per https://skyline.ms/announcements/home/support/thread.view?rowId=6…

…5625 be a little more tolerant of data variants:

In SSL, accept "scan=<number>" as meaning just <number>
In mzML reader, accept MS2 scans that lack precursor values

pwiz_tools/BiblioSpec/src/PwizReader.cpp

@@ -435,7 +435,7 @@ void PwizReader::transferSpec(BiblioSpec::SpecData& returnData,
 
     returnData.id = specInfo->scanNumber;
     returnData.retentionTime = specInfo->retentionTime/60;  // seconds to minutes
-    if (specInfo->msLevel > 1)
+    if (specInfo->msLevel > 1 && !specInfo->precursors.empty())
     {
         returnData.mz = specInfo->precursors[0].mz;
     }

pwiz_tools/BiblioSpec/src/SslReader.h

@@ -64,6 +64,11 @@ class sslPSM : public PSM {
             } catch (bad_lexical_cast) {
                 if (bal::istarts_with(value, "index="))
                     psm.specIndex = boost::lexical_cast<int>(value.substr(6));
+                else if (bal::istarts_with(value, "scan="))
+                {
+                    psm.specKey = boost::lexical_cast<int>(trimLeadingZeros(value.substr(5)));
+                    psm.specIndex = -1;
+                }
                 else
                     psm.specName = value;
             }