tools_aahelper.java

For calculating peptide and fragment masses.

/*
##############################################################################
# File: tools_aahelper.java                                                  #
# Mascot Parser toolkit example code                                         #
# Acknowledgment: Thanks to Tony Major, Celera Genomics for converting this  #
#                 file from the C++ example                                  # 
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2006 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#     $Source: parser/examples/test_java/tools_aahelper.java $ 
#     $Author: villek@matrixscience.com $
#       $Date: 2018-07-30 16:23:53 +0100 $
#   $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_2_8_1-0-gea32989045 $
##############################################################################
*/

import matrix_science.msparser.ms_enzymefile;
import matrix_science.msparser.ms_fragmentationrules;
import matrix_science.msparser.msparserConstants;
import matrix_science.msparser.*;
import java.text.*;

public class tools_aahelper {
    static {
        try {
            System.loadLibrary("msparserj");
        } catch (UnsatisfiedLinkError e) {
            System.err.println("Native code library failed to load. "
                               + "Is msparserj.dll on the path?\n" + e);
            System.exit(0);
        }
    }
    
    public static void main(String argv[]) 
    {
        // We need an enzyme to build a list of peptides
        // and mod_file file if we want to apply any modifications
        if(argv.length < 2) {
            System.out.println("Location of enzymes file and mod_file has to be specified as parameters");
            System.exit(0);
        }
       
        ms_enzymefile enzymefile = new ms_enzymefile(argv[0]);
        if ( !enzymefile.isValid() )
        {
            System.out.println("There are errors. Cannot continue. The last error description:");
            System.out.println(enzymefile.getLastErrorString());
            System.exit(1);
        }
        
        ms_enzyme enzyme = enzymefile.getEnzymeByName("Trypsin");
        if ( enzyme == null )
        {
            System.out.println("Cannot find Trypsin enzyme in the file. Cannot continue.");
            System.exit(1);
        }

        // we need masses file, but can use default masses anyway
        ms_masses masses = new ms_masses();
        ms_modfile modfile = new ms_modfile(argv[1], masses);
        if ( !modfile.isValid() )
        {
            System.out.println("There are errors. Cannot continue. The last error description:");
            System.out.println(modfile.getLastErrorString());
            System.exit(1);
        }

        ms_modification oxidation   = modfile.getModificationByName("Oxidation (M)");
        ms_modification acetylNterm = modfile.getModificationByName("Acetyl (N-term)");
        ms_modification phospho     = modfile.getModificationByName("Phospho (STY)");
        if ( oxidation == null || acetylNterm == null || phospho == null )
        {
            System.out.println("Cannot find necessary modifications in the mod_file. Cannot continue.");
            System.exit(1);
        }

        ms_aahelper aahelper = new ms_aahelper();
        aahelper.setMasses(masses);
        aahelper.setEnzyme(enzyme);

        // Now we can generate peptides for a given protein
        String proteinStr = "MAIFRIDEIRNMSSEELEEELRKLEVELIRERGAVRAGGAPEKPGRIREIRRTIARMKTVQRERVRK";

        aahelper.startIteratePeptides(proteinStr, proteinStr.length(), 0);// no missed cleavages are allowed
        System.out.println("List of peptides");
        while(aahelper.getNextPeptide())
        {
            int start = aahelper.getPepStart()-1; // the method returns 1-based position
            int end = aahelper.getPepEnd();
            String peptideStr = proteinStr.substring(start, end);
            //peptideStr.assign(proteinStr+start, len);
            System.out.println(peptideStr);
        }

        System.out.println("End of list");

        // create a list of fixed modifications
        ms_modvector vecFixed = new ms_modvector();
        vecFixed.appendModification(phospho);

        // create a list of variable modifications
        ms_modvector vecVariable = new ms_modvector();
        vecVariable.appendModification(oxidation);
        vecVariable.appendModification(acetylNterm);

        aahelper.setAvailableModifications(vecFixed, vecVariable);

        // ms_aahelper can also contain errors that might happen when applying modifications
        // for instance, when we have a conflict between two modifications (same residue or same peptide end)
        if ( !aahelper.isValid() )
        {
            System.out.println("There are errors. Cannot continue. The last error description:");
            System.out.println(aahelper.getLastErrorString());
            System.exit(1);
        }
        
        // we will need also a separate error-object for collecting peptide-specific errors
        ms_errs err = new ms_errs();
        
