Spectrum Mill - Peptide Selector
Spectrum Mill
Peptide String Match
Multiple Sequence Aligner
Databases
MS Digest
Help
Selection
Hide HTML links (better Excel cut/paste)
Saved File Parameters
Generate inclusion or MRM list file
MassHunter QQQ MRM list
MassHunter QQQ MRM Optimizer list
MassHunter Q-TOF MS/MS target list
MassHunter AM Database
Xcalibur inclusion list
From results
Filename:
Run time(min):
List Type:
m/z
uncharged
Precursor Charge Min.:
4
3
2
1
Max.:
4
3
2
1
Precursor m/z Min.:
Max.:
Valid Results to Filter
Proteins to select:
Unidentified + Single peptide
Single peptide
Unidentified
Data directories:
(None Selected)
Digest Parameters
Digest:
Maximum # missed cleavages:
0
1
2
3
4
5
6
7
Product Ion Parameters
Show Product Ion Masses
Criteria for Excluding Peptides
Max. # basic residues (RHK):
13
4
3
2
1
Peptide MH
+
Min.:
Max.:
AA Composition Filtering:
AAs Required :
Disallowed:
Peptide exclusion criteria:
Has nearby cleavage site within
1
2
3
4
5
residues
Contains peptide N-terminal Gln to pyroGlu
Contains protein N-terminus Acetylatable
Contains consensus N-linked glycosylation site
Contains no variable modification
Protein Position Filtering:
Each peptide must contain
at least 1 of the following
positions in the protein
(enter 1 position/line)
Modifications
Fixed:
Variable:
Protein(s) to Select From
Database:
User Protein
MS Digest index numbers:
69470
Select Peptides from only the Database Entries
with the accession numbers below
Allowed delimiters (|:,)
P07288 P02741 P00533 P06702 P16860 P03372
User-supplied sequence:
Paste or type sequence in this field. Delete these instructions first. Tabs, returns, and spaces are ignored. USE CAPITAL LETTERS for UNMODIFIED amino acids or those with FIXED Modifications. Use lower case letters to indicate VARIABLE modifications. Only those Variable Modifications that have been selected will be considered. Do NOT use the letters B, J, O, U, X, or Z. Do NOT use 3-letter code amino acid symbols.
Search Mode
Count Peptide Uniqueness in Database by:
None
Sequence
Species:
Scoring
Penalize rather than exclude
Max reported peptides/protein:
Penalty
Excess basic residues
Nearby cleavage site
Disallowed AA composition
Lower relative uniqueness
Feedback to Karl Clauser
clauser@broadinstitute.org