Laboratory of Mass Spectrometry and Gaseous Ion Chemistry
PROWL
ProFound
ProteinInfo
PeptideMap
X! Tandem
X! Hunter
GPMDB
   
PROWL
Chait Lab

The Rockefeller University
The Rockefeller University
1230 York Avenue,
New York, NY 10021
(212) 327-8000


National Center of Research Resources
National Resource
for the Mass Spectrometric
Analysis of Biological
Macromolecules

PeptideMap - Help

Amino Acid Position (Local Modifications)
The position of the amino acid where the modification takes place. NOTE: The first amino acid in the chain should be considered as having position 1.
Amino Acid Sequence
The sequence of the protein to be used in the mapping. To specify an amino acid sequence the one letter codes for the amino acids should be used. All non-letter characters will be ignored except for '/' and '\' which will be interpreted as the end of a peptide chain.

Examples:

A single peptide chain:

MNYLRRRLSDSNFMANLPNGYMTDLQRPQPPPPPPAAPSPGATTGPATATAERASSAAP

or
      1    *   10    *    20    *   30    *    40    *   50
    1 MNYLRRRLSDSNFMANLPNGYMTDLQRPQPPPPPPAAPSPGATTGPATAT
   51 AERASSAAP

Two peptide chains:

MNYLRRRLSDSNFMANLPNGY/MTDLQRPQPPPPPPAAPSPGATT

or
      1    *   10    *    20    *   30    *    40    *   50
    1 MNYLRRRLSDSNFMANLPNGY/
   22 MTDLQRPQPPPPPPAAPSPGATT
or
      1    *   10    *    20    *   30    *    40    *   50
 CHAIN A:
    1 MNYLRRRLSDSNFMANLPNGY/
 CHAIN B:
   22 MTDLQRPQPPPPPPAAPSPGATT

Note: The numbers are only for your convenience, the chains will always be considered as starting at 1.
Average Masses
List the average masses here, separated by a space. All characters are ignored except numbers (0-9) and decimal point (.).
Chain (Local Modifications)
The protein chain number where the modification takes place. NOTE: The first chain should be considered as having chain number 0.
Charge State (of masses)
If MH+ is selected, the mass of H is subtracted from each mass before the comparison; if M is selected, the masses are not changed.
Chemical Formula Format
The following expression describes the format of chemical formulas accepted by PeptideMap. Only letters (Aa-Zz), numbers (0-9), plus(+) and minus(-) are recognized:

          [+|-]element[[#occurence]..[element[#occurence]]]
CHEMISTRY
In this section, enter information about the enzymes that are to be used in the protein digestion.
Cleave Sites (user-defined enzyme)
The cleave sites of the user-defined enzyme. To select more than one site, hold the control key down while clicking on your choices.
Complete Global Modifications (pre-defined)
Complete global modifications add the corresponding modification formula to every occurance of the specified amino acid(s). To select more than one, hold the control key down while clicking on your choices. The following table indications the meanings of the modification names in the list box.


Name Site(s) Formula
4-vinyl-pyridine (Cys) C +C7H7N
Acrylamide (Cys) C +C3H5ON
Iodoacetamide (Cys) C +C2H3ON
Iodoacetic acid (Cys) C +C2H2O2
Performic acid (Cys+O3) C +O3
Performic acid (Met+O2) M +O2
Performic acid (Met+O) M +O

CROSS LINK 
In this section, enter information about the cross link.  Only one cross link is currently supported .  Choose a pre-defined cross link from the list, or specify your own cross link parameters.  The following table indicates the meanings of the cross link names in the list box.

Name Cross Linking Reagent Site(s) 1 Mod. 1 Site(s) 2 Mod. 2
Disulfide - C -H C -H
Cross Linking Reagent
Enter the formula for the cross linking reagent in the text box.
Do not cleave near Proline (user-defined enzyme)
Check this box if the enzyme will not cut next to Proline.
File name (Save Settings)
Enter the name of the file where the current version of the PeptideMap form (with all your current input data) should be saved. Do not enter a directory, because the file will be created in the prowl directory of KNEXUS. To access the file, click on the PeptideMap link from inside Knexus, then change the html file name in the location bar of your browser to the name entered in this text box.
Global Modification Site (user-defined)
The amino acid(s) to which the modification will be added. To select more than one site, hold down the control key while clicking on your choices.
GLOBAL MODIFICATIONS
In this section, enter information about the global modifications to the protein. Global modifications are modifications to 0 or more occurances of an amino acid, called the specificity of the modification. The modifications can be applied to all of the occurances of the amino acid(s) in the sequence (complete modification) or some (i.e. 0 or more) of them (partial modification). If you would like to specify the exact range of the number of occurances to which the modification should apply, add a user-defined modification.
How to remove our company logo for your presentation
Our company logo and name can be removed only when there is a strict restriction on displaying company logos at academic conference presentations. Please contact Proteometrics to obtain a patch for removing the company logo and name.
Link Site(s)
Select the amino acids to which the cross link attaches on one of the sides. To select more than one, hold down the control key while making your choices.

