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Files
Upload spectra file
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Acceptable formats are: DTA, PKL, MGF(GPM), MSP(NIST or ISB), mzXML, mzML, mzData or Thermo Xcalibur(raw).
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Database
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Select a database
NCBI representative
NCBI RefSeq
NCBI Bacteria and Human
NCBI Human gut
NCBI Mouse gut
NCBI Human oral
NCBI Human urine
NCBI Virus
Browse
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A peptide-centric database for pathogen identification.
Families
Genera
Species
Organisms
Distinct peptides
NCBI Bacteria and Human
806
4,124
21,618
21,640
2,784,809,742
NCBI Representative
1,662
5,726
24,595
24,612
4,428,306,761
NCBI RefSeq
2,011
8,825
87,019
429,999
7,715,656,130
NCBI Human oral
96
212
836
4,888
116,957,810
NCBI Human gut
138
539
3,958
44,960
387,856,244
NCBI Human urine
110
209
758
11,858
118,542,436
NCBI Mouse gut
72
163
375
6,526
69,505,602
NCBI Virus
306
2,927
13,896
14,580
20,249,898
GOterm database
No GOterm database...
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NCBI GOterm bacteria
NCBI GOterm bacteria and human
No GOterm analisys
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Select GO term database suitable for peptide-centric database.
Output file prefix
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The prefix is used to name output files created after a job is submitted.
Contaminant fasta file
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MiCId contaminants
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AMR proteins
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NDARO
ResFinder
CARD
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Select one of AMR databases:
NDARO
,
ResFinder
, or
CARD
.
Enzymes
Enzyme type
Trypsin (K,R)
Lys-C (K)
Arg-C (R)
GluC-Phosphate (E,D)
GluC-Bicarbonate (E)
PepsinA (L,F)
Chymotrypsin (F,Y,W,L)
Cyanogen bromide (M)
Cyanogen bromide + Trypsin (M,K,R)
Chymotrypsin + Trypsin (F,Y,W,L,K,R)
V8-DE (N,D,E,Q)
V8-E (E,Q)
Trypsin + PepsinA (K,R,F,L)
Lys-N (K)
Asp-N (D,N)
Asp-N_ambic (D,E)
GluC-Phosphate+Trypsin (K,R,E,D)
GluC-Bicarbonate+Trypsin (K,R,E)
Maximum missed clevage sites
0
1
2
3
4
5
Miscellaneous parametrs
Organism identification level
Infraspecific
Species
Cysteine modification
Unmodified Cysteine
Carboxymethylation (+58 Da)
Carbamidomethylation (+57.02 Da)
Pyridylethylation (+105.06.07 Da)
E-value cutoff
0.01
0.1
1
Statistics
Statistics
R(RAId score)
R(RAId score)
R(Kscore)
R(Hyperscore)
R(XCorr)
R(RAId score)
R(Kscore)
R(Hyperscore)
R(XCorr)
[?]
×
MiCId can assigning statistical significance to identified peptides for different scoring functions by using an extension to the central limit theorem (CLT), Gumbel extreme value distribution (EVD), or by scoring all possible peptides statistics (APPS).
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, MiCId does not include those unpublished heuristics while implementing these scoring functions.
Series to score:
[?]
RAId score:
a-H;
a;
a+H;
b-NH
3
;
b-H
2
O;
b-H;
b;
b+H;
c-H;
c;
c+H;
x-H;
x;
x+H;
y-NH
3
;
y-H
2
O
y-H;
y;
y+H;
z-H;
z;
z+H;
Kscore:
a-H;
a;
a+H;
b-NH
3
;
b-H
2
O;
b-H;
b;
b+H;
c-H;
c;
c+H;
x-H;
x;
x+H;
y-NH
3
;
y-H
2
O
y-H;
y;
y+H;
z-H;
z;
z+H;
Hyperscore:
a-H;
a;
a+H;
b-NH
3
;
b-H
2
O;
b-H;
b;
b+H;
c-H;
c;
c+H;
x-H;
x;
x+H;
y-NH
3
;
y-H
2
O
y-H;
y;
y+H;
z-H;
z;
z+H;
XCorr:
a-H;
a;
a+H;
b-NH
3
;
b-H
2
O;
b-H;
b;
b+H;
c-H;
c;
c+H;
x-H;
x;
x+H;
y-NH
3
;
y-H
2
O
y-H;
y;
y+H;
z-H;
z;
z+H;
MiCId will use specified series to score peptides from the specified database. If nothing is specified, default series are used for each selected scoring function.
Precursor ion
N-Terminal
C-Terminal
TMT Labeling
None
TMT0
TMTpro-zero
TMT2
TMT6
TMT10
TMT11
TMTpro-16
Minimum charge
Maximum charge
Mass tolerance (ppm)
Precursor Ion
Product Ion
This tab is currently under development and is not yet functional.
It works in the standalone version.
Databases list
Organisms database
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Target database
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PTMs
Novel 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
TMT labeling
Curently, in standalone version only.
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