (Cys) 70.005481 C17 Cysteine amide 102.025170 C18 Cysteine methyl disulfide 148.996907 C19 Cysteine methyl ester 117.024836 C20 N-acetylcysteine 145.019751 C21 S-stearoyl cysteine 369.270152 C22 S-12-hydroxyfarnesyl cysteine 323.191901 C23 S-4a-FMN cysteine 559.113801 C24 ADP-ribosylcysteine 644.070295 C25 Phosphocysteine 182.975516 C26 S-6-FMN cysteine 559.113801 C27 Farmesylation 307.196986 C28 Glutathionylation 408.07727 C29 S-Nitrosylation 131.999356 C30 Hex-Glycosylation 265.062015 C31 Carboxymethylation 161.0146499 C32 Carbamidomethylation 160.0306469 C33 Cysteine N-terminal Carbamidomethylation 143.0040979 C34 Pyridylethylation 207.0592089 C35 Cysteine 85.982637 C36 Propionamide 174.04631 C37 4-hydroxyethynylestradiol+CR3 573.207961 C38 4-hydroxyethynylestradiol+CR3(-2H) 571.192311 C39 4-Hydroxyestradiol 389.16608 C40 4-Hydroxyestradiol(-2H) 387.15043 C41 N,N-dimethylcysteine 131.040485 C42 N,N-dimethylcysteine (Deuterium) 135.065592 D01 Cis-14-hydroxy-10,13-dioxo-7-heptadecenoic acid aspartate ester 409.210054 D02 Aspartic acid 1-amide 114.042929 D03 Aspartyl aldehyde 99.032030 D04 N-acetylaspartate 157.037510 D05 4-aspartylphosphate 194.993275 D06 3-hydroxyaspartate 131.021860 D07 3-methylthioaspartic acid 161.014666 D08 N,N-dimethylaspartate 143.058243 D09 N,N-dimethylaspartate (Deuterium) 147.08335 E01 Glutamic acid 1-amide 128.058579 E02 Glutamate methyl ester (Glu) 143.058245 E03 Pyrrolidone carboxylic acid (Glu) 111.032030 E04 4-carboxyglutamate 173.032424 E05 N-acetylglutamate 171.053160 E06 N,N-dimethylglutamate 157.073893 E07 N,N-dimethylglutamate (Deuterium) 161.099 F01 Phenylalanine amide 146.084401 F02 3-phenyllactic acid 148.052433 F03 N-methylphenylalanine 161.084067 F04 N-acetyl-phenylalanine 189.07898 F05 N,N-dimethylphenylalanine 175.099714 F06 N,N-dimethylphenylalanine (Deuterium) 179.124821 G01 Cholesterol glycine ester 425.365766 G02 N-formylglycine 85.016380 G03 1-thioglycine 72.998621 G04 Phosphatidylethanolamine amidated glycine 756.541755 G05 N-acetylglycine 99.032030 G06 Glycine amide 56.037449 G07 N-palmitoyl glycine 295.251131 G08 N-myristoyl glycine 267.219830 G09 N,N-dimethylglycine 85.052764 G10 N,N-dimethylglycine (Deuterium) 89.077871 H01 Pros-8alpha-FAD histidine 920.200398 H02 Tele-methylhistidine 151.074564 H03 Diphthamide 280.177352 H04 Pros-phosphohistidine 217.025244 H05 Histidine amide 136.074898 H06 Pros-methylhistidine 151.074564 H07 Phosphohistidine 217.025244 H08 Tele-8alpha-FMN histidine 591.147879 H09 Methylhistidine 151.074564 H10 Tele-8alpha-FAD histidine 920.200398 H11 Bromohistidine 214.969427 H12 Glucose 299.111743 H13 ADP-Ribosylation 678.119914 H14 N-acetyl-Histidine 179.06948 H15 4-hydroxyethynylestradiol+CR3 607.257688 H16 4-hydroxyethynylestradiol+CR3(-2H) 605.242038 H17 4-Hydroxyestradiol 423.215807 H18 4-Hydroxyestradiol(-2H) 421.200157 H19 N,N-dimethylhistidine 165.090212 H20 N,N-dimethylhistidine (Deuterium) 169.115319 I01 N-methylisoleucine 127.099717 I02 Isoleucine amide 112.100051 I03 N-acetylisoleucine 155.094632 I04 N,N-dimethylisoleucine 141.115364 I05 N,N-dimethylisoleucine (Deuterium) 145.140471 K01 Pyrrolysine 237.147731 K02 Hypusine 215.163381 K03 Lysine amide 127.110951 K04 Lysine methyl ester 142.110617 K05 5-hydroxylysine 144.089882 K06 N6,N6,N6-trimethyl-5-hydroxylysine 186.136832 K07 N,N,N-trimethyllysine 170.141917 K08 N,N-dimethyllysine 156.126267 K09 4,5-dihydroxylysine 160.084796 K10 N6-1-carboxyethyl lysine 200.116096 K11 N6-acetyllysine 170.105532 K12 N6-carboxylysine 172.084796 K13 N6-formyllysine 156.089882 K14 