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This file is part of the masschroq_examples.zip archive (or of the examples 
directory of your MassChroQ Windows installation) which contain 
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ready to use examples to test masschroq v1.0.

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In the masschroq_examples (resp. examples) directory you will find ready-to-use 
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examples to run masschroq. They are intended to illustrate how masschroq 
works and the results it can provide. They are also intended to provide 
usage and parameter values support for your further analysis.
  
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The input masschroqML example files are the ones named 
example_blabla_masschroq.masschroqML.
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To run them go into the masschroq_examples directory and simply type:
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	masschroq example_blabla_masschroq.masschroqML 
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on the command line. 
The mzXML files provided are the LC-MS/MS data files used in these examples. 

The following examples are provided :

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 - example_labelling_dimethylation_masschroq.masschroqML (only in the website archive)
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	This example analysis the BSA_labeling_mix_light_intermediaire.mzXML
	data file produced by a low resolution LTQ spectrometer 
	in a profile mode and where dimethyl labeling (with light and heavy 
	dimethyl groups) has been performed.
	The quantified entities are the heavy and the light isotopes.

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- example_LTQ_and_alignment_masschroq.masschroqML :
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	Here we analyze the BSA_LTQ_1.mzXML and BSA_LTQ_2.mzXML data files
	obtained with a low resolution LTQ spectrometer in centroid mode. 
	The quantification parameters are thereby adapted to LTQ data. 
	An MS2 alignment is performed on the second data file towards the 
	first one. During execution masschroq notifies that these two runs have 35 
	peptides in common (the peptides used to align the two runs). After 
	alignment, notice the two produced files with extension .time (containing 
	the old versus the aligned retention times) and .trace (containing step 
	by step traces of the alignment procedure). 
	
	Also, in this example we ask masschroq to produce trace files for the 
	quantification procedure (xic extraction, filtering and peak detection 
	steps) concerning a given list of peptides (pep0 - pep4). After execution 
	you should notice a newly created directory named peplist_xics_traces 
	containing these traces for each detected peptide in each run.
  
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- example_orbitrap_masschroq.masschroqML
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	In this example we analyze the BSA_Orbitrap.mzXML data file obtained 
	from a high resolution orbitrap spectrometer. The quantification 
	parameters are adapted to this spectrometer. Also, an external peptide 
	text file (peptides_BSA_Orbitrap.txt file) is used to integrate the 
	identified peptides. During execution masschroq notifies that he has found 
	the instruction to parse this peptide file, that he created a new example
	file called parsed_peptides-example_orbitrap_masschroq.xml containing 
	the identified peptides and then he continues analysis on this new file. 
	
	If you run this example with option -p (or --parse-peptides) you will 
	notice that masschroq only creates the new file without analyzing it. 
	You can then run masschroq directly on this new file in order to 
	perform the analysis.

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- masschroq_complete_input_example.xml (only with the Windows installation) 
	This is a complete input masschroqML example file that you can edit with 
	any text or xml editor. This file contains every possible masschroqML 
	instruction. It is intended to be used as a reference for users.