Raw data access

Basic usage

After you successfully build the proteolizard binary, you are ready to connect to a timsTOF TDF-file. This is done by creating a handle to the raw-datset which we can use to fetch parts of the raw-data required. We can also have a look at metadata such as frame types (MS-I vs MS-II), quadrupole settings during PASEF etc.

import pandas as pd
import numpy as np
from proteolizarddata.data import PyTimsDataHandleDDA

handle = PyTimsDataHandle('path/to/dataset.d')
print(handle.meta_data)

	Id	Time	Polarity	ScanMode	MsMsType	TimsId	MaxIntensity	SummedIntensities	NumScans	NumPeaks	MzCalibration	T1	T2	TimsCalibration	PropertyGroup	AccumulationTime	RampTime
0	1	0.554466	+	8	0	0	2312	12276207	918	211960	1	25.6798	25.3503	1	1	99.953	99.953
1	2	0.807918	+	8	8	520192	646	51427	918	715	1	25.6798	25.3501	1	1	99.953	99.953
2	3	0.912566	+	8	8	524288	574	61312	918	830	1	25.6798	25.3501	1	1	99.953	99.953

The simplest form of raw-data fetching is to get a single TimsFrame by its Id, which represents a collection of ion-mobility separated mass spectra at a single retention time:

frame = handle.get_frame(1)
print(frame)

Wich will return a TimsFrame:

TimsFrame(id: 1, num data-points: 211960, sum intensity: 12270522)

You can also query all frames in a given retention time range (caution, rt-start/rt-end values should be given in seconds):

slice = slic = handle.get_slice_rt_range(120, 180)

Wich will return a TimsSlice: TimsSlice(frame start: 1130, frame end: 1691)

Classes

PyTimsDataHandleDDA

Constructor

Properties

Methods

PyTimsDataHandleDIA

Constructor

Properties

Methods