LOCAL MODIFICATIONS
In this section, enter information about the local modifications to the protein. Local modifications are modifications to the amino acid at a specified position in the protein. You must specify the chain number (starting at chain 0) and the amino acid position (starting at pos. 1) of the modification. The minimum and maximum occupancy refer to the number of modification at the specified position.  Once the parameters have been specified, click the "Add Modification" button to add the local modification to the list on the right.  The user-defined local modifications that are in the list on the right will be applied in the program.  If you make a mistake, a local modification(s) may be removed from the box on the right by highlighting it and clicking the "Remove Modification" button.

Mass Tolerance
Enter the error range for the corresponding masses. You can enter an error for both the monoisotopic and average masses. There are three choices for the units: Daltons (Da), percent (%) and parts-per-million (ppm).
Masses
In this section, enter the average and monoisotopic masses to be mapped to the protein, the error tolerance of these masses, and the charge state of the masses.
Maximum Allowed Missed Cleavages
The maximum number of missed cleavages that are to be allowed for this enzyme in the digestion.
Max. number of fragments cross linked
The maximum number of fragments that can be linked by a cross link. Leave blank for no maximum.
Max. number of cross link attachments
The maximum number of cross link attachements in a match. Leave blank for no maximum.
Max. Occupancy
This number represents the maximum number of this modification that will be added to the mass of a peptide during the program calculation.
Min. Occupancy
This number represents the minimum number of this modification that will be added to the mass of a peptide during the program calculation.
Modification (cross link)
Enter the chemical formula of the modification caused by a link at the amino acid(s) chosen in the corresponding list box.
Modification (user-defined enzyme)
The modification associated with the enzyme can be entered as a chemical formula. Format Explanation
Modification Formula (user-defined)
The formula of the modification. Format Explanation
Monoisotopic Masses
List the monoisotopic masses here, separated by a space. All characters are ignored except numbers (0-9) and decimal point (.).
N Terminal (Cross Link)
Check this box if you would like the cross link to link at the N-terminal of each chain, in addition to the defined link sites. You must select Lysine as a link site, and the associated modification will be used as the modification of the cross link at the N-terminal.
Partial Global Modifications (pre-defined)
Partial global modifications add the corresponding modification formula to 0 or more (up to the total number of occurances) occurances of the specified amino acid(s). To select more than one, hold the control key down while clicking on your choices. The following table indications the meanings of the modification names in the list box.


Name Site(s) Formula
4-vinyl-pyridine (Cys) C +C7H7N
Acrylamide (Cys) C +C3H5ON
Iodoacetamide (Cys) C +C2H3ON
Iodoacetic acid (Cys) C +C2H2O2
Performic acid (Cys+O3) C +O3
Performic acid (Met+O2) M +O2
Performic acid (Met+O) M +O
Nitration (Y) Y +NO2-H
Oxidation (M) M +O
Phosphorylation (S,T,Y) STY +HPO3
Phosphorylation (S,T)) ST +HPO3
Phosphorylation (Y) Y +HPO3
Pre-Defined Enzyme
A pre-defined enzyme to be used in the digestion can be selected here. The following table indicates the meanings of the enzyme names in the drop-down list box.


Name Cleave at Don't Cleave at Terminal Modification
Endoproteinase Arg C R P C  
Endoproteinase Asp N D   N  
Endoproteinase Glu C E P C  
Endoproteinase Lys C K P C  
CNBr M   C +CH3S
Trypsin KR P C  
V8 (D,E) DE P C  
V8 (E) E P C  
PROTEIN
In this section, enter information about the protein that is to be used in the mapping.
Protein Name
The name of the protein to be used in the mapping. This is an optional field, as the name is not a necessary input and is only present for the user's convenience.
Terminal (for user-defined enzyme)
The terminal at which the enzyme cuts. Select C (right) or N (left) terminal.
User-Defined Chemistry (section heading)
In this section, specify the parameters for user-defined enzymes. Once the parameters have been specified, click the "Add Enzyme" button to add the enzyme to the list on the right. The user-defined enzymes that are in the list on the right will be used in the digestion.  If you make a mistake, an enzyme(s) may be removed from the box on the right by highlighting it and clicking the "Remove Enzyme" button.
User-Defined Cross Link (section heading)
In this section, specify the parameters for a user-defined cross link. Only one cross link is currently supported.
User-Defined Enzymes List
This box contains a list of the user-defined enzymes that will be used in the digestion. You add enzymes to this list by filling in the fields to the left and then clicking the "Add Enzyme" button. If you make a mistake, an enzyme(s) may be removed from this box by highlighting it and clicking the "Remove Enzyme" button.
User-Defined Global Modifications List
This box contains a list of the user-defined global modifications that will be used in the mass calculations. You add global modifications to this list by filling in the fields to the left and then clicking the "Add Modification" button. If you make a mistake, a modification(s) may be removed from this box by highlighting it and clicking the "Remove Modification" button.
User-Defined Global Modifications (section heading)
In this section, specify the parameters for user-defined global modifications. Once the parameters have been specified, click the "Add Modification" button to add the global modification to the list on the right. The user-defined global modifications that are in the list on the right will be applied in the program. If you make a mistake, a global modification(s) may be removed from the box on the right by highlighting it and clicking the "Remove Modification" button.
User-Defined Local Modifications List
This box contains a list of the user-defined local modifications that will be used in the mass calculations. You add local modifications to this list by filling in the fields to the left and then clicking the "Add Modification" button. If you make a mistake, a modification(s) may be removed from this box by highlighting it and clicking the "Remove Modification" button.