Quantitative Molecular Biological Physics (QMBP)

Upload MS/MS Spectrum [?]
Upload a file with a single spectrum. Acceptable formats are: DTA, MGF, PKL or mzXML. If file contains more than one spectrum only the first spectum will be processed. For dealing with multiple spectra files, please, download the standalone version. Currently, no spectrum was uploaded to the server. Clear

MS/MS spectra mode

[?]

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

Database:	[?]
RAId_DbS will search for peptides in the specified single organism database. To search agains multiple organism specific databases one has to download the standalone version of RAId. More...

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

More parameters

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.

Bounds in the charge state of the precursor ion, allowed range [1,9]:
(If both bounds set to 0 - charge state will be extracted from MS/MS file).

Lower bound:

Upper bound:

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

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

Cysteine modification:	[?] Chemical reduction performed to the side chain of cysteine.
E-value cutoff	[?]
RAId_DbS will report peptides with E-value less than or equal to the specified E-value cutoff.

Series to score [?]

	a;		b;		c;		b-NH₃;		b-H₂O;		b²
	x;		y;		z;		y-NH₃;		y-H₂O;		y²

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

SAPs and PTMs

Novel SAP	[?]
RAId_DbS can search for novel single amino acid polimorphism (SAP) in peptides without any annotated information related to SAP. More...

Number of allowed annotated SAPs/PTMs, allowed range [0,2] per peptide:

SAPs:	[?]	PTMs:	[?]
RAId_DbS will use information about annotated single amino acid polimorphism (SAP) incorporated in the specified database up to the allowed SAPs per peptide.		RAId_DbS will use annotated posttranslational modification (PTM) information incorporated in the specified database up to the allowed PTMs per peptide.
Alowed SAP's [?]	Ala Cys Asp Glu Phe Gly His Ile Lys Leu Met Asn Pro Gln Arg Ser Thr Val Trp Tyr
RAId_DbS can restrict allowed annotated single amino acid polymorphisms (SAPs) to the specified residues. By default, all annotated SAPs are considered. More...

Allowed 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_DbS can restrict allowed annotated posttranslational modifications (PTMs) to the specified modifications. By default, all annotated PTMs are considered. More...