SpectraTutorials

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Tutorial sections and SQLite database for MONA Spectral Database (.msp)

4

Hello jorainer, First of all many thanks for this utterly great and comprehensible tutorial and of course all the wonderful work hidden in the `Spectra` package. I would like to...

Tony-II

precursorMz of hmdb Spectra object are NAs

5

Hi Johannes, I just realized that precursorMz is another important check on the matched spectra between samples and database. Only if both precursorMz matched should the spectra comparison meaningful. I...

gmhhope

export massbank spectra object 2 mgf format encounter error.

2

Sorry for bombarding questions here! This question is not urgent but I would like to see if you can tell what is going wrong. When I try to export massbank...

gmhhope

concatenateSpectra Error

1

I am trying to merge spectra objects based on the function `concatenateSpectra` you used in this session: https://bioconductor.org/packages/devel/bioc/vignettes/Spectra/inst/doc/Spectra.html#33_Filtering,_subsetting_and_merging ## Background - I have performed `filterMz` and subset the original MS2...

gmhhope

Ways to export the spectra object (S4 method object) to a dataframe?

2

Hi Johannes, Since I am working on several dozens of MS2 spectra, rather than one cysteine, I need to try to export the information stored in the spectra objects or...

gmhhope

Filtering spectra within a particular RT range in each precursorMz? functions similar to `filterPrecursorMz`?

2

Could I easily implement filtering spectra within a particular RT range according to their character in the MS1 scan? Something similar to `filterPrecursorMz`? Thanks, Minghao Gong

gmhhope

PrecursorIntensity of all MS2 spectra equal to zero?

6

Hi Johannes, I noticed that in my dataset, all my precursor intensity of all MS2 spectra equal to zero? But I do get peaks when I look into the data....

gmhhope

Reasonable range of dot-product score for a good MS/MS matching

4

Do you have some empirical ideas of a reasonable range of dot-product scores for a good MS/MS matching? Thanks, Minghao

gmhhope

Export options other than mgf?

6

What options for the export function in `Spectra` other than .mgf? Thanks, Minghao

gmhhope

Error when try to setBackend from MsBackendMzR to MsBackendDataFrame

3

Hi Johannes, Here also I want to report issue when I tried to load my own data and `setBackend` from `MzR` to `DataFrame`. It renders following error. ```{r change-backend} #'...

gmhhope