Re: [Mzmine-devel] Identifying spectra in aligned peak-lists

Hi Chris, > For aligned peak-lists, whether the m/z and intensity values are the > average or "best" of each row isn't so much the issue as how to group > the rows in the first place. I somehow assumed that you already had them grouped. I think you wrote something in that sense a few emails back

Re: [Mzmine-devel] Identifying spectra in aligned peak-lists

G'day, > What exactly are you planning to pass to NIST MS search? I'm passing the list of (m/z, intensity) pairs, one pair for each of the peak-list rows that I've grouped together. > I can see two ways: > > 1) Identify the peak list rows that should be grouped together. > Then you take th

Re: [Mzmine-devel] Identifying spectra in aligned peak-lists

Hi Chris, > Sorry, what I'm trying to imply is that if an aligned peak-list has a > set of rows that should clearly be grouped together to form a spectrum > (to pass to NIST MS Search) then there's no guarantee that the values of > PeakListRow.getBestPeak().getRepresentativeScan() for each of the

Re: [Mzmine-devel] Identifying spectra in aligned peak-lists

G'day, >> Suppose you have an aligned peak-list and have (manually) identified a >> set of peak-list rows that are part of the same spectrum. There's no >> guarantee (in fact it's quite likely?) the peak-list rows will all >> return identical values for >> PeakListRow.getBestPeak().getRepresentat

Re: [Mzmine-devel] Identifying spectra in aligned peak-lists

> Suppose you have an aligned peak-list and have (manually) identified a > set of peak-list rows that are part of the same spectrum. There's no > guarantee (in fact it's quite likely?) the peak-list rows will all > return identical values for > PeakListRow.getBestPeak().getRepresentativeScan(). T

Re: [Mzmine-devel] Identifying spectra in aligned peak-lists

Hi Chris, > As far as I understood, I suppose your data is GC-MS and so you use MS scans > and compare them to the NIST library. Yes, that's correct. > Perhaps we can assume that the spectra of aligned peaks should be similar, as > long as the alignment is correct. > Therefore I would suggest

Re: [Mzmine-devel] Identifying spectra in aligned peak-lists

Hi Chris, I am not sure I understand correctly your approach. Is your data coming from GC-MS or LC-MS? Are you searching MS scans or MS/MS scans? As far as I understood, I suppose your data is GC-MS and so you use MS scans and compare them to the NIST library. Perhaps we can assume that the sp

[Mzmine-devel] Identifying spectra in aligned peak-lists

G'day, I'm working on a module that uses the NIST MS Search program to identify peaks. NIST MS Search takes spectra as input for its searches. Each spectrum is defined by a set of one or more (mass, intensity) pairs. Given a peak-list in MZmine 2 I