QuiXoT - Revision history

Mtrevisan: /* The configuration files */

2017-05-26T10:13:46Z

‎The configuration files

Mtrevisan: /* The configuration files */

2017-05-26T10:13:09Z

‎The configuration files

Mtrevisan at 08:52, 24 May 2017

2017-05-24T08:52:21Z

Mtrevisan at 10:47, 4 May 2017

2017-05-04T10:47:24Z

Mtrevisan: /* Part II: Analysing an experiment from scratch */

2017-04-28T10:44:52Z

‎Part II: Analysing an experiment from scratch

Mtrevisan: /* Part II: Analysing an experiment from scratch */

2017-04-28T10:44:40Z

‎Part II: Analysing an experiment from scratch

Mtrevisan: /* Part I: Checking an existent QuiXoT analysis */

2017-04-28T10:43:56Z

‎Part I: Checking an existent QuiXoT analysis

Mtrevisan: /* Part I: Checking an existent QuiXoT analysis */

2017-04-28T10:43:44Z

‎Part I: Checking an existent QuiXoT analysis

Mtrevisan: /* The configuration files */

2017-04-26T09:07:26Z

‎The configuration files

Mtrevisan at 08:32, 26 April 2017

2017-04-26T08:32:46Z

@@ Line 68: / Line 68: @@
 * several '''xml files''' which contain information such as the weights of each isotope, the composition of each amino acid or their posttranslational modifications. They also include the correspondence between the different residues and their symbols; for instance, "Y" means "tysorine", while "*" may refer to an oxidation in methionine, or a SILAC label on arginine. Examples of these files are:
 :* isotopes.xml
 :* aminoacids.xml

@@ Line 61: / Line 61: @@
 In the location where you have copied your version of QuiXoT you will find a '''''conf'' folder''' containing the configuration files. It contains three kinds of file:
-* the '''QuantitationMethods.xml''' file, which contains the parameters of the different methods used. Here it is specified which labelling is associated to a method, or which is the spectrum type that contains the quantitative information (for instance, SILAC quantification is performed in the full scan if a high resolution spectrometre has been used, but if it is a low resolution machine, then the quantification is performed in the zoom scan immediately previous to the MS2 scan). Examples of other parametres that can be determined using this file are:
+* the '''[[QuantitationMethods.xml]]''' file, which contains the parameters of the different methods used. Here it is specified which labelling is associated to a method, or which is the spectrum type that contains the quantitative information (for instance, SILAC quantification is performed in the full scan if a high resolution spectrometre has been used, but if it is a low resolution machine, then the quantification is performed in the zoom scan immediately previous to the MS2 scan). Examples of other parametres that can be determined using this file are:
 :* '''''width''''': the tolerance for the high resolution peaks
 :* '''''deltaR''''': the mass difference between 16O and 18O

