Spectrum Mill - MS/MS Autovalidation
Spectrum Mill
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Data Directories
(None Selected)
Search result files:
*.spo
Validation Parameters
Strategy:
Fixed thresholds
Auto thresholds
Auto thresholds - discriminant
Mode:
Protein details
Peptide
Protein polishing
VM site polishing
Peptide global FDR
Peptide local FDR
Optimize score & R1-R2 score thresholds with max FDR:
% across each:
LC run
Directory
Group proteins across all directories
(unexpanded subgroups)
Group VM sites across all directories, and group missed cleavages containing the same VM site
Variable modification site localization
Method for applying combined thresholds of VM site Score and Minimum number of directories:
Retain VM sites above both thresholds (more strict)
Retain VM sites above either threshold (less strict - retains recurrently observed VM sites with scores below threshold)
Minimum number of directories VM site is observed in:
Minimum VM site score:
Method for applying combined thresholds of Protein Score and Minimum number of directories:
Retain proteins above both thresholds (more strict)
Retain proteins above either threshold (less strict - retains recurrently observed proteins with scores below threshold)
Minimum number of directories protein group is observed in:
Minimum protein score:
Local
Global
FDR:
%
Automatically raise minimum protein score to yield maximum protein FDR:
%
Peptide FDR for validated proteins:
%
Calculate FDR using reversed hits
Precursor charge range:
to
Min Sequence Length:
1
4
5
6
7
8
9
Max Sequence Length:
4
5
6
7
8
9
35
40
60
99
Min Backbone Cleavage Score:
0
3
4
5
Required AAs: Disallowed AAs:
Required species:
Filtering
None (ppm)
None (SC/pI)
Automatic variable range for each run
Auto precursor mass error
Auto SCX Solution Charge, pH3
Auto OGE/IEF peptide pI
Fixed range for all runs
Fixed precursor mass error
Fixed Solution Charge
Fixed peptide pI
Low
High
ppm
Low
High
Low
High
Protein Rules
Rule
Precursor
Charge
Score
Threshold
% SPI
Threshold
Fwd - Rev Score
Threshold
Rank 1-2 score
Threshold
1.
1
2
3
4
5
6
7
8
9
10
2.
1
2
3
4
5
6
7
8
9
10
3.
1
2
3
4
5
6
7
8
9
10
4.
1
2
3
4
5
6
7
8
9
10
5.
1
2
3
4
5
6
7
8
9
10
6.
1
2
3
4
5
6
7
8
9
10
Results