Help:
RAId_DbS/deNovo help
Modes:
Compute TNPP
Generate Histogram
Reassign E-values
Database search
Home
Members
Publications
Resources
RAId_deNovo "Reassign E-values" parameters:
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
centroid
profile
[?]
MS/MS spectrum acquisition mode: "centroid" or "profile".
Upload file with list of peptides
[?]
RAId_deNovo will rescore and compute accurate
P
-values and
E
-values for uploaded file with peptides. Acceptable formats are ouput files from Mascot(.dat), SEQUEST(.out), X!Tandem (.xml) search engines, as well as a list of peptides in a flat file.
Currently,
no sequence
was uploaded to the server.
Clear
Calibrate
E
-value for peptides
yes
no
[?]
RAId_deNovo can calibrate the original score reported to compute an
E
-value/
P
-value for the original score base on an
E
-value calibration procedure. More...
Scoring function:
RAId_DbS
Kscore
Hyperscore
XCorr
[?]
RAId_deNovo scoring functions were implemented to resemble RAId DbS score, SEQUEST XCorr, X!Tandem Hyperscore and X!Tandem Kscore plug-in. More...
Series to score:
[?]
RAId_DbS:
a;
b;
c;
b-NH
3
;
b-H
2
O;
x;
y;
z;
y-NH
3
;
y-H
2
O
Kscore:
a;
b;
c;
b-NH
3
;
b-H
2
O;
x;
y;
z;
y-NH
3
;
y-H
2
O
Hyperscore:
a;
b;
c;
b-NH
3
;
b-H
2
O;
x;
y;
z;
y-NH
3
;
y-H
2
O
XCorr:
a;
b;
c;
b-NH
3
;
b-H
2
O;
x;
y;
z;
y-NH
3
;
y-H
2
O
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:
Cysteine (103.009186 Da)
Carboxymethylation (161.014649 Da)
Carbamidomethylation (160.030646 Da)
Pyridylethylation (208.066421 Da)
[?]
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.
Copyright
|
Disclaimer
|
Privacy
|
Accessibility
Maintained by Aleksey Y. Ogurtsov. Last update: November 9, 2009
Upload spectrum data
Select a file:
or Copy/Paste a text data here:
Close
Upload
Clear
Upload file with list of peptides
Select a file:
or Copy/Paste a text data here:
Close
Upload
Clear