        // Example of how to call calcPeptideMZ
        // It will often be more convenient to create an ms_peptide and then
        // call getMrCalc() on that object.
        vectori numThatMustBeModded = new vectori();
        numThatMustBeModded.add(1);  // 1 acetylNterm modification
        numThatMustBeModded.add(1);  // 1 site is phosphorylated


        double mr = aahelper.calcPeptideMZ(proteinStr, proteinStr.length(), 
                                           1, 10, // peptide ends (1-based)
                                           numThatMustBeModded, 
                                           0, // no charge
                                           msparserConstants.MASS_TYPE_MONO,
                                           err);
        if ( !err.isValid() )
        {
            System.out.println("There have been errors while calculating peptide mass: ");
            System.out.println(err.getLastErrorString());
            // don't need to halt as they are not fatal errors
            err.clearAllErrors(); // prepare to re-use it
        }
        else
        {
            DecimalFormat massFmt = new DecimalFormat("0.000");
            System.out.println("Peptide mass calculated using 'calcPeptideMZ' is " + massFmt.format(mr));
        }

        // Create a peptide - which we can then fragment
        //
        // Specify which residues are modified by which modification.
        // as it has to correspond to a modification string
        // Nterm modification + 9 residues + Cterm modification
        vectori numModded = new vectori();
        numModded.add(2);  // N-term  - modified by "Acetyl (N-term)"
        numModded.add(1);  // M       - modified by "Oxidation (M)"
        numModded.add(0);  // A
        numModded.add(0);  // I
        numModded.add(0);  // F
        numModded.add(0);  // R
        numModded.add(0);  // I
        numModded.add(0);  // D
        numModded.add(0);  // E
        numModded.add(0);  // I
        numModded.add(0);  // R
        numModded.add(0);  // C-term


        // we have to specify (or at least supply an empty vector) which neutral loss value to use
        // in case there are more than one available for a modification
        vectori whichNl = new vectori();
        whichNl.add(0);  // N-term
        whichNl.add(1);  // M - has 2 neutral losses. Specify the first (-98)
        whichNl.add(0);  // A
        whichNl.add(0);  // I
        whichNl.add(0);  // F      
        whichNl.add(0);  // R
        whichNl.add(0);  // I
        whichNl.add(0);  // D
        whichNl.add(0);  // E
        whichNl.add(0);  // I
        whichNl.add(0);  // R
        whichNl.add(0);  // C-term

        ms_peptide peptide = aahelper.createPeptide(proteinStr, proteinStr.length(),
                                                    1,10, // end positions
                                                    numModded, // modification string-like vector
                                                    whichNl, // which neutral loss to use
                                                    0, // no charge
                                                    msparserConstants.MASS_TYPE_MONO,
                                                    err); // collect errors in it
        if ( !err.isValid() )
        {
            System.out.println("There have been errors while creating a peptide: ");
            System.out.println(err.getLastErrorString());
            // don't need to halt as they are not fatal errors
            err.clearAllErrors(); // prepare to re-use it
        }
        else
        {
            System.out.println();
            System.out.println();
            System.out.print("Peptide has been created successfully: ");
            System.out.println(peptide.getPeptideStr());
        }

        vectord ions;
        ms_fragmentvector fragments = new ms_fragmentvector();
        ms_fragmentvector all_fragments = new ms_fragmentvector();  // Keep a list of fragments from all series
                
        ions = aahelper.calcFragments(peptide, // that is why we needed to create a peptide object first
                                      ms_fragmentationrules.FRAG_B_SERIES, // ions series ID
                                      false, // single-charged ions only
                                      100.0, // minimal fragment mass to return
                                      mr,    // maximal fragment mass to return 
                                      msparserConstants.MASS_TYPE_MONO,
                                      fragments,
                                      err); // collect peptide-specific errors

        System.out.println("b-ion series fragments: ");
        printFragmentsTable(fragments);
        all_fragments.copyFrom(fragments);
        ms_fragmentvector b_ions = new ms_fragmentvector();
        b_ions.copyFrom(fragments);

        ions = aahelper.calcFragments(peptide, // that is why we needed to create a peptide object first
                                      ms_fragmentationrules.FRAG_Y_SERIES, // ions series ID
                                      false, // single-charged ions only
                                      100.0, // minimal fragment mass to return
                                      mr,    // maximal fragment mass to return 
                                      msparserConstants.MASS_TYPE_MONO,
                                      fragments,
                                      err); // collect peptide-specific errors

        System.out.println("y-ion series fragments: ");
        printFragmentsTable(fragments);
        for (int i=0; i < fragments.getNumberOfFragments(); i++) 
            all_fragments.appendFragment(fragments.getFragmentByNumber(i));
        
        aahelper.calcFragmentsEx(peptide, // that is why we needed to create a peptide object first
                                 ms_fragmentationrules.FRAG_Y_SERIES, // ions series ID
                                 2, // double-charged only
                                 100.0, // minimal fragment mass to return
                                 mr,    // maximal fragment mass to return 
                                 msparserConstants.MASS_TYPE_MONO,
                                 fragments,
                                 err); // collect peptide-specific errors

