Training Courses 1 - Bruker · Essential Operator Training Courses, In-House C5EA13 General Training part of Instrument purchase 3 days 3 days DAL00905 DAL00901 54 Individual Operator

Training Courses 1.0

Innovation with IntegrityService & Support

On Instrumentation, Software Packagesand Solutions

Power up your skills andshare your knowledge

Training on our instrumentation, software packages and solution is provided by very experienced application experts.

Various courses are available covering the range from absolute beginners to experienced experts.

• Training • Improvement • Practice • Focus • Intelligence • Lesson • Motivation• Success

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Table of Contents

General Remarks and Information for Training Courses ....................... 2

Overview ............................................................................................. 3

Training Center Contact Information ..................................................... 4

Training Course Index

MALDI Operator ................................................................................ 6

ESI Ion Trap Operator ........................................................................ 6

ESI-TOF Operator .............................................................................. 6

FT-ICR-MS Operator ......................................................................... 7

GC Operator ...................................................................................... 7

GC-MS TQ Operator .......................................................................... 7

LC-MS TQ Operator .......................................................................... 7

Software Trainings ............................................................................. 8

Training Course Descriptions

MALDI Operator ................................................................................ 9

ESI Ion Trap Operator ........................................................................ 29

ESI-TOF Operator .............................................................................. 38

FT-ICR-MS Operator ......................................................................... 49

GC Operator ...................................................................................... 53

GC-MS TQ Operator .......................................................................... 56

LC-MS TQ Operator .......................................................................... 60

Software Trainings ............................................................................. 63

Registration Form for Training Courses ................................................ 71

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RegistrationFor registration please access the online reg-istration or fill out the registration form on page 69. Please attach a copy of your training confirmation, which you should have obtained in advance.

ConfirmationAfter receiving your registration form we will confirm your participation. If the selected training course is already fully booked, we will inform you immediately and offer an alternative date.

Training costsTraining costs include the course fees as well as lunch and beverages during the training. Travel and accommodation are excluded.Since the trainings are paid with vouchers, please do not forget to bring the original train-ing voucher with you.

CancellationBruker reserves the right to cancel the training if the minimum number of participants are not achieved one month prior to the training date.Please wait with your travel arrangements until receipt of confirmation.Customers may cancel in writing not later than one month prior to the training date at a full refund of the training price. If customer cancels later than 2 weeks before the training, the full training fee will be charged. Customers may substitute a colleague without extra charge or payment in this case. However, please make sure that we are informed in case a hotel reser-vation has been made.

Course languageAll courses will be held in English unless other-wise explicitly stated or agreed with the cus-tomer.Our general terms and conditions of supply and service apply.

General Remarks and Information for Training Courses

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Training Courses @ Training CenterEssential Operator Training Courses• Introductory courses at a Bruker training

center• Includes instrument control, data acquisition

and processing• Includes sample preparation and application-

specific training• If HPLC is required it includes application

relevant HPLC aspects but does not substi-tute an explicit HPLC training

• The number of participants is usually limited to 5 persons per course

• Price is per person and excludes all travel & lodging expenses

Advanced Operator Training Courses• Pre-requisite for attending a advanced

operator training courses is the successful participation in an essential operator training course.

• Price is per person and excludes all travel & lodging expenses

On-site Training CoursesOn-site Operator Training Courses• Contents are defined prior to the training

between the customer and Bruker training center.

• Time need should be calculated analogously to the factory training courses. Parameter optimization in your lab and of your instrument requires approx. an additional half day.

• The number of participants in the training is not limited but should not exceed a reason-able number to ensure a good interaction between trainees and trainer (usually up to 5 persons)

• Bruker reserves the right to convert an ordered on-site training into an in-house training in case of war, civil war, political instability, the risk of terrorist activity or natural disasters which pose a significant threat for Bruker employees. In this case Bruker will carry the costs for traveling in economy class to the Bruker training center providing the training as well as lodging costs for a maximum of three training partici-pants. Travel costs of accompanying persons not participating in the training cannot be covered.

