524d / mzrecal

Recalibrate Mass Spectrometry data in mzML format

Hi there 👋, I'm Rob Marissen

• 🔭 I'm working at the Center for Proteomics and Metabolomics of the Leiden University Medical Center

• 💻 Some of my current projects are: mzRecal, CompareMS2,

• 🧠 My interests are: mass spectromety, software security, software reliability and testability, user interface design

• ⚡ Fun fact: Some interesting facts about the number 42 are revealed by John Baez

Some of the computer languages and tools I use:

mzrecal's Issues

Add SDRF support for mzRecal

It would be great if mzRecal could recalilbrate all files in an SDRF file, or we supply a script that takes certain parameters and file names from the SDRF and runs through a workflow that does the recalibration.

@di-hardt is working on a SDRF to Comet conversion (presumably using "comment[precursor mass tolerance]", "comment[fragment mass tolerance]", "comment[modification parameters]", "comment[cleavage agent details]" etc. to determine the Comet parameters, and "characteristics[organism]" to select a FASTA file). We can focus on the mzRecal-specific parameters, which I think are only "comment[precursor mass tolerance]" and "comment[instrument]" (and the input file names of course).

There are many instruments in the tree, but we can make a look-up table for them. This would allow the used to override the instruments specified in the mzML file for specific datasets. In the future, it may be easier to maintain this functionality in the SDRF to mzRecal script than in mzRecal itself.

Improving documentation and README.md

As the manuscript nears completion, could we update the README Markdown to reflect the narrative in the manuscript, and using a similar figure as in the manuscript? It does not have to be the same dataset, but presented in the same style for clarity and consistency. The "aim" of the software is also described well in the manuscript. Perhaps we can borrow and condense that narrative here?

Add mzQC output

Generate an mzQC file as (optional) output with runQuality metrics such as mass measurement error distribution moments and an array of spectrum-level metrics such as the number of internal calibrants found and used per spectrum, and their errors before and after recalibration. All of this information is already available.

Make max_peaks data-dependent

Allocate just enough memory to store the largest spectrum.