Matrix Science header

resfile_summary.cpp

Example program for extracting the peptide or protein summary.

/*
##############################################################################
# file: resfile_summary.cpp                                                  #
# 'msparser' toolkit example code                                            #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2005 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#    $Source: /vol/cvsroot/parser/examples/test_cxx/resfile_summary.cpp,v $  #
#     $Author: francoisr $                                                   #
#       $Date: 2016/06/20 16:03:03 $                                         #
#   $Revision: 1.4 $                                                         #
# $NoKeywords::                                                            $ #
##############################################################################
*/
#include "msparser.hpp"
#include <iostream>
#include <iomanip>
#include <fstream>

// All the classes are part of the matrix_science namespace
using namespace matrix_science;


/*****************************************************************************/
/* Local functions                                                           */
/*****************************************************************************/
static void displayPeptideInfo(bool showFullDetails,
                               ms_peptide * pep,
                               ms_mascotresults * r,
                               bool isDuplicate,
                               bool isBold,
                               bool showCheckBox);
static bool showResults(ms_mascotresfile &  file,
                        bool                peptideSummary,
                        const int           flags,
                        const double        minProbability        =  0,
                        const int           maxHitsToDisplay      = 50,
                        const double        ignoreIonsScoreBelow  =  0,
                        const int           minPepLenInPepSummary =  0,
                        const int           flags2                = ms_peptidesummary::MSPEPSUM_NONE);
static void displayYellowPopupInfo(ms_mascotresults * results, int q);
static bool checkErrors(ms_mascotresfile & file);


/*****************************************************************************/
/* main                                                                      */
/* Call this program with a single argument - the name of the .dat file      */
/*****************************************************************************/
int main(int argc, char * argv[])
{
    int returnValue = EXIT_FAILURE;

    if (argc == 2)
    {
        ms_mascotresfile file(argv[1]);

        if (checkErrors(file))
        {
            bool         usePeptideSummary;
            unsigned int flags, flags2, minPepLenInPepSummary;
            int          maxHitsToReport;
            double       minProbability, ignoreIonsScoreBelow;

            /*
             * The parameters passed to ms_peptidesummary or ms_proteinsummary determine
             * the type of grouping and the number of proteins and peptides displayed.
             * Default parameters can be returned using ms_mascotresfile::get_ms_mascotresults_params().
             * The return values from this function depend on the type of search,
             * and also on values in the mascot.dat configuration file if that is available.
             */

            ms_datfile datfile("../config/mascot.dat"); //You may need to change this path

            //if the mascot.dat isn't available, use defaults
            ms_mascotoptions mascotOptions;

            if (datfile.isValid())
            {
                mascotOptions = *(datfile.getMascotOptions());
            }

            std::string scriptName = file.get_ms_mascotresults_params(
                                           mascotOptions,
                                           &flags,
                                           &minProbability,
                                           &maxHitsToReport,
                                           &ignoreIonsScoreBelow,
                                           &minPepLenInPepSummary,
                                           &usePeptideSummary,
                                           &flags2);

            bool bResult;
            if (usePeptideSummary)
            {
                /*
                 * For peptide summary
                 *
                 * Flags defined for hierarchical clustering algorithm:
                 *     flags: ms_mascotresults::MSRES_CLUSTER_PROTEINS
                 *            | ms_mascotresults::MSRES_SHOW_SUBSETS
                 *            | ms_mascotresults::MSRES_MUDPIT_PROTEIN_SCORE;
                 *     flags2: ms_peptidesummary::MSPEPSUM_USE_HOMOLOGY_THRESH;
                 *
                 * Flags defined for original simple parsimony algorithm:
                 *     flags: ms_mascotresults::MSRES_GROUP_PROTEINS | ms_mascotresults::MSRES_SHOW_SUBSETS;
                 */

                std::cout << "-------------------------------------------------------------" << std::endl;
                std::cout << "---   Peptide summary report                              ---" << std::endl;
                std::cout << "-------------------------------------------------------------" << std::endl;

                bResult = showResults(file,
                                      usePeptideSummary,
                                      flags,
                                      minProbability,
                                      maxHitsToReport,
                                      ignoreIonsScoreBelow,
                                      minPepLenInPepSummary,
                                      flags2);
            }
            else
            {
                // Show results from full protein summary, remove grouping
                flags &= ~ms_mascotresults::MSRES_GROUP_PROTEINS;
                flags &= ~ms_mascotresults::MSRES_SHOW_SUBSETS;

                std::cout << "-------------------------------------------------------------" << std::endl;
                std::cout << "---   Full Protein summary report                         ---" << std::endl;
                std::cout << "-------------------------------------------------------------" << std::endl;
                bResult = showResults(file,
                                      usePeptideSummary,
                                      flags,
                                      minProbability,
                                      maxHitsToReport,
                                      ignoreIonsScoreBelow,
                                      minPepLenInPepSummary,
                                      flags2);

                if (bResult && checkErrors(file))
                {
                    std::cout << std::endl;