Overview

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EuropeBruker Daltonik GmbH Fahrenheitstrasse 4 28359 Bremen Germany Phone: +49 (421) 2205-1464 Fax: +49 (421) 2205-104 Email: [email protected] Training center code: BRE

Bruker UK Ltd. Banner Lane Coventry CV 4 9GH United Kingdom Phone: +44 (2476) 855200 Email: [email protected] Training center code: COV

Bruker Daltonique S.A. 4, Alleé Lorentz, Parc de la Haute Maison - Bât.A5 77447 Marne la Vallee Cedex 2 France Phone: +33 (0) 160954750 Email: [email protected] Training center code: PAR

Bruker Española S.A Parque Empresarial Rivas Futura C/Marie Curie, 5 Edificio Alfa, Planta Baja 28529-Rivas Vaciamadrid Madrid, Spain Phone: +34 (91) 4994080 Email: [email protected] Training center code: MAD

AmericaBruker Daltonics Inc. 40 Manning Road, Manning Park Billerica, MA 01821 USA Phone: +1 (978) 663-3660 Email: [email protected] Training center code: BIL

Bruker Daltonics Inc. 3500 West Warren Avenue Fremont, CA 94538 USA Phone: +1 (510) 683-4300 Email: [email protected] Training center code: FRE

Bruker do Brasil Ltda. Condomínio BBP – Barão de Mauá Rod.D.Pedro I, km 87.5 (pista norte) 12954-260 Atibaia, SP Brazil Phone: +55 (11) 98917-3992 Fax: +55 (11) 2119-1772 Email: [email protected] Training center code: SAO

AsiaBruker Daltonics K.K.Technical Support Center 3-9, Moriya, Kanagawa Yokohama, Kanagawa 221-0022, Japan Phone: +81 (45) 4400478 Fax: +81 (45) 4532458 Email: [email protected] Training center code: YOK Training course available in Japanese language

Bruker (Beijing) Scientific Technology Co., Ltd Everbright International Trust Mansion, Suite 5109, 11 Zhong Guan Cun South Avenue Beijing 100081, China Phone: +86 (800) 8190181 Fax: +86 (10) 5833 3030 Email: [email protected] Training center code: BEI Training course is available in Mandarin language

Bruker (Beijing) Scientific Technology Co., Ltd Shanghai Office 19F, Xingyuan Technology Building 418 Guiping Rd, Caohejing Development Zone Shanghai 200233, China Phone: +86 (800) 8190181 Fax: +86 (021) 5172 0880 Email: [email protected] Training center code: SHA Training course is available in Mandarin language

AustraliaBruker Biosciences Pty. LTD. P.O. Box 8432 Northland Centre, Victoria 3072, Australia Phone: +61 (3) 9474 7000 Fax: +61 (3) 9474 7070 Email: [email protected] Training center code: MEL

Training Center Codes: Please refer to the bottom of each Training Course Description page for local availability by training center codes. Language: Check language availability at your training center.

