Issue Running with .mzML file

[danielgeiszler]

Hello,

I'm having a problem trying to run FlashLFQ. Here is my command line execution and error message:

& '..\FlashLFQ\FlashLFQ\FlashLFQExecutable' --idt flashLFQinput.psmtsv --raw FileName.mzML --rep . --chg false

Opening PSM file flashLFQinput.psmtsv Done reading PSMs Setup is OK; read in 12894 identifications; starting FlashLFQ engine Assigning MS1 peaks to bins Quantifying peptides for FileName Unhandled Exception: System.AggregateException: One or more errors occurred. ---> System.ArgumentOutOfRangeException: Index was out of range. Must be non-negative and less than the size of the collection. Parameter name: index at System.ThrowHelper.ThrowArgumentOutOfRangeException(ExceptionArgument argument, ExceptionResource resource) at FlashLFQ.FlashLFQEngine.FilterPeaksByIsotopicDistribution(IEnumerable1 peaks, Identification identification, Int32 chargeState, Boolean lookForBadIsotope, Dictionary2 allMs1Scans) at FlashLFQ.FlashLFQEngine.<>cDisplayClass31_0.b4(Tuple`2 range, ParallelLoopState loopState) at System.Threading.Tasks.Parallel.<>cDisplayClass42_0`2.b1() at System.Threading.Tasks.Task.InnerInvokeWithArg(Task childTask) at System.Threading.Tasks.Task.<>c__DisplayClass176_0.b__0(Object ) --- End of inner exception stack trace --- at System.Threading.Tasks.Task.ThrowIfExceptional(Boolean includeTaskCanceledExceptions) at System.Threading.Tasks.Task.Wait(Int32 millisecondsTimeout, CancellationToken cancellationToken) at System.Threading.Tasks.Parallel.PartitionerForEachWorker[TSource,TLocal](Partitioner1 source, ParallelOptions parallelOptions, Action1 simpleBody, Action2 bodyWithState, Action3 bodyWithStateAndIndex, Func4 bodyWithStateAndLocal, Func5 bodyWithEverything, Func1 localInit, Action1 localFinally) at System.Threading.Tasks.Parallel.ForEach[TSource](Partitioner1 source, ParallelOptions parallelOptions, Action2 body) at FlashLFQ.FlashLFQEngine.QuantifyMS2IdentifiedPeptides(RawFileInfo fileInfo, Dictionary2 mzBins, Dictionary2 allMs1Scans) at FlashLFQ.FlashLFQEngine.Run() at FlashLFQExecutable.FlashLFQExecutable.Main(String[] args) in C:\Users\rmillikin\Source\Repos\FlashLFQ\FlashLFQ Executable\FlashLFQExecutable.cs:line 112

Also, your GitHub page says that this supports a custom filetype with the headers "File Name", "Base Sequence", "Full Sequence", "Peptide Monoisotopic Mass", "Scan Retention Time", "Precursor Charge", and "Protein Accession". When I tried to build an input file with these parameters, it failed saying that it was an Unknown file type. I don't see anywhere in the PsmReader.cs source code where this would be supported either.

Please let me know if you can help me with this issue.

Thanks, Danny

[trishorts]

we'll get on this shortly.

[rmillikin]

Sorry about that - the latest version should be able to parse generic PSM input. The readme has been updated slightly too, since some of the parameters have changed recently and the readme was out of date.

The crash is a little more involved. I can take a stab at it and guess that the monoisotopic mass in your PSM file may not be consistent between Modified Sequences. Can you double check that you only have one monoisotopic mass per Mod Sequence?

If it's not that (or if you're not sure), are you able to share your PSM file along with one or more of your mzML files?

You may email them to me at rmillikin@wisc.edu .

[KaiLiCn]

I also met this issue. The data I used was from FlashLFQ-master\Test\SampleFiles in the download package.

[trishorts]

We'll look at it shortly.

[rmillikin]

Hello Kai,

Please make sure your FlashLFQ is the latest version. I'm also not sure if that mzML included in that particular sample file is up to date. I'll upload a new sample files package here, attached.

SampleFiles.zip

[cksakura]

Hello,

Thank you for your advice. Currently, I only use the raw files directly and it works very well.

Best regards,

Kai

On 19 April 2018 at 11:01, rmillikin notifications@github.com wrote:

Hello Kai,

Please make sure your FlashLFQ is the latest version. I'm also not sure if that mzML included in the sample files is up to date. I'll upload a new sample files package here, attached.

SampleFiles.zip https://github.com/smith-chem-wisc/FlashLFQ/files/1928626/SampleFiles.zip

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