                    // Show results from concise protein summary, add grouping
                    flags |= ms_mascotresults::MSRES_GROUP_PROTEINS;
                    flags |= ms_mascotresults::MSRES_SHOW_SUBSETS;

                    std::cout << "-------------------------------------------------------------" << std::endl;
                    std::cout << "---   Concise Protein summary report                      ---" << std::endl;
                    std::cout << "-------------------------------------------------------------" << std::endl;
                    bResult = showResults(file,
                                          usePeptideSummary,
                                          flags,
                                          minProbability,
                                          maxHitsToReport,
                                          ignoreIonsScoreBelow,
                                          minPepLenInPepSummary,
                                          flags2);
                }
            }

            if (bResult && checkErrors(file))
            {
                returnValue = EXIT_SUCCESS;
            }
        }
    }
    else
    {
        std::cout << "Must supply the name of a .dat file as a command line argument" << std::endl;
    }

    return returnValue;
}




/*****************************************************************************/
/* showResults                                                               */
/* Shows results using either the peptide summary or the protein summary     */
/*****************************************************************************/
static bool showResults(ms_mascotresfile &  file,
                        bool                peptideSummary,
                        const int           flags,
                        const double        minProbability,
                        const int           maxHitsToDisplay,
                        const double        ignoreIonsScoreBelow,
                        const int           minPepLenInPepSummary,
                        const int           flags2)
{
    ms_mascotresults * results;

    if (peptideSummary)
    {
        results = new ms_peptidesummary(file, flags, minProbability, maxHitsToDisplay,
                                        0, ignoreIonsScoreBelow, minPepLenInPepSummary, "", flags2);
    }
    else
    {
        results = new ms_proteinsummary(file, flags, minProbability, maxHitsToDisplay);
    }

    //Stop there is any fatal error occurred
    if (!checkErrors(file))
    {
        return false;
    }

    int family = 1;
    int hit = 1;
    ms_protein * prot = results->getHit(hit);

    while (prot)
    {
        std::string accession   = prot->getAccession();
        std::string description = results->getProteinDescription(accession.c_str());
        double      mass        = results->getProteinMass(accession.c_str());
        int dbIdx               = prot->getDB();

        std::cout << "Protein Hit " << hit;
        if (flags & ms_mascotresults::MSRES_CLUSTER_PROTEINS)
        {
            std::cout << "." << family;
        }
        std::cout << "\n===================\n";
        std::cout << "Accession   : " << accession             << std::endl;
        std::cout << "Description : " << description           << std::endl;
        std::cout << "Score       : " << prot->getScore()      << std::endl;
        std::cout << "Mass        : " << mass                  << std::endl;
        std::cout << "Frame       : " << prot->getFrame()      << std::endl;
        std::cout << "Coverage    : " << prot->getCoverage()   << std::endl;
        std::cout << "Peptides    : " << prot->getNumDisplayPeptides()<< std::endl;

        int i;

        // Each protein has a number of peptides that matched - list them:
        for (i=1; i <= prot->getNumPeptides(); i++)
        {
            int query = prot->getPeptideQuery(i);
            int p     = prot->getPeptideP(i);

            if (p != -1
                && query != -1
                && prot->getPeptideDuplicate(i) != ms_protein::DUPE_DuplicateSameQuery)
            {
                ms_peptide * pep;

                if (results->getPeptide(query, p, pep))
                {
                    displayPeptideInfo(false, pep, results,
                                       prot->getPeptideDuplicate(i) == ms_protein::DUPE_Duplicate,
                                       prot->getPeptideIsBold(i),
                                       prot->getPeptideShowCheckbox(i));
                }
            }
        }

        // Now display list of all proteins that contain a subset or a same set of the matching peptides
        if ( (flags & ms_mascotresults::MSRES_GROUP_PROTEINS) || (flags & ms_mascotresults::MSRES_CLUSTER_PROTEINS) )
        {
            std::cout << "Proteins matching the same set of peptides:" << std::endl;
            i = 1;
            while ((prot = results->getNextSimilarProteinOf(accession.c_str(), dbIdx, i)) != 0)
            {
                std::string accession = prot->getAccession();
                if (flags & ms_mascotresults::MSRES_CLUSTER_PROTEINS)
                {
                    int dbIdx = prot->getDB();
                    if (dbIdx > 1)
                    {
                        std::cout << dbIdx << "::";
                    }
                }
                std::cout << accession.c_str()
                          << " - Total score: " << prot->getScore()
                          << " - Peptides matched: " << prot->getNumDisplayPeptides()
                          << std::endl;
                i++;
            }

            if (flags & ms_mascotresults::MSRES_SHOW_SUBSETS)
            {
                std::cout << "Proteins matching a subset of these peptides:" << std::endl;
                i = 1;
                while ((prot = results->getNextSubsetProteinOf(accession.c_str(), dbIdx, i)) != 0)
                {
                    std::string accession = prot->getAccession();
                    int dbIdx             = prot->getDB();
                    if ( (flags & ms_mascotresults::MSRES_CLUSTER_PROTEINS) && dbIdx > 1)
                    {
                        std::cout << dbIdx << "::";
                    }
                    std::cout << accession.c_str()
                              << " - Total score: " << prot->getScore()
                              << " - Peptides matched: " << prot->getNumDisplayPeptides()
                              << std::endl;

