MSRawData

class MSRawData.MSRawData(filepath, logger=None, ingui=True)

Bases: object

A class to describe raw data obtained from the MS machine

Parameters:

• filePath (str) – file path of the input MRM transition name file

• logger (object) – logger object created by start_logger in MSOrganiser

• ingui (bool) – if True, print analysis status to screen

remove_whiteSpaces(df)

Strip the whitespaces for each string columns of a df

Parameters:

df (pandas DataFrame) – A panda data frame

Returns:

df (pandas DataFrame) – A panda data frame with white space removed

class MSRawData.AgilentMSRawData(filepath, logger=None, ingui=True)

Bases: MSRawData.MSRawData

To describe raw data obtained from the Agilent MS machine

Parameters:

• filePath (str) – file path of the input MRM transition name file

• logger (object) – logger object created by start_logger in MSOrganiser

• ingui (bool) – if True, print analysis status to screen

get_table(column_name, is_numeric=True)

Function to get the table from MassHunter Raw Data

Parameters:

column_name (str) – The name of the column given in the Output_Options.

Returns:

A data frame of sample as rows and transition names as columns with values from the chosen column name

class MSRawData.SciexMSRawData(filepath, logger=None, ingui=True)

Bases: MSRawData.MSRawData

To describe raw data obtained from the Sciex MS machine

Parameters:

• filePath (str) – file path of the input MRM transition name file

• logger (object) – logger object created by start_logger in MSOrganiser

• ingui (bool) – if True, print analysis status to screen

get_table(column_name, is_numeric=True)

Function to get the table from Sciex MultiQuant Raw Data

Parameters:

column_name (str) – The name of the column given in the Output_Options.

Returns:

A data frame of sample as rows and transition names as columns with values from the chosen column name

AgilentColumnName_to_SciexColumnName(column_name)

Function to convert the column_name (Output Option) from Agilent to Sciex form

Note

By default the Output Option name follows Agilent.

Parameters:

column_name (str) – The name of the column given in the Output_Options.

Returns:

column_name (str) – Name converted to Sciex form