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GPM Cyclone XE, Advanced Search Page
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1. algorithm & taxon
Use X!
Tandem
P3
Hunter
The value set in this control determines which of the X! series search engine will be used to identify your proteins. The choices are:
X! Tandem
- compares spectra to full protein sequences.
X! P3
- compares spectra to proteotypic peptides to improve the search process.
X! Hunter
- compares spectra to annotated spectrum libraries (ASLs).
NOTE: X! P3 and X! Hunter are not available for all species listed below.
cos(θ) >:
parameter name = "spectrum, minimum cosine theta" (
more ...
)
This parameter sets how closely an observed spectrum matches a library spectrum. Values can be between 0 and 1, where 0 is no match at all and 1 is a perfect match.
NOTE: if this value is set to 0, a default value will be used instead.
peptide sequences:
parameter name = "protein, allowed peptides"
This parameter can be used to enter one or more peptide sequences, separated by commas. When sequences are entered, X! Hunter will only search for those peptide sequences, ignoring all other entries in the annotation libraries. The peptide sequences must be represented as continuous strings of uppercase characters. The following are examples of valid entries for this parameter:
VLIPDETVK LIPDEFHR,YGFTQQQQQR,LIVMK
protein accessions:
parameter name = "protein, allowed accessions"
This parameter can be used to enter one or more protein accession numbers, separated by commas. When accession numbers are entered, X! Hunter will only search for peptides from the proteins with those accession numbers, ignoring all other entries in the annotation libraries. The accession numbers must be represented in exactly the same way that they are shown in X! Hunter output displays. The following are examples of valid entries for this parameter:
ENSP00000249364 YLR347C,YLR335W,YGL244W
spectra
ASCII format only
parameter name = "spectrum, path" (
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)
DTA, PKL, MGF, mzData, mzXML or Tandem BIOML format files only
Files may be compressed in either ZIP or GZIP formats.
taxon
Select one or more.
parameter name = "protein, taxon" (
more ...
)
This selection determines which selection of organisms was the source of your proteins. Some common experimental contaminants, such as bovine serum albumin and trypsin are included in each of the current spectrum libraries by default. See the
cRAP
documentation for a complete list.
You may select one or more species from the lists below to perform your search.
Eukaryotes
Prokaryotes
Viruses
1. Reversed sequences: |
no |
yes |
only |
2. Use masses for amino acids with all
15
N:
yes
3. Check parent ions for charges 1, 2 & 3
yes
with peptide log(e) <
0
-1
-2
-3
-4
-5
-6
-7
-8
-9
and protein log(e) <
0
-1
-2
-3
-4
-5
-6
-7
-8
-9
sample information
name:
additional sample information ...
institution:
email:
project:
description:
organelle:
(
GO
)
cell type:
(
CELL
)
cell culture:
(
BRENDA
)
tissue type:
(
BRENDA
)
2. measurement errors
Fragment mass error:
Da
ppm
Parent mass error: +
-
Da
ppm
Isotope error:
yes
no
Fragment type:
monoisotopic
average
3. signal processing
Remove redundant:
yes
no, angle:
(0-90)
Maximum parent charge:
Spectrum synthesis:
yes
no
Noise suppression:
yes
no
Minmum parent M+H:
Minimum fragment m/z:
Total peaks:
Minimum peaks:
Fragment types:
a
b
c
x
y
z
4. protein modifications
Complete modifications (
unimod
)
Set 1
specify your own
Set 2
more sets ...
Set 3
Set 4
Potential modifications (
unimod
)
specify your own
Potential motif:
Use sequence annotations
yes
no
Protein N-terminus:
Da
Protein C-terminus:
Da
5. refinement specification
Refine model:
yes
no
Use sequence annotations
yes
no
Point mutations:
yes
no
Single amino acid polymorphisms:
yes
no
Potential modifications (
unimod
):
round 1
round 2
mods:
motifs:
mods:
motifs:
round 3
round 4
mods:
motifs:
mods:
motifs:
Semi-cleavage:
yes
no
Use these modifications throughout:
yes
no
Unantipated cleaves ([X]|[X]):
yes
no
Potential N-terminus modifications:
Potential C-terminus modifications:
Valid expectation: <
0
-1
-2
-3
-4
-5
-6
-7
-8
-9
6. protein cleavage specification
Cleavage site:
specify your own
Semi-cleavage:
yes
no
N-terminus limit:
none
10
20
30
40
Missed cleavage sites allowed:
Cleavage C-terminal change:
Da
Cleavage N-terminal change:
Da