                    if (flags & ms_mascotresults::MSRES_CLUSTER_PROTEINS)
                    {
                        int j = 1;
                        if (results->getNextSimilarProteinOf(accession.c_str(), dbIdx, j))
                        {
                            std::cout << "  Proteins matching the same set of peptides for this subset:" << std::endl;
                        }
                        ms_protein * similar_subset_prot;
                        while ((similar_subset_prot =
                                results->getNextSimilarProteinOf(accession.c_str(), dbIdx, j)) != 0)
                        {
                            std::string similar_subset_accession = similar_subset_prot->getAccession();
                            int similar_subset_dbIdx             = similar_subset_prot->getDB();
                            std::cout << "  ";
                            if (similar_subset_dbIdx > 1)
                            {
                                std::cout << similar_subset_dbIdx << "::";
                            }
                            std::cout << similar_subset_accession.c_str()
                                      << " - Total score:" << similar_subset_prot->getScore()
                                      << " - Peptides matched: " << similar_subset_prot->getNumDisplayPeptides()
                                      << std::endl;
                            j++;
                        }
                    }

                    i++;
                }
            }
        }

        if (flags & ms_mascotresults::MSRES_CLUSTER_PROTEINS)
        {
            prot = results->getNextFamilyProtein(hit, family++);

            if (!prot)
            {
                hit++;
                prot = results->getHit(hit);
                family = 1;
            }
        }
        else
        {
            hit++;
            prot = results->getHit(hit);
        }
        std::cout << std::endl;
    }

    results->createUnassignedList(ms_mascotresults::SCORE);
    if (results->getNumberOfUnassigned())
    {
        std::cout << "Unassigned list" << std::endl
                  << "---------------" << std::endl;
        for (int u = 1; u <= results->getNumberOfUnassigned(); u++)
        {
            ms_peptide pep = results->getUnassigned(u);
            displayPeptideInfo(false, &pep, results, false, true, true);
        }
    }

    if (peptideSummary)
        displayYellowPopupInfo(results, 1);
    delete results;

    return true;
}

/*****************************************************************************/
/* displayYellowPopupInfo                                                    */
/* Shows the equivalent of the yellow popup box for given query              */
/*****************************************************************************/
static void displayYellowPopupInfo(ms_mascotresults * results, int q)
{
    std::cout << "Score Delta      Hit Protein Peptide" << std::endl;

    int p;

    for (p=1; p <= 10; p++)
    {
        ms_peptide pep = results->getPeptide(q, p);
        std::string seq = pep.getPeptideStr();
        if (!seq.empty())
        {
            std::string tmp = results->getProteinsWithThisPepMatch(q, p, true);

            std::string hit = "   ";
            std::string protein = "      ";
            if (!tmp.empty())
            {
                hit = tmp.substr(0, tmp.find(':'));
                std::string::size_type start = tmp.find(":\"");
                if (start != tmp.rfind(":\""))
                    hit += "+";
                protein = tmp.substr(2 + start, tmp.find("\" ") - start -2);
            }
            std::cout << pep.getIonsScore()   << "  "
                      << pep.getDelta()       << "  "
                      << hit                  <<  "  "
                      << protein              <<  "  "
                      << pep.getPeptideStr()  << std::endl;
        }
    }

    p = 1;
    std::cout << "Accessions that matched query " << q
              << " rank " << p << ":- "
              << results->getProteinsWithThisPepMatch(q, p)
              << std::endl << std::endl;

}


/*****************************************************************************/
/* displayPeptideInfo                                                        */
/* Shows information about a peptide                                         */
/*****************************************************************************/
static void displayPeptideInfo(bool showFullDetails,
                               ms_peptide * p,
                               ms_mascotresults * r,
                               bool isDuplicate,
                               bool isBold,
                               bool showCheckBox)
{
    int q = p->getQuery();

    if (showFullDetails)
    {
        std::cout << "Peptide hit" << std::endl;
        if (p->getAnyMatch())
        {

            std::cout << "  Query       : " << q                          << std::endl;
            std::cout << "  Rank        : " << p->getRank()               << std::endl;
            std::cout << "  Matched     : " << p->getAnyMatch()           << std::endl;
            std::cout << "  missedCleave: " << p->getMissedCleavages()    << std::endl;
            std::cout << "  mrCalc      : " << p->getMrCalc()             << std::endl;
            std::cout << "  delta       : " << p->getDelta()              << std::endl;
            std::cout << "  observed    : " << p->getObserved()           << std::endl;
            std::cout << "  charge      : " << p->getCharge()             << std::endl;
            std::cout << "  mrExp       : " << p->getMrExperimental()     << std::endl;
            std::cout << "  ionsMatched : " << p->getNumIonsMatched()     << std::endl;
            std::cout << "  peptideStr  : " << p->getPeptideStr()         << std::endl;
            std::cout << "  peaksUsed1  : " << p->getPeaksUsedFromIons1() << std::endl;
            std::cout << "  varModsStr  : " << p->getVarModsStr()         << std::endl;
            std::cout << "  readable mod: " << r->getReadableVarMods(q, p->getRank()) << std::endl;
            std::cout << "  tag matches : " << r->getTagString(q, 1) << std::endl;
            std::cout << "  first tag   : 1:" << r->getTagStart(q,1,1)
                                              << ":" << r->getTagEnd(q,1,1)
                                              << ":" << r->getTagSeries(q,1,1) << std::endl;
            std::cout << "  etag drange : " << r->getTagDeltaRangeStart(q, 1)
                                          << "," << r->getTagDeltaRangeEnd(q, 1) << std::endl;
            std::cout << "  ionsScore   : " << p->getIonsScore()          << std::endl;
            std::cout << "  seriesUsed  : " << p->getSeriesUsedStr()      << std::endl;
            std::cout << "  peaksUsed2  : " << p->getPeaksUsedFromIons2() << std::endl;
            std::cout << "  peaksUsed3  : " << p->getPeaksUsedFromIons3() << std::endl;
            std::cout << "  idth, hth, p: "
                      << r->getPeptideIdentityThreshold(q,20) << ", "
                      << r->getHomologyThreshold(q, 20)       << ", "
                      << r->getProbOfPepBeingRandomMatch(p->getIonsScore(), q)
                      << std::endl;
        }
        else
            std::cout << "  No match" << std::endl;
    }
    else
    {
        if (showCheckBox)
            std::cout << "CB ";
        else
            std::cout << "-- ";

