diff --git a/pwiz/data/msdata/Serializer_MGF.cpp b/pwiz/data/msdata/Serializer_MGF.cpp
index fe06378b39..f94375780f 100644
--- a/pwiz/data/msdata/Serializer_MGF.cpp
+++ b/pwiz/data/msdata/Serializer_MGF.cpp
@@ -1,57 +1,57 @@
-//
-// $Id$
-//
-//
-// Original author: Matt Chambers <matt.chambers .@. vanderbilt.edu>
-//
-// Copyright 2011 Vanderbilt University - Nashville, TN 37232
-//
-// Licensed under the Apache License, Version 2.0 (the "License"); 
-// you may not use this file except in compliance with the License. 
-// You may obtain a copy of the License at 
-//
-// http://www.apache.org/licenses/LICENSE-2.0
-//
-// Unless required by applicable law or agreed to in writing, software 
-// distributed under the License is distributed on an "AS IS" BASIS, 
-// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 
-// See the License for the specific language governing permissions and 
-// limitations under the License.
-//
-
-
-#define PWIZ_SOURCE
-
-#include "Serializer_MGF.hpp"
-#include "SpectrumList_MGF.hpp"
-#include "pwiz/utility/misc/Filesystem.hpp"
-#include "pwiz/utility/misc/Std.hpp"
-#include <boost/spirit/include/karma.hpp>
-#include "SpectrumWorkerThreads.hpp"
-
-
-namespace pwiz {
-namespace msdata {
-
-
-using boost::iostreams::stream_offset;
-using namespace pwiz::util;
-
-
-class Serializer_MGF::Impl
-{
-    public:
-
-    Impl()
-    {}
-
-    void write(ostream& os, const MSData& msd,
-               const pwiz::util::IterationListenerRegistry* iterationListenerRegistry,
-               bool useWorkerThreads, bool continueOnError) const;
-
-    void read(shared_ptr<istream> is, MSData& msd) const;
-};
-
+//
+// $Id$
+//
+//
+// Original author: Matt Chambers <matt.chambers .@. vanderbilt.edu>
+//
+// Copyright 2011 Vanderbilt University - Nashville, TN 37232
+//
+// Licensed under the Apache License, Version 2.0 (the "License"); 
+// you may not use this file except in compliance with the License. 
+// You may obtain a copy of the License at 
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software 
+// distributed under the License is distributed on an "AS IS" BASIS, 
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 
+// See the License for the specific language governing permissions and 
+// limitations under the License.
+//
+
+
+#define PWIZ_SOURCE
+
+#include "Serializer_MGF.hpp"
+#include "SpectrumList_MGF.hpp"
+#include "pwiz/utility/misc/Filesystem.hpp"
+#include "pwiz/utility/misc/Std.hpp"
+#include <boost/spirit/include/karma.hpp>
+#include "SpectrumWorkerThreads.hpp"
+
+
+namespace pwiz {
+namespace msdata {
+
+
+using boost::iostreams::stream_offset;
+using namespace pwiz::util;
+
+
+class Serializer_MGF::Impl
+{
+    public:
+
+    Impl()
+    {}
+
+    void write(ostream& os, const MSData& msd,
+               const pwiz::util::IterationListenerRegistry* iterationListenerRegistry,
+               bool useWorkerThreads, bool continueOnError) const;
+
+    void read(shared_ptr<istream> is, MSData& msd) const;
+};
+
 template <typename T>
 struct nosci10_policy : boost::spirit::karma::real_policies<T>   
 {
@@ -59,25 +59,25 @@ struct nosci10_policy : boost::spirit::karma::real_policies<T>
     static unsigned int precision(T) { return 10; }
     //  we want the numbers always to be in fixed format
     static int floatfield(T) { return boost::spirit::karma::real_policies<T>::fmtflags::fixed; }
-};
-
-
-void Serializer_MGF::Impl::write(ostream& os, const MSData& msd,
-    const pwiz::util::IterationListenerRegistry* iterationListenerRegistry,
-    bool useWorkerThreads, bool continueOnError) const
-{
-    bool titleIsThermoDTA = false;
-    if (msd.fileDescription.sourceFilePtrs.size() >= 1)
-        titleIsThermoDTA = msd.fileDescription.sourceFilePtrs[0]->hasCVParam(MS_Thermo_nativeID_format);
-    const string& thermoFilename = titleIsThermoDTA ? msd.fileDescription.sourceFilePtrs[0]->name : "";
-    string thermoBasename = titleIsThermoDTA ? bfs::basename(thermoFilename) : "";
-
-    int scansWritten = 0;
-
-    os << std::setprecision(10); // 1234.567890
-    SpectrumList& sl = *msd.run.spectrumListPtr;
-    SpectrumWorkerThreads spectrumWorkers(sl, useWorkerThreads, continueOnError);
-    for (size_t i=0, end=sl.size(); i < end; ++i)
+};
+
+
+void Serializer_MGF::Impl::write(ostream& os, const MSData& msd,