@@ Line 9: / Line 9: @@
 }}
-'''QuiXoT''' is an open source software created for the quantitation and statistical analysis of quantitative proteomics experiments, and the central program of the '''[[QuiXoT software package|homonymous software package]]'''. It has been developed at the Cardiovascular Proteomics Laboratory of Prof Jesús Vázquez, at the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
+'''QuiXoT''' is an open source software created for the quantification and statistical analysis of quantitative proteomics experiments, and the central program of the '''[[QuiXoT software package|homonymous software package]]'''. It has been developed at the Cardiovascular Proteomics Laboratory of Prof Jesús Vázquez, at the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
 == Download ==
@@ Line 43: / Line 43: @@
 {{main|QuiXML}}
-QuiXoT makes use of a '''QuiXML files''', which is an ''ad hoc'' XML format created to manage the three levels of information treated: identification, quantitation and statistical information. To check a list of the different fields used in QuiXML files (i.e., the columns appearing in the main window of QuiXoT), you can check the article [[DataGrid information in QuiXoT]].
+QuiXoT makes use of a '''QuiXML files''', which is an ''ad hoc'' XML format created to manage the three levels of information treated: identification, quantification and statistical information. To check a list of the different fields used in QuiXML files (i.e., the columns appearing in the main window of QuiXoT), you can check the article [[DataGrid information in QuiXoT]].
-[[File:Screenshot QuiXoT-SelectMethod.PNG|350px|right|thumb|After dragging and dropping the QuiXML file, you will have to choose the quantitation method.]]
+[[File:Screenshot QuiXoT-SelectMethod.PNG|350px|right|thumb|After dragging and dropping the QuiXML file, you will have to choose the quantification method.]]
-If you just want to see an existing QuiXoT analysis, you only need the corresponding QuiXML file. Just drag and drop that file on the main form, and select the quantitation method used, which will depend on the SIL method used (such as 18O, SILAC, etc) and the spectrometre used (sich as high or low resolution).
+If you just want to see an existing QuiXoT analysis, you only need the corresponding QuiXML file. Just drag and drop that file on the main form, and select the quantification method used, which will depend on the SIL method used (such as 18O, SILAC, etc) and the spectrometre used (sich as high or low resolution).
 ==== The binStack folder ====
@@ Line 53: / Line 53: @@
 The spectra are saved in a folder called '''[[binStack]]''', which contains one or more .bfr files and one index.idx file. You do not need this folder if you just want to check the results of a QuiXoT analysis (such as the statistics, identifications or the quantitative information).
-However, you will need it if you want to requantitate a spectrum, or see the spectrum itself (for example to compare the theoretical and experimental isotopic envelope, which are respectively in red and blue colours). If this is your case, then you should always have the QuiXML file and its corresponding binStack in the same folder (do not forget to move them together).
+However, you will need it if you want to re-quantify a spectrum, or see the spectrum itself (for example to compare the theoretical and experimental isotopic envelope, which are respectively in red and blue colours). If this is your case, then you should always have the QuiXML file and its corresponding binStack in the same folder (do not forget to move them together).
 As far as the binStack and the QuiXML file are in the same place, you do not need to do anything else to load the spectral information.
@@ Line 61: / Line 61: @@
 In the location where you have copied your version of QuiXoT you will find a '''''conf'' folder''' containing the configuration files. It contains three kinds of file:
-* the '''QuantitationMethods.xml''' file, which contains the parameters of the different methods used. Here it is specified which labelling is associated to a method, or which is the spectrum type that contains the quantitative information (for instance, SILAC quantitation is performed in the full scan if a high resolution spectrometre has been used, but if it is a low resolution machine, then the quantitation is performed in the zoom scan immediately previous to the MS2 scan). Examples of other parametres that can be determined using this file are:
+* the '''QuantitationMethods.xml''' file, which contains the parameters of the different methods used. Here it is specified which labelling is associated to a method, or which is the spectrum type that contains the quantitative information (for instance, SILAC quantification is performed in the full scan if a high resolution spectrometre has been used, but if it is a low resolution machine, then the quantification is performed in the zoom scan immediately previous to the MS2 scan). Examples of other parametres that can be determined using this file are:
 :* '''''width''''': the tolerance for the high resolution peaks
 :* '''''deltaR''''': the mass difference between 16O and 18O
@@ Line 72: / Line 72: @@
 :* aminoacids_SILAC.xml
-* several '''xsd files''', which are the XML schemas that contain the structure of the QuiXML file depending on each quantitation method. Some examples of these files are
+* several '''xsd files''', which are the XML schemas that contain the structure of the QuiXML file depending on each quantification method. Some examples of these files are
 :* identifications_schema_18Ohighres.xsd
 :* identifications_schema_mascot_SILAC.xsd
@@ Line 82: / Line 82: @@
 ==== Labelling efficiency for 18O labelling ====
-If you have used 18O-labelling, you can check the labelling efficiency, prior to other analyses. Plot ''q_f'' versus ''Xs'' (consult how to create graphs). Since this plot does not differentiate between good and bad quantitations and hence plots together more and less accurate estimations of ''q_f'', it is a good idea to eliminate bad quantitations from the plot by filtering out the data that do not have an arbitrary minimum ''Vs'' value (for instance ''Vs > 30'' in ZoomScan-quantitated spectrum). Labelling efficiency must be above 0.8 for the vast majority of peptides. A cloud of points with ''q_f'' below 0.7 tending to curve towards the right (increasing ''Xs'' values) are indicative of a poorly-labeled experiment.
+If you have used 18O-labelling, you can check the labelling efficiency, prior to other analyses. Plot ''q_f'' versus ''Xs'' (consult how to create graphs). Since this plot does not differentiate between good and bad quantifications and hence plots together more and less accurate estimations of ''q_f'', it is a good idea to eliminate bad quantifications from the plot by filtering out the data that do not have an arbitrary minimum ''Vs'' value (for instance ''Vs > 30'' in ZoomScan-quantified spectrum). Labelling efficiency must be above 0.8 for the vast majority of peptides. A cloud of points with ''q_f'' below 0.7 tending to curve towards the right (increasing ''Xs'' values) are indicative of a poorly-labeled experiment.
 === Part II: Analysing an experiment from scratch ===
@@ Line 100: / Line 100: @@
 * if your spectra are stored '''in a different file format''', you should use an external converter to get a mgf file, and then use [[mgfToBinStack]]
-==== Quantitating ====
+==== Quantifying ====
 [[File:Screenshot QuiXoT-18Ospectrum1.PNG|thumb|300px|A high resolution spectrum from an 18O-labelled experiment. Notice the light species (the four peaks at the left) and the heavy species (the peaks 5th to 8th). The theoretical peaks are red colour, while the original, experimental spectrum is blue colour. You can see a contaminant (or perhaps another less abundant peptide) on the right side of the spectrum (of course, only blue colour, as it does not match a theoretical spectrum in this case).]]
-To quantitate a single spectrum just select a row by clicking on its left side, and the press the quantitation button. You will see that several columns that were empty (such as ''q_A'' or ''q_log2Ratio'') are now filled. Additionally, if you are visualising the spectrum, you will see that a red colour spectrum has appeared, superposed to the blue colour experimental spectrum. Both spectra may match better or worse depending on the spectrometre performance, level of noise, artefacts, and the fact that the identification might be correct or not. The more similar the theoretical and the experimental spectra are, the higher the assigned weight will be (which you will find in column ''Vs''). On the other hand, if the spectrum is very bad (for example because it contains several contaminants that are mixing with the signal from the peptide), then it will be assigned a low weight, which means it will have a very low impact in the posterior statistics compared to other spectra.
+To quantify a single spectrum just select a row by clicking on its left side, and the press the ''quantitate'' button. You will see that several columns that were empty (such as ''q_A'' or ''q_log2Ratio'') are now filled. Additionally, if you are visualising the spectrum, you will see that a red colour spectrum has appeared, superposed to the blue colour experimental spectrum. Both spectra may match better or worse depending on the spectrometre performance, level of noise, artefacts, and the fact that the identification might be correct or not. The more similar the theoretical and the experimental spectra are, the higher the assigned weight will be (which you will find in column ''Vs''). On the other hand, if the spectrum is very bad (for example because it contains several contaminants that are mixing with the signal from the peptide), then it will be assigned a low weight, which means it will have a very low impact in the posterior statistics compared to other spectra.
-To quantify the whole experiment, simply select all the rows (by clicking on the top-left corner of the datagrid) and press the ''quantitate'' button. Take into account that this might take between a few seconds to several hours depending on the amount of spectra and the quantitation method used.
+To quantify the whole experiment, simply select all the rows (by clicking on the top-left corner of the datagrid) and press the ''quantitate'' button. Take into account that this might take between a few seconds to several hours depending on the amount of spectra and the quantification method used.
 ==== Performing the first statistics ====

