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XCMS Online
&
Understanding XCMS
algorithms
H. Paul Benton PhD
The Siuzdak Laboratory -The Scripps Research Institute
How to select text in pdf reader - search text inside PDF file in C#.net, ASP.NET, MVC, Ajax, WinForms, WPF
Learn how to search text in PDF document and obtain text content and location information
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How to select text in pdf reader - VB.NET PDF Text Search Library: search text inside PDF file in vb.net, ASP.NET, MVC, Ajax, WinForms, WPF
Learn How to Search Text in PDF Document and Obtain Text Content and Location Information in VB.NET application
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To do this morning
•Learn how to fly a rocket ship
•Get to look at chaos itself
•Shine light into the depths of nature
C# PDF Image Extract Library: Select, copy, paste PDF images in C#
C#: Select All Images from One PDF Page. C# programming sample for extracting all images from a specific PDF page. C#: Select An Image from PDF Page by Position.
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VB.NET PDF Image Extract Library: Select, copy, paste PDF images
VB.NET : Select An Image from PDF Page by Position. Sample for extracting an image from a specific position on PDF in VB.NET program.
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Ok really what are we going to do
• Learn how to fly a rocket ship
–Computing hundreds of calculations at the speed of intel
–using XCMS Online
• Get to look at chaos itself
– Its your data not mine ! 
• Data can be messy
• Chaos can being about order metabolism is highly ordered
• Shine light into the depths of nature
–We get to look at some of the most complex questions 
at the smallest biological level –metabolites.
C# PDF Text Redact Library: select, redact text content from PDF
Free online C# source code to erase text from adobe PDF file in Visual Studio. NET class without adobe reader installed. Provide
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VB.NET PDF Text Redact Library: select, redact text content from
PDF Image Extract; VB.NET Write: Insert text into PDF; VB.NET Annotate: PDF Markup & Drawing. XDoc.Word for C#; C#; XImage.OCR for C#; XImage.Barcode Reader for C#
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Getting started with XCMSOnline
C# HTML5 PDF Viewer SDK to view PDF document online in C#.NET
Barcoding. XImage.Barcode Reader. XImage.Barcode Generator. Others. XDoc.Tiff. XDoc.Dicom. 1. Select tool. Select text and image on PDF document. 2. Hand tool.
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VB.NET PDF- View PDF Online with VB.NET HTML5 PDF Viewer
Barcoding. XImage.Barcode Reader. XImage.Barcode Generator. Others. XDoc.Tiff. XDoc.Dicom. 1. Select tool. Select text and image on PDF document. 2. Hand tool.
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What did we do
• Registered on XCMS Online
–Confirmed real email address
• Uploaded some data
–In the old days we had to convert data ourselves –
you are all very lucky!
–XO supports –Agilent .d , Waters .RAW, Bruker.d, 
AB Sciex.wiff(remember the .wiff.scanfiles) and 
open source formats (mzML, mzXML, mzData, 
netCDF)
VB.NET PDF - View PDF with WPF PDF Viewer for VB.NET
Barcoding. XImage.Barcode Reader. XImage.Barcode Generator. Hand. Pan around the PDF document. Ⅱ. Select text and image to copy and paste using Ctrl+C and Ctrl+V
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C# WPF PDF Viewer SDK to view PDF document in C#.NET
Barcoding. XImage.Barcode Reader. XImage.Barcode Generator. Hand. Pan around the PDF document. Ⅱ. Select text and image to copy and paste using Ctrl+C and Ctrl+V
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Processing Data 
C# Image: Select Document or Image Source to View in Web Viewer
Supported document formats: TIFF, PDF, Office Word, Excel, PowerPoint, Dicom; Supported Viewer Library enables Visual C# programmers easily to select and load
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C# WPF PDF Viewer SDK to annotate PDF document in C#.NET
Click to select drawing annotation with default properties. Other Tab. Item. Name. Description. 17. Text box. Click to add a text box to specific location on PDF
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Now step by step
• We’ve loaded up two datasets –2 classes to 
compare
• Set our parameters and launched a job
–Looking at the parameters and what they mean.
–Junk in, junk out. –Biologist
–Good data in, bad parameter selection, junk out –
bioinformticist
Overview of XCMS
Peak Picking
Grouping similar peaks
across replicates
Retention time 
alignment
Statistical 
analysis of Peaks
Between classes
Peak detection choice
Peak Picking
matchedFilter
centWave
Profile Data
Low resolution data
Original algorithm 
Centroid data
High resolution data
New published algorithm
Rockets are like ions !!
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