        if (isBold)
            std::cout << "BOLD ";
        else
            std::cout << "dim  ";
        std::cout << std::setiosflags(std::ios::left) << std::setw(4)  << std::setfill(' ') << q;
        std::cout << std::setiosflags(std::ios::left) << std::setw(11) << std::setfill(' ') << p->getObserved();
        std::cout << std::setiosflags(std::ios::left) << std::setw(3)  << std::setfill(' ') << p->getRank();
        std::cout << "(";
        std::cout << std::setiosflags(std::ios::left) << std::setw(3)  << std::setfill(' ') << p->getPrettyRank();
        std::cout << ")";
        std::cout << std::setiosflags(std::ios::left) << std::setw(20) << std::setfill(' ') << p->getPeptideStr()
                  << "\t";
        if (isDuplicate)
            std::cout << "(" << p->getIonsScore() << ")";
        else
            std::cout << p->getIonsScore();
        std::cout << "\t";
        std::cout << r->getReadableVarMods(q, p->getRank());
        std::cout << std::endl;
    }
}

/*****************************************************************************/
/* checkErrors                                                               */
/* Print errors and return false if a critical error occurred                */
/*****************************************************************************/
static bool checkErrors(ms_mascotresfile &  file)
{
    if (file.getLastError())
    {
        for (int i=1; i <= file.getNumberOfErrors(); i++)
        {
            std::cout << "Error number: "
                      << file.getErrorNumber(i)
                      << " : "
                      << file.getErrorString(i)
                      << std::endl;
        }
    }

    //Call isValid before clearAllErrors, otherwise this method always returns true
    bool bIsValid = file.isValid();
    file.clearAllErrors();

    return bIsValid;
}

/*

will give the output:


-------------------------------------------------------------
---   Peptide summary report                              ---
-------------------------------------------------------------
Protein Hit 1
===================
Accession   : Q9XZJ2
Description : HEAT SHOCK PROTEIN 70.- Crassostrea gigas (Pacific oyster).
Score       : 286.477
Mass        : 79480.1
Frame       : 0
Coverage    : 57
CB BOLD 1   671.9      1  (1  )DAGTISGLNVLR             95.12
CB BOLD 2   808.3      1  (1  )TTPSYVAFTDTER            74.55
CB BOLD 3   973.9      1  (1  )NQVAMNPNNTIFDAK          89.84
-- BOLD 4   1084.9     3  (3  )IINEPTAAAIAYGLDKK        30.07
Proteins matching the same set of peptides:
Q94805 Total score: 283.374
Proteins matching a subset of these peptides:
AAF09496 Total score: 211.927  Peptides matched: 3
BAB72169 Total score: 199.74  Peptides matched: 3
Q24789 Total score: 199.74  Peptides matched: 3
Q9I9Q5 Total score: 199.74  Peptides matched: 3
AAB93665 Total score: 196.637  Peptides matched: 3
Q9W6Y1 Total score: 196.637  Peptides matched: 3
Q95V47 Total score: 194.46  Peptides matched: 3
Q91993 Total score: 193.534  Peptides matched: 3
T45476 Total score: 191.357  Peptides matched: 3
O01948 Total score: 169.67  Peptides matched: 2
O97150 Total score: 166.567  Peptides matched: 2
AAA64872 Total score: 125.19  Peptides matched: 2
B44261 Total score: 125.19  Peptides matched: 2
P81159 Total score: 125.19  Peptides matched: 2
Q9NJ92 Total score: 125.19  Peptides matched: 2
Q9NJ93 Total score: 125.19  Peptides matched: 2
Q9PUF9 Total score: 125.19  Peptides matched: 2
S21175 Total score: 125.19  Peptides matched: 2
T45473 Total score: 125.19  Peptides matched: 2
JC4610 Total score: 122.087  Peptides matched: 2
O73788 Total score: 122.087  Peptides matched: 2
1ATR Total score: 104.62  Peptides matched: 2
1ATS Total score: 104.62  Peptides matched: 2
1BA0 Total score: 104.62  Peptides matched: 2
1BA1 Total score: 104.62  Peptides matched: 2
1BUPA Total score: 104.62  Peptides matched: 2
1HSC Total score: 104.62  Peptides matched: 2
1KAX Total score: 104.62  Peptides matched: 2
1KAY Total score: 104.62  Peptides matched: 2
1KAZ Total score: 104.62  Peptides matched: 2
1NGC Total score: 104.62  Peptides matched: 2
1NGD Total score: 104.62  Peptides matched: 2
1NGE Total score: 104.62  Peptides matched: 2
1NGF Total score: 104.62  Peptides matched: 2
1NGG Total score: 104.62  Peptides matched: 2
1NGH Total score: 104.62  Peptides matched: 2
1NGI Total score: 104.62  Peptides matched: 2
2BUPA Total score: 104.62  Peptides matched: 2
A25646 Total score: 104.62  Peptides matched: 2
A27077 Total score: 104.62  Peptides matched: 2
A35922 Total score: 104.62  Peptides matched: 2
A44985 Total score: 104.62  Peptides matched: 2
A45635 Total score: 104.62  Peptides matched: 2
A45935 Total score: 104.62  Peptides matched: 2
A48439 Total score: 104.62  Peptides matched: 2
AAA30130 Total score: 104.62  Peptides matched: 2
AAA30569 Total score: 104.62  Peptides matched: 2
AAA33009 Total score: 104.62  Peptides matched: 2
CAA81523 Total score: 104.62  Peptides matched: 2
HHKW7A Total score: 104.62  Peptides matched: 2
HHUM7B Total score: 104.62  Peptides matched: 2
JC2215 Total score: 104.62  Peptides matched: 2
JC4786 Total score: 104.62  Peptides matched: 2
JC5642 Total score: 104.62  Peptides matched: 2
O61003 Total score: 104.62  Peptides matched: 2
O61004 Total score: 104.62  Peptides matched: 2
O73885 Total score: 104.62  Peptides matched: 2
O76274 Total score: 104.62  Peptides matched: 2
O96541 Total score: 104.62  Peptides matched: 2
O96911 Total score: 104.62  Peptides matched: 2
P79984 Total score: 104.62  Peptides matched: 2
PQ0138 Total score: 104.62  Peptides matched: 2
Q27031 Total score: 104.62  Peptides matched: 2
Q43532 Total score: 104.62  Peptides matched: 2
Q93146 Total score: 104.62  Peptides matched: 2
Q93147 Total score: 104.62  Peptides matched: 2
Q94614 Total score: 104.62  Peptides matched: 2
Q95LN9 Total score: 104.62  Peptides matched: 2
Q9GPK0 Total score: 104.62  Peptides matched: 2
Q9GRE8 Total score: 104.62  Peptides matched: 2
Q9H3R6 Total score: 104.62  Peptides matched: 2
Q9M4E6 Total score: 104.62  Peptides matched: 2
Q9M6R1 Total score: 104.62  Peptides matched: 2
Q9NCC8 Total score: 104.62  Peptides matched: 2
Q9NGK9 Total score: 104.62  Peptides matched: 2
Q9NJB7 Total score: 104.62  Peptides matched: 2
Q9SAU8 Total score: 104.62  Peptides matched: 2
Q9TW75 Total score: 104.62  Peptides matched: 2
Q9U545 Total score: 104.62  Peptides matched: 2
Q9UAE9 Total score: 104.62  Peptides matched: 2
S07197 Total score: 104.62  Peptides matched: 2
S11456 Total score: 104.62  Peptides matched: 2
S27004 Total score: 104.62  Peptides matched: 2
S31716 Total score: 104.62  Peptides matched: 2
S36753 Total score: 104.62  Peptides matched: 2
S37165 Total score: 104.62  Peptides matched: 2
T21394 Total score: 104.62  Peptides matched: 2
T45478 Total score: 104.62  Peptides matched: 2
T45479 Total score: 104.62  Peptides matched: 2
A55719 Total score: 101.517  Peptides matched: 2
AAA37859 Total score: 101.517  Peptides matched: 2
AAD11466 Total score: 101.517  Peptides matched: 2
B36590 Total score: 101.517  Peptides matched: 2
B86295 Total score: 101.517  Peptides matched: 2
CAA33735 Total score: 101.517  Peptides matched: 2
HS74_YEAST Total score: 101.517  Peptides matched: 2
Q99KD7 Total score: 101.517  Peptides matched: 2
Q9TUG3 Total score: 101.517  Peptides matched: 2
Q9TX61 Total score: 101.517  Peptides matched: 2
S08211 Total score: 101.517  Peptides matched: 2
S10859 Total score: 101.517  Peptides matched: 2
AAA49563 Total score: 95.12  Peptides matched: 1
1HJOA Total score: 74.55  Peptides matched: 1
1NGA Total score: 74.55  Peptides matched: 1
1QQMA Total score: 74.55  Peptides matched: 1
1QQNA Total score: 74.55  Peptides matched: 1
1QQOA Total score: 74.55  Peptides matched: 1
A25773 Total score: 74.55  Peptides matched: 1
A29160 Total score: 74.55  Peptides matched: 1
A45871 Total score: 74.55  Peptides matched: 1
A48872 Total score: 74.55  Peptides matched: 1
A49242 Total score: 74.55  Peptides matched: 1
AAA03451 Total score: 74.55  Peptides matched: 1
AAA17441 Total score: 74.55  Peptides matched: 1
AAA57233 Total score: 74.55  Peptides matched: 1
AAA78276 Total score: 74.55  Peptides matched: 1
AAB03704 Total score: 74.55  Peptides matched: 1
AAD21815 Total score: 74.55  Peptides matched: 1
AAD21816 Total score: 74.55  Peptides matched: 1
AAL34314 Total score: 74.55  Peptides matched: 1
BAB72167 Total score: 74.55  Peptides matched: 1
BAB72168 Total score: 74.55  Peptides matched: 1
BAB72233 Total score: 74.55  Peptides matched: 1
BAB78505 Total score: 74.55  Peptides matched: 1
CAA52328 Total score: 74.55  Peptides matched: 1
E980236 Total score: 74.55  Peptides matched: 1
HS71_SCHPO Total score: 74.55  Peptides matched: 1
I37564 Total score: 74.55  Peptides matched: 1
I51129 Total score: 74.55  Peptides matched: 1
I54542 Total score: 74.55  Peptides matched: 1
JH0095 Total score: 74.55  Peptides matched: 1
JU0164 Total score: 74.55  Peptides matched: 1
O18474 Total score: 74.55  Peptides matched: 1
O73922 Total score: 74.55  Peptides matched: 1
PC1156 Total score: 74.55  Peptides matched: 1
Q26357 Total score: 74.55  Peptides matched: 1
Q26936 Total score: 74.55  Peptides matched: 1
Q26937 Total score: 74.55  Peptides matched: 1
