Can this method "Peak identification carried out by cumulative lines" being intergrated into existing non-targeted LCMS analysis up-stream pipeline?

[YUANMENG-1]

I would like to ask if there are existing tools that use this principle for peak lifting, if not, do you plan to build new upstream analysis tools based on this?

[YUANMENG-1]

Did this have some paper?

[xieguigang]

hi,

The algorithm for peak detection based on signal accumulation lines is a prevalent approach within the field of signal processing. This methodology is extensively utilized in biological image processing applications, such as the detection of cell and tissue boundaries. Nevertheless, its application for peak detection in liquid chromatography-mass spectrometry is not routine, as the prevailing technique for deconvolution analysis in LCMS remains curve fitting methods.

An implementation of the signal accumulation line method is available within the mzkit software, and we have conducted a series of tests that have yielded promising results. I will furnish you with detailed test outcomes in due course and will ensure to inform you accordingly. Your attention to the progress of this endeavor would be appreciated.

code details of algorithm implements in mzkit

1. Chromatogram data calls the PopulateROI function for finding ROI peaks:
   https://github.com/xieguigang/mzkit/blob/402ade786b1a653ad10429ab3a366ae501e5f200/src/mzmath/mz_deco/Deconvolution.vb#L81

2. then function PopulateROI reference to the ElevationAlgorithm module for find signal peaks:
   https://github.com/xieguigang/mzkit/blob/402ade786b1a653ad10429ab3a366ae501e5f200/src/mzmath/mz_deco/Signals/Chromatogram/AccumulateROI.vb#L120

3. where finnaly in ElevationAlgorithm module use the method of signal accumulation lines for finding the signal peaks as the LCMS peak ROI output:
   

   sciBASIC/Data_science/Mathematica/SignalProcessing/SignalProcessing/PeakFinding/Algorithm.vb

   Line 96 in bebb0a7

   Public Iterator Function FindAllSignalPeaks(Of T As ITimeSignal)(signals As IEnumerable(Of T)) As IEnumerable(Of SignalPeak)

The above algorithm invocation process has been encapsulated as a public API in an mzkit_hpc R# language package, allowing for the method to be called through script programming.

[YUANMENG-1]

I was very surprised to see this idea of peak raising, and hope to have tools available！！

[YUANMENG-1]

I am doing an evaluation of as many new peak picking algorithms as possible. According to the link you sent, can I input mzML to get the peak table? Sincerely expecting referencing your tools!!🙋‍♂️🙋‍♂️

[YUANMENG-1]

您好请问我可以github_install mzkit_hpc来完成整个mzkit_hpc的这三个步骤吗？ Chromatogram data calls the PopulateROI function for finding ROI peaks: then function PopulateROI reference to the ElevationAlgorithm module for find single peaks: where finnaly in ElevationAlgorithm module use the method of signal accumulation lines for finding the single peaks as the LCMS peak ROi outcomes: At 2024-07-02 11:08:28, "この中二病に爆焔を！" ***@***.***> wrote: hi, The algorithm for peak detection based on signal accumulation lines is a prevalent approach within the field of signal processing. This methodology is extensively utilized in biological image processing applications, such as the detection of cell and tissue boundaries. Nevertheless, its application for peak detection in liquid chromatography-mass spectrometry is not routine, as the prevailing technique for deconvolution analysis in LCMS remains curve fitting methods. An implementation of the signal accumulation line method is available within the mzkit software, and we have conducted a series of tests that have yielded promising results. I will furnish you with detailed test outcomes in due course and will ensure to inform you accordingly. Your attention to the progress of this endeavor would be appreciated. code details of algorithm implements in mzkit Chromatogram data calls the PopulateROI function for finding ROI peaks: https://github.com/xieguigang/mzkit/blob/402ade786b1a653ad10429ab3a366ae501e5f200/src/mzmath/mz_deco/Deconvolution.vb#L81 then function PopulateROI reference to the ElevationAlgorithm module for find single peaks: https://github.com/xieguigang/mzkit/blob/402ade786b1a653ad10429ab3a366ae501e5f200/src/mzmath/mz_deco/Signals/Chromatogram/AccumulateROI.vb#L120 where finnaly in ElevationAlgorithm module use the method of signal accumulation lines for finding the single peaks as the LCMS peak ROi outcomes: https://github.com/xieguigang/sciBASIC/blob/bebb0a718729db13725bf593b08ad7b32b9fe938/Data_science/Mathematica/SignalProcessing/SignalProcessing/PeakFinding/Algorithm.vb#L96 The above algorithm invocation process has been encapsulated as a public API in an mzkit_hpc R# language package, allowing for the method to be called through script programming. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[xieguigang]

你好，这个非常抱歉哈，这个目前还没有办法兼容R语言。因为目前这个包是使用我自己设计的R#(rsharp-lang/R-sharp)编程语言来开发的，R#语言不是传统意义上的R语言，所以没有办法使用github_install来进行安装 。😅😅😅😅😅