Allysine 127.063333 K15 N6-palmitoyl lysine 366.324633 K16 N6-myristoyl lysine 338.293332 K17 N6-methylated lysine 170.141917 K18 N6-methyllysine 142.110617 K19 Glucose 290.147796 K20 Galactose 290.147796 K21 4-hydroxyethynylestradiol+CR3 598.293739 K22 4-hydroxyethynylestradiol+CR3(-2H) 596.278089 K23 4-Hydroxyestradiol 414.251858 K24 4-Hydroxyestradiol(-2H) 412.236208 K25 TMT-0 352.247445 K26 TMT-2 353.2508 K27 TMT-6/10/11 357.257899 K28 N,N-dimethyllysine (Deuterium) 160.15137 K29 N,N,N,N-tetramethyllysine 184.157567 K30 N.N,N,N-tetramethyllysine (Deuterium) 192.207781 L01 N-methylleucine 127.099717 L02 Leucine methyl ester 127.099717 L03 Leucine amide 112.100051 L04 N-acetyl-Leucine 155.09463 L05 N,N-dimethylleucine 141.115364 L06 N,N-dimethylleucine (Deuterium) 145.140471 M01 N-acetylmethionine 173.051052 M02 N-methylmethionine 145.056137 M03 Methionine sulfone 163.030316 M04 Methionine amide 130.056471 M05 N-formylmethionine 159.035402 M06 Methionine Hydroxylated 147.035402 M07 Methionine Sulfoxide 147.035402 M08 N,N-dimethylmethionine 159.071785 M09 N,N-dimethylmethionine (Deuterium) 163.096892 N01 3-hydroxyasparagine 130.037844 N02 Deamidated asparagine 115.026945 N03 N4-methylasparagine 128.058579 N04 N,N-dimethylasparagine 142.074229 N05 Asparagine amide 113.058913 N06 Aspartyl isopeptide (Asn) 115.026945 N07 ADP-ribosylasparagine 655.104038 N08 N-Acetylglucosamine 317.12231 N09 GlcNAc-GlcNAc 502.19112 N10 GlcNAc-GlcNAc-Man 664.24395 N11 GlcNAc-GlcNAc-Man-Man 826.29678 N12 GlcNAc-GlcNAc-Man-Man-Man 988.34961 N13 Glucose 276.09576 N14 Hex-Glycosylation 276.09576 N15 N-acetyl-Asparagine 156.05349 N16 N,N-dimethylasparagine (Deuterium) 146.099334 P01 Proline amide 96.068750 P02 Hydroxyproline 113.047681 P03 4-hydroxyproline 113.047681 P04 3-hydroxyproline 113.047681 P05 3,4-dihydroxyproline 129.042595 P06 N-methylproline 111.068416 P07 N-acetylproline 139.063331 P08 N,N-dimethylproline 125.084066 P09 N,N-dimethylproline (Deuterium) 129.109171 Q01 Glutamine amide 127.074564 Q02 Omega-hydroxyceramide glutamate ester 888.789442 Q03 Glutamate methyl ester (Gln) 143.058246 Q04 2-methylglutamine 142.074230 Q05 N-acetyl-glutamine 170.06914 Q06 Pyrrolidone carboxylic acid 111.032031 Q07 Deamidated glutamine 129.042596 Q08 Glucose 290.111409 Q09 N-methylglutamine 142.074230 Q10 N,N-dimethylglutamine 156.089878 Q11 N,N-dimethylglutamine (Deuterium) 160.114985 R01 ADP-ribosylarginine 697.162224 R02 5-methylarginine 170.116765 R03 4-hydroxyarginine 172.096030 R04 N,N-dimethylarginine 184.132415 R05 3,4-dihydroxyarginine 188.090944 R06 Arginine amide 155.117099 R07 Citrulline 157.085131 R08 Phosphoarginine 236.067445 R09 N2-acetylarginine 198.111680 R10 Omega-N-methylated arginine 184.132415 R11 Omega-N-methylarginine 170.116765 R12 N5-methylarginine 170.116765 R13 N,N-dimethylarginine (Deuterium) 188.157518 S01 O-palmitoyl serine 325.261696 S02 Serine amide 86.048014 S03 Serine microcin E492 siderophore ester 918.229071 S04 Lactic acid 72.021131 S05 ADP-ribosylserine 628.093139 S06 Phosphoserine 166.998360 S07 O-octanoyl serine 213.136495 S08 3-oxoalanine (Ser) 85.016380 S09 O-decanoyl serine 241.167795 S10 O-acetylserine 129.042595 S11 O-(sn-1-glycerophosphoryl)serine 241.035140 S12 FMN phosphoryl serine 525.126080 S13 D-alanine (Ser) 71.037115 S14 Sulfoserine 166.988845 S15 Pyruvic acid (Ser) 70.005481 S16 N-acetylserine 129.042595 S17 2,3-didehydroalanine (Ser) 69.021465 S18 N-Acetylgalactosamine 274.11649 S19 Beta-D-Gal(1:3)Beta-D-GalNAc 452.164243 S20 Alpha-0-SilicAcid(2:3)Beta-D-Gal(1:3) Beta-D-GalNAc 