Q63256 Total score: 74.55  Peptides matched: 1
Q63718 Total score: 74.55  Peptides matched: 1
Q98896 Total score: 74.55  Peptides matched: 1
Q98899 Total score: 74.55  Peptides matched: 1
Q98900 Total score: 74.55  Peptides matched: 1
Q98901 Total score: 74.55  Peptides matched: 1
Q9I8F9 Total score: 74.55  Peptides matched: 1
Q9IAC1 Total score: 74.55  Peptides matched: 1
Q9LU13 Total score: 74.55  Peptides matched: 1
Q9N1U2 Total score: 74.55  Peptides matched: 1
Q9NFT1 Total score: 74.55  Peptides matched: 1
Q9QWJ5 Total score: 74.55  Peptides matched: 1
S09036 Total score: 74.55  Peptides matched: 1
S25585 Total score: 74.55  Peptides matched: 1
S31766 Total score: 74.55  Peptides matched: 1
S37394 Total score: 74.55  Peptides matched: 1
S53357 Total score: 74.55  Peptides matched: 1
S67431 Total score: 74.55  Peptides matched: 1
T19211 Total score: 74.55  Peptides matched: 1
T22169 Total score: 74.55  Peptides matched: 1
T41121 Total score: 74.55  Peptides matched: 1
T43724 Total score: 74.55  Peptides matched: 1
T45468 Total score: 74.55  Peptides matched: 1
JQ1515 Total score: 71.4471  Peptides matched: 1
PC7036 Total score: 71.4471  Peptides matched: 1
Q9UVM0 Total score: 71.4471  Peptides matched: 1
A25089 Total score: 30.07  Peptides matched: 1
A32475 Total score: 30.07  Peptides matched: 1
A42582 Total score: 30.07  Peptides matched: 1
A48469 Total score: 30.07  Peptides matched: 1
AAA28075 Total score: 30.07  Peptides matched: 1
AAA34139 Total score: 30.07  Peptides matched: 1
AAA65099 Total score: 30.07  Peptides matched: 1
AAA92743 Total score: 30.07  Peptides matched: 1
AAA99920 Total score: 30.07  Peptides matched: 1
AAB06397 Total score: 30.07  Peptides matched: 1
AAB53051 Total score: 30.07  Peptides matched: 1
AAB63968 Total score: 30.07  Peptides matched: 1
AAF88019 Total score: 30.07  Peptides matched: 1
BAA13948 Total score: 30.07  Peptides matched: 1
BAB08435 Total score: 30.07  Peptides matched: 1
CAA02784 Total score: 30.07  Peptides matched: 1
CAA27330 Total score: 30.07  Peptides matched: 1
CAA28976 Total score: 30.07  Peptides matched: 1
CAA31393 Total score: 30.07  Peptides matched: 1
CAA31663 Total score: 30.07  Peptides matched: 1
CAA54419 Total score: 30.07  Peptides matched: 1
CAC84456 Total score: 30.07  Peptides matched: 1
D44261 Total score: 30.07  Peptides matched: 1
D90093 Total score: 30.07  Peptides matched: 1
H96605 Total score: 30.07  Peptides matched: 1
HHBYA1 Total score: 30.07  Peptides matched: 1
HS71_CANAL Total score: 30.07  Peptides matched: 1
HS71_PICAN Total score: 30.07  Peptides matched: 1
HS71_YEAST Total score: 30.07  Peptides matched: 1
HS72_PICAN Total score: 30.07  Peptides matched: 1
HS72_YEAST Total score: 30.07  Peptides matched: 1
HS7E_SPIOL Total score: 30.07  Peptides matched: 1
JC7132 Total score: 30.07  Peptides matched: 1
JQ0966 Total score: 30.07  Peptides matched: 1
O45038 Total score: 30.07  Peptides matched: 1
O48563 Total score: 30.07  Peptides matched: 1
O62564 Total score: 30.07  Peptides matched: 1
O65171 Total score: 30.07  Peptides matched: 1
O76306 Total score: 30.07  Peptides matched: 1
O93935 Total score: 30.07  Peptides matched: 1
O94104 Total score: 30.07  Peptides matched: 1
O94106 Total score: 30.07  Peptides matched: 1
P90655 Total score: 30.07  Peptides matched: 1
P91738 Total score: 30.07  Peptides matched: 1
P97966 Total score: 30.07  Peptides matched: 1
Q05829 Total score: 30.07  Peptides matched: 1
Q17310 Total score: 30.07  Peptides matched: 1
Q23712 Total score: 30.07  Peptides matched: 1
Q24895 Total score: 30.07  Peptides matched: 1
Q24928 Total score: 30.07  Peptides matched: 1
Q24952 Total score: 30.07  Peptides matched: 1
Q27078 Total score: 30.07  Peptides matched: 1
Q27121 Total score: 30.07  Peptides matched: 1
Q27146 Total score: 30.07  Peptides matched: 1
Q27147 Total score: 30.07  Peptides matched: 1
Q40924 Total score: 30.07  Peptides matched: 1
Q91624 Total score: 30.07  Peptides matched: 1
Q943K7 Total score: 30.07  Peptides matched: 1
Q94439 Total score: 30.07  Peptides matched: 1
Q961X6 Total score: 30.07  Peptides matched: 1
Q96IS6 Total score: 30.07  Peptides matched: 1
Q96W30 Total score: 30.07  Peptides matched: 1
Q9ATB8 Total score: 30.07  Peptides matched: 1
Q9DC27 Total score: 30.07  Peptides matched: 1
Q9FSY7 Total score: 30.07  Peptides matched: 1
Q9GPM5 Total score: 30.07  Peptides matched: 1
Q9GTX3 Total score: 30.07  Peptides matched: 1
Q9LHA8 Total score: 30.07  Peptides matched: 1
Q9M4E7 Total score: 30.07  Peptides matched: 1
Q9M4E8 Total score: 30.07  Peptides matched: 1
Q9NAX9 Total score: 30.07  Peptides matched: 1
Q9NCC9 Total score: 30.07  Peptides matched: 1
Q9NCD0 Total score: 30.07  Peptides matched: 1
Q9NCD1 Total score: 30.07  Peptides matched: 1
Q9NCD2 Total score: 30.07  Peptides matched: 1
Q9NCD3 Total score: 30.07  Peptides matched: 1
Q9NCD4 Total score: 30.07  Peptides matched: 1
Q9NCD5 Total score: 30.07  Peptides matched: 1
Q9NCD6 Total score: 30.07  Peptides matched: 1
Q9NCD7 Total score: 30.07  Peptides matched: 1
Q9NCD8 Total score: 30.07  Peptides matched: 1
Q9NCD9 Total score: 30.07  Peptides matched: 1
Q9NCE0 Total score: 30.07  Peptides matched: 1
Q9NHB4 Total score: 30.07  Peptides matched: 1
Q9P8E0 Total score: 30.07  Peptides matched: 1
Q9U540 Total score: 30.07  Peptides matched: 1
Q9ZS55 Total score: 30.07  Peptides matched: 1
S03250 Total score: 30.07  Peptides matched: 1
S14949 Total score: 30.07  Peptides matched: 1
S14950 Total score: 30.07  Peptides matched: 1
S18181 Total score: 30.07  Peptides matched: 1
S20139 Total score: 30.07  Peptides matched: 1
S21879 Total score: 30.07  Peptides matched: 1
S21880 Total score: 30.07  Peptides matched: 1
S24782 Total score: 30.07  Peptides matched: 1
S41372 Total score: 30.07  Peptides matched: 1
S42488 Total score: 30.07  Peptides matched: 1
S44168 Total score: 30.07  Peptides matched: 1
S46302 Total score: 30.07  Peptides matched: 1
S49303 Total score: 30.07  Peptides matched: 1
S51682 Total score: 30.07  Peptides matched: 1
S51712 Total score: 30.07  Peptides matched: 1
S53126 Total score: 30.07  Peptides matched: 1
S71171 Total score: 30.07  Peptides matched: 1
T03581 Total score: 30.07  Peptides matched: 1
T04078 Total score: 30.07  Peptides matched: 1
T04080 Total score: 30.07  Peptides matched: 1
T06358 Total score: 30.07  Peptides matched: 1
T06598 Total score: 30.07  Peptides matched: 1
T15513 Total score: 30.07  Peptides matched: 1
T34037 Total score: 30.07  Peptides matched: 1
T45298 Total score: 30.07  Peptides matched: 1
T45474 Total score: 30.07  Peptides matched: 1
T45475 Total score: 30.07  Peptides matched: 1
T45477 Total score: 30.07  Peptides matched: 1
T45517 Total score: 30.07  Peptides matched: 1
T45522 Total score: 30.07  Peptides matched: 1
T46574 Total score: 30.07  Peptides matched: 1
T46650 Total score: 30.07  Peptides matched: 1
T48270 Total score: 30.07  Peptides matched: 1
T48271 Total score: 30.07  Peptides matched: 1
AAB08760 Total score: 26.9671  Peptides matched: 1
AAC05418 Total score: 26.9671  Peptides matched: 1
AAF23276 Total score: 26.9671  Peptides matched: 1
P93937 Total score: 26.9671  Peptides matched: 1
Q91688 Total score: 26.9671  Peptides matched: 1
Q9NCC5 Total score: 26.9671  Peptides matched: 1
Q9NCC6 Total score: 26.9671  Peptides matched: 1
Q9NCC7 Total score: 26.9671  Peptides matched: 1