@@ Line 2: / Line 2: @@
 |screenshot = Screenshot QuiXoT general.PNG|name = QuiXoT
 |screenshot_description = Screenshot of QuiXoT, depicting different spectra and graphs used.
-|last_release = 1.5.00|date = 31st Mar 2017
+|last_release = 1.5.02|date = 24th Apr 2017
-|link = File:QuiXoT v.1.5.00.zip
+|link = File:QuiXoT v.1.5.02.zip
 |requirements =
 * [http://www.microsoft.com/en-us/download/details.aspx?id=1639 .NET Framework 2.0] or higher
@@ Line 13: / Line 13: @@
 == Download ==
-You can download QuiXoT 1.5.00 from this link: '''[[File:QuiXoT v.1.5.00.zip]]'''
+You can download QuiXoT 1.5.02 from this link: '''[[File:QuiXoT v.1.5.02.zip]]'''
 == Installation instructions ==
-QuiXoT v1.5.00 is a portable, standalone application, so you do not need to install it to execute it.
+QuiXoT is a portable, standalone application, so you do not need to install it to execute it.
-Unzip the '''''QuiXoT 1.5.00''''' folder (which you will find within the above-linked zip file) where you prefer in your computer. Then execute the QuiXoT.exe file (make sure it is the executable file, which has the QuiXoT logo, and not the QuiXoT.exe.config file, which will look as if it were called "QuiXoT.exe" when hiding file extensions). You may want to create a shortcut on your desktop or elsewhere to have fast access to QuiXoT.
+Unzip the '''''QuiXoT 1.5.02''''' folder (which you will find within the above-linked zip file) where you prefer in your computer. Then execute the QuiXoT.exe file (make sure it is the executable file, which has the QuiXoT logo, and not the QuiXoT.exe.config file, which will look as if it were called "QuiXoT.exe" when hiding file extensions). You may want to create a shortcut on your desktop or elsewhere to have fast access to QuiXoT.
 === Additional information ===

@@ Line 86: / Line 86: @@
 === Part II: Analysing an experiment from scratch ===
-You can see more details about how to analyse an experiment in ''[[exploring QuiXoT features]]''.
+You can see more details about how to analyse an experiment in '''[[exploring QuiXoT features]]'''.
 ==== Generating the files ====

← Older revision		Revision as of 10:44, 28 April 2017
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	=== Part II: Analysing an experiment from scratch ===		=== Part II: Analysing an experiment from scratch ===
		+
		+	You can see more details about how to analyse an experiment in ''[[exploring QuiXoT features]]''.

	==== Generating the files ====		==== Generating the files ====

@@ Line 38: / Line 38: @@
 === Part I: Checking an existent QuiXoT analysis ===
-You can see more detailed explanations with zip files for different experiments in [[unit tests for QuiXoT]].
+You can see more detailed explanations with zip files for different experiments in '''[[unit tests for QuiXoT]]'''.
 ==== The QuiXML files ====