        System.out.println("y++-ion series fragments: ");
        printFragmentsTable(fragments);
        for (int i=0; i < fragments.getNumberOfFragments(); i++) 
            all_fragments.appendFragment(fragments.getFragmentByNumber(i));

        ions = aahelper.calcFragments(peptide, // that is why we needed to create a peptide object first
                                      ms_fragmentationrules.FRAG_INTERNAL_YB, // ions series ID
                                      false, // single-charged ions only
                                      100.0, // minimal fragment mass to return
                                      700.0,    // maximal fragment mass to return 
                                      msparserConstants.MASS_TYPE_MONO,
                                      fragments,
                                      err); // collect peptide-specific errors

        System.out.println("internal yb-ion series fragments: ");
        printFragmentsTable(fragments);
        for (int i=0; i < fragments.getNumberOfFragments(); i++) 
            all_fragments.appendFragment(fragments.getFragmentByNumber(i));


        System.out.println("Run a search under Mascot to verify the output above");
        System.out.println("Paste the following into a Mascot search query window:");
        displayMascotTestSearch(vecFixed, vecVariable, 
                                enzyme, 
                                mr, 
                                b_ions); // Or you can use all_fragments

        
        System.exit(0);        
    }

    public static void printFragmentsTable(ms_fragmentvector fragments) 
    {
        System.out.print("Number of fragments: ");
        System.out.println(fragments.getNumberOfFragments());

        System.out.println("Col\tStart\tEnd\tLabel\t\t Mass\t  NL\tName\tImmon\tIntern\tReg");
        int i;
        for (i=0; i < fragments.getNumberOfFragments(); i++)
        {
            ms_fragment frag = fragments.getFragmentByNumber(i);
            DecimalFormat fragMassFmt = new DecimalFormat("0.00");
                        
            System.out.print(frag.getColumn());
            System.out.print("\t");
            System.out.print(frag.getStart());
            System.out.print("\t");
            System.out.print(frag.getEnd());
            System.out.print("\t");
            System.out.print(padding(frag.getLabel(), 10, " "));
            System.out.print("\t");
            System.out.print(padout(fragMassFmt.format(frag.getMass()),7," "));
            System.out.print("\t");
            System.out.print(fragMassFmt.format(frag.getNeutralLoss()));
            System.out.print("\t");
            System.out.print(frag.getSeriesName());
            System.out.print("\t");
            if (frag.isImmonium())
                System.out.print("1\t");
            else
                System.out.print("0\t");
            if (frag.isInternal())
                System.out.print("1\t");
            else
                System.out.print("0\t");
            if (frag.isRegular())
                System.out.print("1\n");
            else
                System.out.print("0\n");
        }
        System.out.println();
    }
    
    public static void displayMascotTestSearch(ms_modvector      vecFixed,
                                               ms_modvector      vecVariable,
                                               ms_enzyme         enzyme,
                                               double            mr,
                                               ms_fragmentvector fragments)
    {
        /* fragments contains a list of b-ions from a peptide
         * vecVariable contains a list of variable mods applied to the peptide
         * vecFixed contains a list of fixed mods applied to the peptide
         * Use this information to generate an test search that can be run on Mascot.
         */
        
        int i;
        for (i=0; i < vecFixed.getNumberOfModifications(); i++)
        {
            System.out.print("MODS=");
            System.out.println(vecFixed.getModificationByNumber(i).getTitle());
        }
        for (i=0; i < vecVariable.getNumberOfModifications(); i++)
        {
            System.out.print("IT_MODS=");
            System.out.println(vecVariable.getModificationByNumber(i).getTitle());
        }
        System.out.println("CHARGE=Mr");
        System.out.print("CLE=");
        System.out.println(enzyme.getTitle());
        System.out.println("INSTRUMENT=MALDI-TOF-TOF");
        DecimalFormat massFmt = new DecimalFormat("#0.000");
        System.out.print(massFmt.format(mr) + " ions(" );
        for(i=0; i < fragments.getNumberOfFragments(); i++)
        {
            if (i > 0)
                System.out.print(", ");
            double mz = fragments.getFragmentByNumber(i).getMass();
            System.out.print(massFmt.format(mz));
        }
        System.out.println(")");
    }

    private static String padout(String toPrint, int length,String padding) {
    
        String returnValue="";
    
        if(toPrint.length() < length) {
            for(int queryLoop = 1; queryLoop <= length - toPrint.length(); queryLoop++) {
                returnValue += padding;
            }   
            returnValue += toPrint;
        }
        else returnValue = toPrint;
   
        return returnValue;
    }

    private static String padding(String toPrint, int length,String padding) {
    
        String returnValue=toPrint;
    
        if(toPrint.length() < length) {
            for(int queryLoop = 1; queryLoop <= length - toPrint.length(); queryLoop++) {
                returnValue += padding;
            }   
        }   
        return returnValue;
    }