Protein Hit 2
===================
Accession   : S14992
Description : dnaK-type molecular chaperone hsp70 - soybean
Score       : 166.04
Mass        : 78349.7
Frame       : 0
Coverage    : 45
-- dim  2   808.3      1  (1  )TTPSYVAFTDTER            74.55
-- dim  3   973.9      2  (2  )NQVAMNPQNTVFDAK          61.42
-- dim  4   1084.9     3  (3  )IINEPTAAAIAYGLDKK        30.07
Proteins matching the same set of peptides:
S53498 Total score: 166.04
Proteins matching a subset of these peptides:
AAA74906 Total score: 135.97  Peptides matched: 2
B45871 Total score: 135.97  Peptides matched: 2
HHXL70 Total score: 135.97  Peptides matched: 2
I49761 Total score: 135.97  Peptides matched: 2
O75634 Total score: 135.97  Peptides matched: 2
O88686 Total score: 135.97  Peptides matched: 2
Q96QC9 Total score: 135.97  Peptides matched: 2
Q9R2A1 Total score: 135.97  Peptides matched: 2
S21365 Total score: 135.97  Peptides matched: 2
S41415 Total score: 135.97  Peptides matched: 2
AAA27868 Total score: 61.42  Peptides matched: 1
Q17228 Total score: 61.42  Peptides matched: 1
Q17289 Total score: 61.42  Peptides matched: 1
Q27379 Total score: 61.42  Peptides matched: 1
A34041 Total score: 58.3171  Peptides matched: 1


