OpenMS::MS1LabelState Namespace Reference

The label state of an identification in MS1-labeled (SILAC, Dimethyl, ...) data. More...

Classes
struct	Keys
	The registry indices of the three keys, resolved once for a loop over many hits. More...

Functions
const std::vector< std::string > &	keys ()
	The three keys, in the order they are reported.
bool	hasMatchedSequence (const PeptideHit &hit)
bool	hasMatchedSequence (const PeptideHit &hit, const Keys &keys)
	Index-based variant of hasMatchedSequence() for loops over many hits.
AASequence	matchedSequence (const PeptideHit &hit)
	The peptidoform hit was matched to the spectrum with.
AASequence	matchedSequence (const PeptideHit &hit, const Keys &keys)
	Index-based variant of matchedSequence() for loops over many hits.
PeptideHit	withMatchedSequence (const PeptideHit &hit)
	A copy of hit whose sequence is matchedSequence(); an unchanged copy when no label state is recorded.

Variables
const std::string	LABELED_SEQUENCE = "MS1Label:labeled_sequence"
	Meta value key: the peptidoform the spectrum was matched with (see the namespace documentation)
const std::string	REMOVED_LABELS = "MS1Label:removed_labels"
	Meta value key: the labels removed from the matched peptidoform, or "none".
const std::string	CHANNEL = "MS1Label:channel"
	Meta value key: the 1-based channel the spectrum belongs to (0 = unknown)

Detailed Description

The label state of an identification in MS1-labeled (SILAC, Dimethyl, ...) data.

In MS1-labeled data the label belongs to the channel, not to the peptide: the light and the heavy spectrum of one peptide have to name one peptide for linking, match between runs, inference and quantification. MS1LabeledWorkflow therefore reduces the sequence of every identification to that peptide identity (the label modifications removed) and records the label state on the PeptideHit as meta values:

• MS1Label:labeled_sequence: the peptidoform the spectrum was matched with, e.g. PEPTIDEK(Label:13C(6)15N(2))
• MS1Label:removed_labels: the labels removed from it, in the FeatureFinderMultiplex vocabulary (e.g. Lys8, or Arg10,Lys8), or none
• MS1Label:channel: the 1-based channel the spectrum belongs to, i.e. the Label of the experimental design (1 = light); 0 if it could not be determined

PSM-level output describes the spectrum match and therefore reports the matched peptidoform (mzTab PSM section, QPX psm view), so that the calculated mass fits the precursor; feature-level output reports the peptide identity. The QPX feature and psm views additionally carry the three values as cv_params.

Function Documentation

hasMatchedSequence() [1/2]

bool hasMatchedSequence

(

const PeptideHit &

hit

)

Does hit record a non-empty MS1Label:labeled_sequence, i.e. was it reduced to a peptide identity? Presence only: the recorded peptidoform may equal the hit's own sequence, as it does for an unlabeled channel. An empty value counts as absent, since it records no peptidoform.

hasMatchedSequence() [2/2]

bool hasMatchedSequence	(	const PeptideHit &	hit,
		const Keys &	keys
	)

Index-based variant of hasMatchedSequence() for loops over many hits.

keys()

const std::vector< std::string > & keys

(

)

The three keys, in the order they are reported.

matchedSequence() [1/2]

AASequence matchedSequence

(

const PeptideHit &

hit

)

The peptidoform hit was matched to the spectrum with.

The hit's sequence, unless the hit records a MS1Label:labeled_sequence, in which case that one.

Never throws. The value comes from a file and may be absent, empty or unparsable; any of those yields the hit's own sequence, with a warning logged once per process for an unparsable one. Callers stream their output, so failing a whole export on one bad row would abandon a half-written file.

matchedSequence() [2/2]

AASequence matchedSequence	(	const PeptideHit &	hit,
		const Keys &	keys
	)

Index-based variant of matchedSequence() for loops over many hits.

withMatchedSequence()

PeptideHit withMatchedSequence

(

const PeptideHit &

hit

)

A copy of hit whose sequence is matchedSequence(); an unchanged copy when no label state is recorded.

Variable Documentation

CHANNEL

const std::string CHANNEL = "MS1Label:channel"

inline

Meta value key: the 1-based channel the spectrum belongs to (0 = unknown)

LABELED_SEQUENCE

const std::string LABELED_SEQUENCE = "MS1Label:labeled_sequence"

inline

Meta value key: the peptidoform the spectrum was matched with (see the namespace documentation)

REMOVED_LABELS

const std::string REMOVED_LABELS = "MS1Label:removed_labels"

inline

Meta value key: the labels removed from the matched peptidoform, or "none".