Revision 1 (June 2014)

Quick Start Guide

Processing Bruker shotgunproteomics data using

MaxQuant 1.5.x

www.bruker.com Language: en

Bruker

Processing Bruker proteomics data using MaxQuant

MaxQuant is a proteomics software package designed for quantitative analysis of large, high-resolutionMS data sets. This document describes the processing of shotgun proteomics data obtained on Brukerinstruments usingMaxQuant software.

Note These instructions apply to unlabeled complex shotgun proteomics data (autoMS/MS).

Software requirements

l Download and install the latest MaxQuant version on your computer(www.maxquant.org/downloads.htm) 1

l Processing Bruker data (*.d files) requires SQLite setups for 64-bit Windows (.NET Framework4.5). Download and install the latest relevant version on your computer(http://system.data.sqlite.org/index.html/doc/trunk/www/downloads.wiki)

1. Start MaxQuant by double-clickingMaxQuant.exe in the folder where you installed the application.2. OpenWindowsExplorer, select the *.d files to be processed, and drag them into theRaw files >

File area of MaxQuant.

l Alternatively, click Raw files > Load folder in MaxQuant and select the folder containing thedata to be processed.

3. SelectGroup-specific parameters > General and select > or deselect < the requiredVariablemodifications and one or more enzymes from theEnzyme list.

1All software available for download via the MaxQuant website(s) is copyright Max-Planck Institute of Biochemistry,Department of Proteomics and Signal Transduction unless otherwise stated.

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4. ClickGlobal parameters > General > Add file and select one or more .fasta files from the librarydownloaded from theMaxQuant website.

Note Before using your own .fasta file, it must be adapted in the Andromeda configurationtab. For more information, visit the MaxQuant Help Google group(https://groups.google.com/forum/#!forum/maxquant-list).

l If required, further parameters, such as mass tolerances at the MS and MS/MS level can beadapted by selectingGlobal parameters > Identification orGlobal parameters > MS/MS -TOF.

l In MaxQuant, a tooltip gives a brief explanation of most parameters.

IMPORTANT Default settings have been carefully optimized for data and instrumenttypes and should not be changed!

5. Select theNumber of threads to be run in parallel.

This number should be equal to the number of cores available to your CPU. Each file is analyzed byone process and usingmultiple processeswill considerably shorten analysis time.

6. ClickStart to start data processing.

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l You will receive your analysis in the form of .txt files. These files are located in the foldercombined > txt, which is created in the same directory as the data files loaded in step 2.

Note Reprocessing data in the same folder will overwrite the contents of the combined > txtfolder.

l Open the file proteinGroups.txt in Excel to view a list of identified protein groups and parameterssuch as number of unique peptides and sequence coverage.

l Open the file summary.txt in Excel to view peptide ID statistics, including:o Raw file→data file nameo MS→number of MS scanso MS/MS→number of MS/MS scanso MS/MS identified→number of identifiedMS/MS spectra ("PSMs")o MS/MS identified (%)→ identification rateo Peptide Sequences Identified→number of unique peptide sequenceso Isotope patterns→number of detected isotope patterns at MS levelo MassStandard Deviation [ppm]→average standard deviation of identified precursor ions(ppm)

A comprehensive description of all MaxQuant result files can be found in the document tables.pdf.

For more information on MaxQuant software, visit the MaxQuant homepage (www.maxquant.org) ortheMaxQuant Help Google group (https://groups.google.com/forum/#!forum/maxquant-list).

Disclaimer: The use of MaxQuant software is undertaken at your own discretion and risk and with agreement that youwill be solely responsible for any damage to your computer system or loss of data that results from such activities. Youare solely responsible for adequate protection and backup of the data and equipment used in connection withMaxQuant software, and Bruker will not be liable for any damages that you may suffer in connection with downloading,installing, using, modifying or distributing such software. No advice or information, whether oral or written, obtainedfrom Bruker shall create any warranty for MaxQuant software.

For research use only. Not for use in diagnostic procedures.

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Descriptions and specifications supersede all previous information and are subject to change without notice.

© Copyright 2014 Bruker Daltonik GmbH

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