+    const pwiz::util::IterationListenerRegistry* iterationListenerRegistry,
+    bool useWorkerThreads, bool continueOnError) const
+{
+    bool titleIsThermoDTA = false;
+    if (msd.fileDescription.sourceFilePtrs.size() >= 1)
+        titleIsThermoDTA = msd.fileDescription.sourceFilePtrs[0]->hasCVParam(MS_Thermo_nativeID_format);
+    const string& thermoFilename = titleIsThermoDTA ? msd.fileDescription.sourceFilePtrs[0]->name : "";
+    string thermoBasename = titleIsThermoDTA ? bfs::basename(thermoFilename) : "";
+
+    int scansWritten = 0;
+
+    os << std::setprecision(10); // 1234.567890
+    SpectrumList& sl = *msd.run.spectrumListPtr;
+    SpectrumWorkerThreads spectrumWorkers(sl, useWorkerThreads, continueOnError);
+    for (size_t i=0, end=sl.size(); i < end; ++i)
     {
         SpectrumPtr s;
         try
@@ -89,164 +89,164 @@ void Serializer_MGF::Impl::write(ostream& os, const MSData& msd,
         {
             if (continueOnError)
             {
-                cerr << "Skipping spectrum " << i << " \"" << (s ? s->id : sl.spectrumIdentity(i).id) << "\": " << e.what() << endl;
-                continue;
+                cerr << "Skipping spectrum " << i << " \"" << (s ? s->id : sl.spectrumIdentity(i).id) << "\": " << e.what() << endl;
+                continue;
             }
             else
                 throw;
-        }
-
-        Scan* scan = !s->scanList.empty() ? &s->scanList.scans[0] : 0;
-
-        if (s->cvParam(MS_ms_level).valueAs<int>() > 1 &&
-            !s->precursors.empty() &&
-            !s->precursors[0].selectedIons.empty())
-        {
-            os << "BEGIN IONS\n";
-
-            const SelectedIon& si = s->precursors[0].selectedIons[0];
-            CVParam scanTimeParam = scan ? scan->cvParam(MS_scan_start_time) : CVParam();
-            CVParam chargeParam = si.cvParam(MS_charge_state);
-
-            CVParam spectrumTitle = s->cvParam(MS_spectrum_title);
-            if (!spectrumTitle.empty())
-                os << "TITLE=" << spectrumTitle.value << '\n';
-            else if (titleIsThermoDTA)
-            {
-                string scan = id::value(s->id, "scan");
-                os << "TITLE=" << thermoBasename << '.' << scan << '.' << scan << '.' << chargeParam.value << '\n';
-            }
-            else
-                os << "TITLE=" << s->id << '\n';
-
-            if (!scanTimeParam.empty())
-                os << "RTINSECONDS=" << scanTimeParam.timeInSeconds() << '\n';
-
-            // many MGF parsers can't handle scientific notation (!) so explicitly use fixed
-            os << "PEPMASS=" << si.cvParam(MS_selected_ion_m_z).valueFixedNotation();
-            
-            bool negativePolarity = s->hasCVParam(MS_negative_scan) ? true : false;
-
-            CVParam intensityParam = si.cvParam(MS_peak_intensity);
-            if (!intensityParam.empty())
-                os << " " << intensityParam.valueFixedNotation();
-            os << '\n';
-
-            CVParam inverseReduceIonMobility = si.cvParam(MS_inverse_reduced_ion_mobility);
-            if (!inverseReduceIonMobility.empty())
-                os << "INVREION=" << inverseReduceIonMobility.valueFixedNotation();
-            os << '\n';
-
-            CVParam collisionalCrossSectionalArea = si.cvParam(MS_collisional_cross_sectional_area);
-            if (!collisionalCrossSectionalArea.empty())
-                os << "COLLCROSSSA=" << collisionalCrossSectionalArea.valueFixedNotation();
-            os << '\n';
-
-            if (chargeParam.empty())
-            {
-                vector<string> charges;
-                BOOST_FOREACH(const CVParam& param, si.cvParams)
-                {
-                    if (param.cvid == MS_possible_charge_state)
-                        charges.push_back(param.value + (negativePolarity ? '-' : '+'));
-                }
-                if (!charges.empty())
-                    os << "CHARGE=" << bal::join(charges, " and ") << '\n';
-            }
-            else
-                os << "CHARGE=" << chargeParam.value << (negativePolarity ? '-' : '+') << '\n';
-
-            const BinaryDataArray& mzArray = *s->getMZArray();
-            const BinaryDataArray& intensityArray = *s->getIntensityArray();
+        }
+
+        const Scan& scan = !s->scanList.empty() ? s->scanList.scans[0] : Scan();
