ms

README

#ms: A Go library to deal with Mass Spectrometry data.

Includes the unthermo library that can read Thermo Finnigan RAW files without external API's, a successor to unfinnigan.

Usable tools:

• XIC, prints the mass chromatogram for a given m/z.

  linux amd64 executable

  windows amd64 executable

  macos amd64 executable

  Documentation over here

Documentation

Overview

Package ms is a library for mass spectrometry data

Index

• type Analyzer
• type Peak
• type Scan
• type Spectrum
  • func (a Spectrum) Len() int
  • func (a Spectrum) Less(i, j int) bool
  • func (a Spectrum) Swap(i, j int)

Types

type Analyzer

type Analyzer int

Analyzer is the mass analyzer

const (
	ITMS Analyzer = iota
	TQMS
	SQMS
	TOFMS
	FTMS
	Sector
	Undefined
)

The analyzer types are documented in literature

type Peak

type Peak struct {
	Mz float64
	I  float32
}

Peak represents an ion peak

type Scan

type Scan struct {
	Analyzer Analyzer
	MSLevel  uint8
	//Spectrum is a function forcing the read of a spectrum,
	//which is "delayed" for efficiency reasons. If it was not delayed
	//and Spectrum were a data structure, it would always have to
	//be read, which is very expensive. Now if only another property of
	//Scan (cheaper to obtain) is requested, resources are saved.
	Spectrum func(centroided ...bool) Spectrum
	//PrecursorMzs is only filled with mz values at MSx scans.
	PrecursorMzs []float64
	Time         float64
}

Scan represents the peak acquisition event of the mass spectrometer

type Spectrum

type Spectrum []Peak

A Spectrum is a collection of peaks

func (Spectrum) Len

func (a Spectrum) Len() int

func (Spectrum) Less

func (a Spectrum) Less(i, j int) bool

func (Spectrum) Swap

func (a Spectrum) Swap(i, j int)