}


/*


will give the output: 



C:\msparser\example_java>java  -classpath .;../java/msparser.jar tools_aahelper c:\Inetpub\MASCOT\config\enzymes c:\Inetpub\MASCOT\config\mod_file


List of peptides
M
MEDYLDELR
EDYLDELR
HK
IPSFIVELLK
NNLK
NR
NLTR
NQLNK
IVNR
VSDLYFGK
KPEDK
K
AAELTNK
INDLSHK
LDALMK
VATVSSATK
VSDDIK
K
EIDNLDELDL
End of list
Peptide mass calculated using 'calcPeptideMZ' is 1320.494


Peptide has been created successfully: MEDYLDELR
b-ion series fragments:
Number of fragments: 8
Col     Start   End     Label            Mass     NL    Name    Immon   Intern  Reg
1       1       -1      b(1)             190.05 0.00    b       0       0       1
2       2       -1      b(2)             319.10 0.00    b       0       0       1
3       3       -1      b(3)             434.12 0.00    b       0       0       1
4       4       -1      b(4) -97         579.18 97.98   b       0       0       1
5       5       -1      b(5) -97         692.26 97.98   b       0       0       1
6       6       -1      b(6) -97         807.29 97.98   b       0       0       1
7       7       -1      b(7) -97         936.33 97.98   b       0       0       1
8       8       -1      b(8) -97        1049.41 97.98   b       0       0       1

y-ion series fragments:
Number of fragments: 8
Col     Start   End     Label            Mass     NL    Name    Immon   Intern  Reg
8       8       -1      y(8) -97        1034.48 97.98   y       0       0       1
7       7       -1      y(7) -97         905.44 97.98   y       0       0       1
6       6       -1      y(6) -97         790.41 97.98   y       0       0       1
5       5       -1      y(5)             645.36 0.00    y       0       0       1
4       4       -1      y(4)             532.27 0.00    y       0       0       1
3       3       -1      y(3)             417.25 0.00    y       0       0       1
2       2       -1      y(2)             288.20 0.00    y       0       0       1
1       1       -1      y(1)             175.12 0.00    y       0       0       1

internal yb-ion series fragments:
Number of fragments: 18
Col     Start   End     Label            Mass     NL    Name    Immon   Intern  Reg
2       2       3       ED               245.08 0.00    yb      0       1       0
2       2       4       EDY -97          390.13 97.98   yb      0       1       0
2       2       5       EDYL -97         503.21 97.98   yb      0       1       0
2       2       6       EDYLD -97        618.24 97.98   yb      0       1       0
3       3       4       DY -97           261.09 97.98   yb      0       1       0
3       3       5       DYL -97          374.17 97.98   yb      0       1       0
3       3       6       DYLD -97         489.20 97.98   yb      0       1       0
3       3       7       DYLDE -97        618.24 97.98   yb      0       1       0
4       4       5       YL -97           259.14 97.98   yb      0       1       0
4       4       6       YLD -97          374.17 97.98   yb      0       1       0
4       4       7       YLDE -97         503.21 97.98   yb      0       1       0
4       4       8       YLDEL -97        616.30 97.98   yb      0       1       0
5       5       6       LD               229.12 0.00    yb      0       1       0
5       5       7       LDE              358.16 0.00    yb      0       1       0
5       5       8       LDEL             471.24 0.00    yb      0       1       0
6       6       7       DE               245.08 0.00    yb      0       1       0
6       6       8       DEL              358.16 0.00    yb      0       1       0
7       7       8       EL               243.13 0.00    yb      0       1       0

Run a search under Mascot to verify the output above
Paste the following into a Mascot search query window:
MODS=Oxidation (M)
IT_MODS=Acetyl (N-term)
IT_MODS=Phospho (STY)
CHARGE=Mr
CLE=Trypsin
INSTRUMENT=MALDI-TOF-TOF
1320.494 ions(190.053, 319.096, 434.123, 579.176, 692.260, 807.287, 936.329, 1049.413)

*/