+
+        if (s->cvParam(MS_ms_level).valueAs<int>() > 1 &&
+            !s->precursors.empty() &&
+            !s->precursors[0].selectedIons.empty())
+        {
+            os << "BEGIN IONS\n";
+
+            const SelectedIon& si = s->precursors[0].selectedIons[0];
+            CVParam scanTimeParam = scan.cvParam(MS_scan_start_time);
+            CVParam chargeParam = si.cvParam(MS_charge_state);
+
+            CVParam spectrumTitle = s->cvParam(MS_spectrum_title);
+            if (!spectrumTitle.empty())
+                os << "TITLE=" << spectrumTitle.value << '\n';
+            else if (titleIsThermoDTA)
+            {
+                string scan_string = id::value(s->id, "scan");
+                os << "TITLE=" << thermoBasename << '.' << scan_string << '.' << scan_string << '.' << chargeParam.value << '\n';
+            }
+            else
+                os << "TITLE=" << s->id << '\n';
+
+            if (!scanTimeParam.empty())
+                os << "RTINSECONDS=" << scanTimeParam.timeInSeconds() << '\n';
+
+            // many MGF parsers can't handle scientific notation (!) so explicitly use fixed
+            os << "PEPMASS=" << si.cvParam(MS_selected_ion_m_z).valueFixedNotation();
+            
+            bool negativePolarity = s->hasCVParam(MS_negative_scan) ? true : false;
+
+            CVParam intensityParam = si.cvParam(MS_peak_intensity);
+            if (!intensityParam.empty())
+                os << " " << intensityParam.valueFixedNotation();
+            os << '\n';
+
+            CVParam inverseReduceIonMobility = scan.cvParam(MS_inverse_reduced_ion_mobility);
+            if (!inverseReduceIonMobility.empty())
+                os << "INVREION=" << inverseReduceIonMobility.valueFixedNotation();
+            os << '\n';
+
+            CVParam collisionalCrossSectionalArea = scan.cvParam(MS_collisional_cross_sectional_area);
+            if (!collisionalCrossSectionalArea.empty())
+                os << "COLLCROSSSA=" << collisionalCrossSectionalArea.valueFixedNotation();
+            os << '\n';
+
+            if (chargeParam.empty())
+            {
+                vector<string> charges;
+                BOOST_FOREACH(const CVParam& param, si.cvParams)
+                {
+                    if (param.cvid == MS_possible_charge_state)
+                        charges.push_back(param.value + (negativePolarity ? '-' : '+'));
+                }
+                if (!charges.empty())
+                    os << "CHARGE=" << bal::join(charges, " and ") << '\n';
+            }
+            else
+                os << "CHARGE=" << chargeParam.value << (negativePolarity ? '-' : '+') << '\n';
+
+            const BinaryDataArray& mzArray = *s->getMZArray();
+            const BinaryDataArray& intensityArray = *s->getIntensityArray();
             using namespace boost::spirit::karma;
             typedef real_generator<double, nosci10_policy<double> > nosci10_type;
             static const nosci10_type nosci10 = nosci10_type();
-            char buffer[256];
-            for (size_t p=0; p < s->defaultArrayLength; ++p)
-            {
-                char* b = buffer;
-                generate(b, nosci10, intensityArray.data[p]);
-                *b = 0;
-                os << mzArray.data[p] << ' ' << buffer << '\n';
-            }
-
-            os << "END IONS\n";
-            ++scansWritten;
-        }
-
-        // update any listeners and handle cancellation
-        IterationListener::Status status = IterationListener::Status_Ok;
-
-        if (iterationListenerRegistry)
-            status = iterationListenerRegistry->broadcastUpdateMessage(
-                IterationListener::UpdateMessage(i, end));
-
-        if (status == IterationListener::Status_Cancel) 
-            break;
-    }
-
-    if (sl.size() == 0)
-        sl.warn_once("Warning: MGF output is empty because the spectrum list is empty (possibly due to filtering)");
-    else if (scansWritten == 0)
-        sl.warn_once("Warning: MGF output is empty because the spectrum list has no MS2+ spectra (either due to filtering or the acquisition method)");
-}
-
-
-void Serializer_MGF::Impl::read(shared_ptr<istream> is, MSData& msd) const
-{
-    if (!is.get() || !*is)
-        throw runtime_error("[Serializer_MGF::read()] Bad istream.");
-
