Quantitative Molecular Biological Physics (QMBP)

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MS/MS spectra mode

[?]

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

Scoring function:	[?]
RAId_deNovo scoring functions were implemented to resemble RAId DbS score, SEQUEST XCorr, X!Tandem Hyperscore and X!Tandem Kscore plug-in. More...

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

Series to score: [?]

RAId_DbS:

a; b; c; b-NH₃; b-H₂O; x; y; z; y-NH₃; y-H₂O

Kscore:

a; b; c; b-NH₃; b-H₂O; x; y; z; y-NH₃; y-H₂O

Hyperscore:

a; b; c; b-NH₃; b-H₂O; x; y; z; y-NH₃; y-H₂O

XCorr:

a; b; c; b-NH₃; b-H₂O; x; y; z; y-NH₃; y-H₂O

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

More parameters

Cysteine modification:

[?]

Chemical reduction performed to the side chain of cysteine.

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.

Mass tolerance (Da), allowed range (0,1]:

Parent ion:	[?]	Daughter ion:	[?]
RAId_deNovo will consider all peptides with mass within ± 3×(Parent ion mass tolerance) range of the precursor ion molecular weight.		RAId_deNovo will score all fragment ions with molecular weight within ± 3×(Daughter ion mass tolerance) range of an experimental fragment.

Amino Acids and PTMs

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

PTMs [?]

Name

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

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

208.066421

C35

Cysteine

85.982637

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

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

F01

Phenylalanine amide

146.084401

F02

3-phenyllactic acid

148.052433

F03

N-methylphenylalanine

161.084067

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

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

I01

N-methylisoleucine

127.099717

I02

Isoleucine amide

112.100051

I03

N-acetylisoleucine

155.094632

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

N6,N6,N6-trimethyllysine

170.141917

K08

N6,N6-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

L01

N-methylleucine

127.099717

L02

Leucine methyl ester

127.099717

L03

Leucine amide

112.100051

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

N01

3-hydroxyasparagine

130.037844

N02

Deamidated asparagine

115.026945

N03

N4-methylasparagine

128.058579

N04

N4,N4-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

P01

Proline amide

96.068750

P02

Hydroxyproline

113.047681

P03

4-hydroxyproline

113.047681

P04

N,N-dimethylproline

125.084066

P05

3-hydroxyproline

113.047681

P06

3,4-dihydroxyproline

129.042595

P07

N-methylproline

111.068416

P08

N-acetylproline

139.063331

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

N5-methylglutamine

142.074230

Q06

Pyrrolidone carboxylic acid

111.032031

Q07

Deamidated glutamine

129.042596

Q08

Glucose

290.111409

R01

ADP-ribosylarginine

697.162224

R02

5-methylarginine

170.116765

R03

4-hydroxyarginine

172.096030

R04

Symmetric dimethylarginine

184.132415

R05

3,4-dihydroxyarginine

188.090944

R06

Arginine amide

155.117099

R07

Asymmetric dimethylarginine

184.132415

R08

Citrulline

157.085131

R09

Phosphoarginine

236.067445

R10

N2-acetylarginine

198.111680

R11

Omega-N-methylated arginine

184.132415

R12

Omega-N-methylarginine

170.116765

R13

N5-methylarginine

170.116765

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

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

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

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

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

325.11616

RAId_deNovo will use selected posttranslational modifications to score denovo peptides and generate a histogram of the scores.