Exploring QuiXoT features - Revision history

Mtrevisan at 10:43, 4 May 2017

2017-05-04T10:43:00Z

Mtrevisan at 10:45, 28 April 2017

2017-04-28T10:45:29Z

Mtrevisan at 10:38, 28 April 2017

2017-04-28T10:38:49Z

Mtrevisan at 10:38, 28 April 2017

2017-04-28T10:38:30Z

Mtrevisan: /* Analysing the three levels at once */

2017-04-28T10:33:37Z

‎Analysing the three levels at once

Mtrevisan at 08:54, 28 April 2017

2017-04-28T08:54:39Z

Mtrevisan: /* Combining different graphs */

2017-04-28T08:53:26Z

‎Combining different graphs

Mtrevisan at 08:43, 28 April 2017

2017-04-28T08:43:53Z

Mtrevisan at 08:35, 28 April 2017

2017-04-28T08:35:00Z

Mtrevisan at 08:17, 28 April 2017

2017-04-28T08:17:00Z

@@ Line 7: / Line 7: @@
 ==== 1.1 Getting started ====
-Open ''QuiXoT.exe'', drag and drop anywhere on its window the abovementioned QuiXML file, and select the ''18, HR, SEQUEST'' strategy. You should see this window:
+After downloading '''QuiXoT''' (find the latest release in the '''[[QuiXoT|specific article]]''') and the files for the experiment from '''[ftp://ftp.cnic.es/ftpsvc/pub/test1_full.zip test1_full.zip]''', unzip the files and open ''QuiXoT.exe''.
 [[File:QuiXoT analysis 1a.png]]

← Older revision		Revision as of 10:45, 28 April 2017
Line 1:		Line 1:
−	.Here we describe some of the features of '''[[QuiXoT]]''' you can use in everyday's work analysing quantitative proteomics experiments. If this is the first time you run the program, you might be interested first in checking the '''[[unit tests for QuiXoT]]'''.	+	Here we describe some of the features of '''[[QuiXoT]]''' you can use in everyday's work analysing quantitative proteomics experiments. If this is the first time you run the program, you might be interested first in checking the '''[[unit tests for QuiXoT]]'''.

	=== Analysis 1: 18O, HR ===		=== Analysis 1: 18O, HR ===

← Older revision		Revision as of 10:38, 28 April 2017
Line 262:		Line 262:
	Or alternatively right click > export to csv, and represent the data using another software. Doing this, the whole QuiXML is saved in table format, including in the last columns the data from the concerning graph.		Or alternatively right click > export to csv, and represent the data using another software. Doing this, the whole QuiXML is saved in table format, including in the last columns the data from the concerning graph.

−	[[File:QuiXoT analysis ~~1ar~~.png]]	+	[[File:QuiXoT analysis 1av.png]]

@@ Line 260: / Line 260: @@
 [[File:QuiXoT analysis 1ar.png]]
-Or alternatively right click > export to csv, and represent the data using another software.
+Or alternatively right click > export to csv, and represent the data using another software. Doing this, the whole QuiXML is saved in table format, including in the last columns the data from the concerning graph.
 [[Category:QuiXoT]]

@@ Line 236: / Line 236: @@
 ===== Analysing the three levels at once =====
 [[File:QuiXoT analysis 1ao.png]]
-[[File:QuiXoT analysis 1aq.png]]
+Then, we can check how a specific group of proteins behave. For example, all the proteins containing the text "tubulin" in the description (their FASTA header). We can do this by filtering ''FASTAProteinDescription like '%tubulin%''', selecting the whole set of rows, removing the filter, and updating the graphs:
 [[File:QuiXoT analysis 1ar.png]]
 === Analysis 2 ===

@@ Line 212: / Line 212: @@
 ===== Combining different graphs =====
 [[File:QuiXoT analysis 1am.png]]
 [[File:QuiXoT analysis 1an.png]]
 [[File:QuiXoT analysis 1as.png]]
 [[File:QuiXoT analysis 1ap.png]]
 ...
@@ Line 228: / Line 243: @@
 [[File:QuiXoT analysis 1ar.png]]
 === Analysis 2 ===

@@ Line 190: / Line 190: @@
 [[File:QuiXoT analysis 1ag.png]]
-Apparently two spectra are present. We will take a closer look at the spectra directly (you can do this only if you have the binStack in the same folder as the QuiXML), just by selecting the rows (on the left).
+Apparently two spectra are present.
 [[File:QuiXoT analysis 1ah.png]]
@@ Line 205: / Line 210: @@
 We have highlighted the FDR value in the identification panel: it seems the reason of the bad quantification is that this was a bad identification; it had an identification FDR of 3%, with an XCorr = 2, which is relatively low, while the other spectrum pointing to the same peptide (see above) had been identified with 0% FDR and a higher XCorr = 2.96.

← Older revision		Revision as of 08:17, 28 April 2017
Line 169:		Line 169:

	[[File:QuiXoT analysis 1ac.png]]		[[File:QuiXoT analysis 1ac.png]]
		+
		+	Now we can see easily what is the behaviour of the poorly labelled peptides compared to the rest of peptides.
		+
		+	Now we will check which scans are quantifying differently, compared to other scans pointing to the same peptide. This is done by applying the filter ''FDRs < 0.05'' (using a 5% FDR). After selecting, we should have this:
		+
		+	[[File:QuiXoT analysis 1ad.png]]
		+
		+	If, for example, we want to see the leftmost of these scans, we can select it with the mouse,
		+
		+	[[File:QuiXoT analysis 1ae.png]]
		+
		+	Now QuiXoT should show us only the row containing that datapoint:
		+
		+	[[File:QuiXoT analysis 1af.png]]
		+
		+	Notice how the filter colour changed from purple to green. This is to tell us that two filters are being used at the same time: the zoom filter and text filter.
		+
		+	We will now filter out all the spectra pointing to the same peptide; we can do this by using the texto ''sequence like '%LLLFPFLSPQK%''':
		+
		+	[[File:QuiXoT analysis 1ag.png]]
		+
		+	Apparently two spectra are present. We will take a closer look at the spectra directly (you can do this only if you have the binStack in the same folder as the QuiXML), just by selecting the rows (on the left).
		+
		+	[[File:QuiXoT analysis 1ah.png]]
		+
		+	[[File:QuiXoT analysis 1ai.png]]
		+
		+	It looks like the first one is a bad quantification. We will zoom that region of the spectrum (by selecting horizontally, as we have seen):
		+
		+	[[File:QuiXoT analysis 1ak.png]]
		+
		+	And, yes, it seems a bad quantification:
		+
		+	[[File:QuiXoT analysis 1aj.png]]
		+
		+	We have highlighted the FDR value in the identification panel: it seems the reason of the bad quantification is that this was a bad identification; it had an identification FDR of 3%, with an XCorr = 2, which is relatively low, while the other spectrum pointing to the same peptide (see above) had been identified with 0% FDR and a higher XCorr = 2.96.
		+

	=== Analysis 2 ===		=== Analysis 2 ===