-    is->seekg(0);
-
-    // read mzML file-level metadata stored in comment tags by the MGF writer like:
-    // # fileContent CVParam MS:12345678 (term name)
-    // # sourceFile id=foo name=bar location=file:///foo/bar
-    /*string lineStr;
-    while (is->peek() != (int) 'B')
-    {
-        getline(*is_, lineStr);
-        if (lineStr[0] == '#')
-        {
-            vector<string> tokens;
-            bal::split(tokens, lineStr, bal::is_space());
-            if (tokens[1] == "fileContent")
-                addParamToContainer(msd.fileDescription.fileContent, */
-
-    // we treat all MGF data is MSn (PMF MGFs not currently supported)
-    msd.fileDescription.fileContent.set(MS_MSn_spectrum);
-    msd.fileDescription.fileContent.set(MS_centroid_spectrum);
-    msd.run.spectrumListPtr = SpectrumList_MGF::create(is, msd);
-    msd.run.chromatogramListPtr.reset(new ChromatogramListSimple);
-}
-
-
-//
-// Serializer_MGF
-//
-
-
-PWIZ_API_DECL Serializer_MGF::Serializer_MGF()
-:   impl_(new Impl())
-{}
-
-
-PWIZ_API_DECL void Serializer_MGF::write(ostream& os, const MSData& msd,
-    const pwiz::util::IterationListenerRegistry* iterationListenerRegistry,
-    bool useWorkerThreads, bool continueOnError) const
-  
-{
-    return impl_->write(os, msd, iterationListenerRegistry, useWorkerThreads, continueOnError);
-}
-
-
-PWIZ_API_DECL void Serializer_MGF::read(shared_ptr<istream> is, MSData& msd) const
-{
-    return impl_->read(is, msd);
-}
-
-
-} // namespace msdata
-} // namespace pwiz
-
-
+            char buffer[256];
+            for (size_t p=0; p < s->defaultArrayLength; ++p)
+            {
+                char* b = buffer;
+                generate(b, nosci10, intensityArray.data[p]);
+                *b = 0;
+                os << mzArray.data[p] << ' ' << buffer << '\n';
+            }
+
+            os << "END IONS\n";
+            ++scansWritten;
+        }
+
+        // update any listeners and handle cancellation
+        IterationListener::Status status = IterationListener::Status_Ok;
+
+        if (iterationListenerRegistry)
+            status = iterationListenerRegistry->broadcastUpdateMessage(
+                IterationListener::UpdateMessage(i, end));
+
+        if (status == IterationListener::Status_Cancel) 
+            break;
+    }
+
+    if (sl.size() == 0)
+        sl.warn_once("Warning: MGF output is empty because the spectrum list is empty (possibly due to filtering)");
+    else if (scansWritten == 0)
+        sl.warn_once("Warning: MGF output is empty because the spectrum list has no MS2+ spectra (either due to filtering or the acquisition method)");
+}
+
+
+void Serializer_MGF::Impl::read(shared_ptr<istream> is, MSData& msd) const
+{
+    if (!is.get() || !*is)
+        throw runtime_error("[Serializer_MGF::read()] Bad istream.");
+
+    is->seekg(0);
+
+    // read mzML file-level metadata stored in comment tags by the MGF writer like:
+    // # fileContent CVParam MS:12345678 (term name)
+    // # sourceFile id=foo name=bar location=file:///foo/bar
+    /*string lineStr;
+    while (is->peek() != (int) 'B')
+    {
+        getline(*is_, lineStr);
+        if (lineStr[0] == '#')
+        {
+            vector<string> tokens;
+            bal::split(tokens, lineStr, bal::is_space());
+            if (tokens[1] == "fileContent")
+                addParamToContainer(msd.fileDescription.fileContent, */
+
+    // we treat all MGF data is MSn (PMF MGFs not currently supported)
+    msd.fileDescription.fileContent.set(MS_MSn_spectrum);
+    msd.fileDescription.fileContent.set(MS_centroid_spectrum);
+    msd.run.spectrumListPtr = SpectrumList_MGF::create(is, msd);
+    msd.run.chromatogramListPtr.reset(new ChromatogramListSimple);
+}
+
+
+//
+// Serializer_MGF
+//
+
+
+PWIZ_API_DECL Serializer_MGF::Serializer_MGF()
+:   impl_(new Impl())
+{}
+
+
+PWIZ_API_DECL void Serializer_MGF::write(ostream& os, const MSData& msd,
+    const pwiz::util::IterationListenerRegistry* iterationListenerRegistry,
+    bool useWorkerThreads, bool continueOnError) const
+  
+{
+    return impl_->write(os, msd, iterationListenerRegistry, useWorkerThreads, continueOnError);
+}
+
+
+PWIZ_API_DECL void Serializer_MGF::read(shared_ptr<istream> is, MSData& msd) const
+{
+    return impl_->read(is, msd);
+}
+
+
+} // namespace msdata
+} // namespace pwiz
+
+