743.259653 S21 Alpha-0-SilicAcid(2:3)Beta-D-Gal(1:3)Beta-D-GalNAc<-Alpha-0-SilicAcid(2:6) 1050.349986 S22 Fucose 233.08994 S23 Glucose 249.084859 S24 Xylose 221.08994 S25 Hex-Glycosylation 249.084859 S26 N,N-dimethylserine 115.063328 S27 N,N-dimethylserine (Deuterium) 119.088435 T01 Threonine amide 100.063665 T02 N-acetylthreonine 143.058246 T03 2,3-didehydrobutyrine 83.037116 T04 Sulfothreonine 181.004496 T05 2-oxobutanoic acid 84.021132 T06 O-acetylthreonine 143.058246 T07 O-decanoyl threonine 255.183446 T08 O-octanoyl threonine 227.152146 T09 O-palmitoyl threonine 339.277347 T10 Phosphothreonine 181.014011 T11 FMN phosphoryl threonine 539.141731 T12 N-Acetylgalactosamine 304.127064 T13 Beta-D-Gal(1:3)Beta-D-GalNAc 466.179894 T14 Alpha-0-SilicAcid(2:3)Beta-D-Gal(1:3) Beta-D-GalNAc 757.275304 T15 Alpha-0-SilicAcid(2:3)Beta-D-Gal(1:3)Beta-D-GalNAc<-Alpha-0-SilicAcid(2:6) 1064.35947 T16 Glucose 263.10051 T17 Fucose 247.105591 T18 Hex-Glycosylation 263.10051 T19 N,N-dimethylthreonine 129.078979 T20 N,N-dimethylthreonine (Deuterium) 133.104086 V01 N-pyruvate 2-iminyl-valine 169.073896 V02 D-4-hydroxyvaline 115.063332 V03 N-acetylvaline 141.078982 V04 Valine amide 98.084401 V05 Glucose 261.121246 V06 N,N-dimethylvaline 127.099714 V07 N,N-dimethylvaline (Deuterium) 131.124821 W01 3'-geranyl-2',N2-cyclotryptophan 322.204517 W02 3-hydroxytryptophan 202.074231 W03 6'-bromotryptophan 263.989829 W04 6'-chlorotryptophan 220.040344 W05 N2-succinyltryptophan 286.095360 W06 Tryptophan amide 185.095300 W07 Tryptophylquinone 216.053495 W08 N-Linked (Manose) 348.13215 W09 C-Linked (Manose) 348.13215 W10 Hex-Glycosylation 348.13215 W11 N-acetyl-Tryptophan 228.089881 W12 Tryptophan 218.069145 W13 N,N-dimethyltryptophan 214.110613 W14 N,N-dimethyltryptophan (Deuterium) 218.13572 Y01 (Z)-2,3-didehydrotyrosine 161.047681 Y02 Thyroxine 758.676118 Y03 Triiodothyronine 632.779475 Y04 Tyrosine amide 162.079315 Y05 Sulfotyrosine 243.020146 Y06 2,3-didehydrotyrosine 161.047681 Y07 (E)-2,3-didehydrotyrosine 161.047681 Y08 2',4',5'-topaquinone 193.037510 Y09 3',4'-dihydroxyphenylalanine 179.058246 Y10 Phosphotyrosine 243.029661 Y11 O-8alpha-FAD tyrosine 946.204815 Y12 N-methyltyrosine 177.078981 Y13 Nitrated tyrosine 208.048409 Y14 N-acetyltyrosine 205.073896 Y15 Glucose 325.11616 Y16 Hex-Glycosylation 325.116160 Y17 N,N-dimethyltyrosine 191.094629 Y18 N,N-dimethyltyrosine (Deuterium) 195.119736
RAId will use selected posttranslational modifications to score denovo peptides and generate a histogram of the scores.

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QMBP

raidaps

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Upload MS/MS Spectrum [?]	Upload Nothing uploaded...
Acceptable formats are: DTA, PKL, MGF(GPM), MSP(NIST or ISB), mzXML, mzML or mzData. Currently, no spectrum was uploaded to the server. Clear

Scoring function:	[?]
RAId scoring functions were implemented to resemble RAId DbS score, SEQUEST XCorr, X!Tandem Hyperscore and X!Tandem Kscore plug-in. For each scoring function other than RAId_score, many heuristics are employed in the original version. Because these heuristics are neither described nor justified in the original papers, RAId does not include those unpublished heuristics while implementing these scoring functions.

Choose enzyme type:	[?]
Specify the protease which was used to digest the protein mixture.

Amino acids [?]	Ala Cys Asp Glu Phe Gly His Ile Lys Leu Met Asn Pro Gln Arg Ser Thr Val Trp Tyr
RAId will use selected amino acid to score denovo peptides and generate a histogram of the scores.