Protein Hit 3
===================
Accession   : A36333
Description : dnaK-type molecular chaperone Hsc70-4 - fruit fly (Drosophila melanogaster)
Score       : 147.45
Mass        : 77814.5
Frame       : 0
Coverage    : 45
-- dim  2   808.3      1  (1  )TTPSYVAFTDTER            74.55
-- dim  3   973.9      3  (3  )NQVAMNPTQTIFDAK          42.83
-- dim  4   1084.9     3  (3  )IINEPTAAAIAYGLDKK        30.07
Proteins matching the same set of peptides:
AAF55150 Total score: 147.45
Proteins matching a subset of these peptides:


Protein Hit 4
===================
Accession   : A03309
Description : dnaK-type molecular chaperone Dsim/Hsc70-1 - fruit fly (Drosophila simulans) (fragments)
Score       : 147.03
Mass        : 25558.9
Frame       : 0
Coverage    : 28
-- dim  2   808.3      3  (3  )TTPSYVAFTESER            57.19
-- dim  3   973.9      1  (1  )NQVAMNPNNTIFDAK          89.84
Proteins matching the same set of peptides:
AAA28632 Total score: 147.03
JN0668 Total score: 143.927
Proteins matching a subset of these peptides:
B03309 Total score: 57.19  Peptides matched: 1
Q9BIS1 Total score: 57.19  Peptides matched: 1
Q9BIS3 Total score: 57.19  Peptides matched: 1


Protein Hit 5
===================
Accession   : Q95PU3
Description : HEAT SHOCK PROTEIN (HSP70).- Euplotes crassus.
Score       : 113.66
Mass        : 80429.7
Frame       : 0
Coverage    : 30
-- dim  2   808.3      1  (1  )TTPSYVAFTDTER            74.55
CB dim  4   1084.9     1  (1  )IIIEPTAAAIAYGLDKK        39.11
Proteins matching the same set of peptides:
Proteins matching a subset of these peptides:


Protein Hit 6
===================
Accession   : 1NGB
Description : Heat-shock cognate 70kd protein (44kd atpase n-terminal Fragment) (EC 3.6.1.3) mutant with glu 175 replace
d by Gln (e175q) - bovine
Score       : 109.89
Mass        : 45220.2
Frame       : 0
Coverage    : 30
-- dim  2   808.3      1  (1  )TTPSYVAFTDTER            74.55
-- dim  4   1084.9     2  (2  )IINQPTAAAIAYGLDKK        35.34
Proteins matching the same set of peptides:
Proteins matching a subset of these peptides:


Protein Hit 7
===================
Accession   : O61226
Description :
Score       : 90.71
Mass        : 0
Frame       : 0
Coverage    : 30
-- dim  2   808.3      2  (2  )TTPSYVAFTNTER            60.64
-- dim  4   1084.9     3  (3  )IINEPTAAAIAYGLDKK        30.07
Proteins matching the same set of peptides:
Proteins matching a subset of these peptides:


Protein Hit 8
===================
Accession   : P87036
Description :
Score       : 81.27
Mass        : 0
Frame       : 0
Coverage    : 29
-- dim  1   671.9      3  (3  )DAGTIAGLEVLR             51.2
-- dim  4   1084.9     3  (3  )IINEPTAAAIAYGLDKK        30.07
Proteins matching the same set of peptides:
Proteins matching a subset of these peptides:
A25398 Total score: 51.2  Peptides matched: 1
AAA30204 Total score: 51.2  Peptides matched: 1
AG2111 Total score: 51.2  Peptides matched: 1
CAB59514 Total score: 51.2  Peptides matched: 1
O76958 Total score: 51.2  Peptides matched: 1
S06158 Total score: 51.2  Peptides matched: 1
S74372 Total score: 51.2  Peptides matched: 1
A45515 Total score: 48.0971  Peptides matched: 1
CAA36551 Total score: 48.0971  Peptides matched: 1
Q94594 Total score: 48.0971  Peptides matched: 1
Q9GYW3 Total score: 48.0971  Peptides matched: 1
Q9HG01 Total score: 48.0971  Peptides matched: 1
S11448 Total score: 48.0971  Peptides matched: 1
S52727 Total score: 48.0971  Peptides matched: 1


Score Delta      Hit Protein Peptide
Accessions that matched query 97 rank 1:-

*/
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:50