Training Center Contact Information

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Register Number

Training Name DurationOrder

NumberPage

MALDI Operator

Essential Operator Training Courses, In-House

C1EP13 Proteomincs using BioTools Training part of Instrument purchase

3 days 3.5 days

3-3.5 days

DAL00905 DAL00916 DAL00901

10

C1EP24 Proteomics using ProteinScape™ Training part of Instrument purchase

3.5 days 3.5 days

DAL00916 DAL00901

11

C1EC12 MALDI Biotyper non IVD Training part of Instrument purchase

1.5 days 1.5 days

DAL00914 DAL00901

12

C1EC21 MALDI Biotyper IVD Training part of Instrument purchase

1 day 1 day

DAL00903 DAL00901

13

C1EI12 MALDI Imaging Training part of Instrument purchase

2 days 2 days

DAL00904 DAL00901

14

C1ES13 Synthetic Chemistry and Polymers Training part of Instrument purchase

3 days 3 days

DAL00905 DAL00901

15

Advanced Operator Training Courses, In-House

C1AP12 LC-MALDI 1.5 days DAL00914 16

C1AC11 Database entry creation 1 day DAL00903 17

C1AC21 MALDI Biotyper Sample Preparation 0.5 day DAL00913 18

C1AC31 MALDI Biotyper Mycobacteria Identification 0.5 day DAL00913 19

C1AC41 MALDI Biotyper Filamentous Funghi Identification

0.5 day DAL00913 20

C1AC62 MALDI Biotyper strain typing course 1.5 days DAL00914 21

C1AC71 STAR-BL Module 1 day DAL00903 22

C1AC81 MALDI Biotyper Sepsityper IVD 1 day DAL00903 23

C1AI11 MALDI Small Molecule Imaging 1 day DAL00903 24

C1AI21 MALDI Statistical data analysis Training part of Instrument purchase

1 day 1 day

DAL00903 DAL00901

25

C1AI31 MALDI Image ID Workflow 1 day DAL00903 26

C1AS11 Polymers and PolyTools 1 day DAL00903 27

Individual Operator Training Courses, On-Site

S1AA01 MALDI 1 day DAL00908 28

S1AA02 MALDI 2 days DAL00909 28




Please click on the page number to be taken directly to that Course Description.


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Register Number


NumberPage

ESI Ion Trap Operator


C2EL13 Low Molecular Weight Applications Training part of Instrument purchase

2.5 days 2.5 days

DAL00915 DAL00901

30

C2ET12 Toxtyper Applications Training part of Instrument purchase

2 days 2 days

DAL00904 DAL00901

31

C2EP13 Proteomics Applications Training part of Instrument purchase

3 days 3 days

DAL00905 DAL00901

32


C2AA12 Toxtyper 1.5 days DAL00914 33

C2AA21 Small Molecule Quantitation 1 day DAL00903 34

C2AA31 Bottom-up analysis using ETD Training part of Instrument purchase

1 day 1 day

DAL00903 DAL00901

35

C2AA41 Top-down analysis using ETD/PTR 0.5 day DAL00913 36


S2AA01 ESI Ion Trap 1 day DAL00908 37

S2AA02 ESI Ion Trap 2 days DAL00909 37




ESI-TOF Operator


C3EL13 micrOTOF, Low Molecular Weight Applications Training part of Instrument purchase

2.5 days 2.5 days

DAL00915 DAL00901

39

C3EL23 ESI-(Q)TOF, Low Molecular Weight Applications Training part of Instrument purchase

2.5 days 2.5 days

DAL00915 DAL00901

40

C3EP13 micrOTOF, Proteomics Applications Training part of Instrument purchase

2.5 days 2.5 days

DAL00915 DAL00901

41

C3EP23 ESI-(Q)TOF, Proteomics Applications Training part of Instrument purchase

2.5 days 2.5 days

DAL00905 DAL00901

42

C3ES13 Screener Solution 2.5 days DAL00915 43


C3AA11 ESI-(Q)TOF, Small Molecule Quantitation 1 day DAL00903 44

C3AA21 ESI-(Q)TOF, GC-APCI Source Operation 0.5 day DAL00913 45

C3AA32 ESI-(Q)TOF, ETD on maXis Training part of Instrument purchase

1.5 days 1.5 days

DAL00914 DAL00901

46

C3AP42 BioPharmaCompass 2 days DAL00909 47


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Register Number


NumberPage


S3AA01 ESI-(Q)TOF 1 day DAL00908 48

S3AA02 ESI-(Q)TOF 2 days DAL00909 48




FT-ICR-MS Operator


C4EP15 Proteomics Applications Training part of Instrument purchase

5 days 5 days

DAL00907 DAL00901

50

C4EL15 Low Molecular Weight Applications Training part of Instrument purchase

5 days 5 days

DAL00907 DAL00901

51


S4AA03 FT-ICR-MS 3 days DAL00910 52

S4AA05 FT-ICR-MS 5 days DAL00912 52

GC Operator


C5EA13 General Training part of Instrument purchase

3 days 3 days

DAL00905 DAL00901

54


S5AA01 GC 1 day DAL00908 55

S5AA03 GC 3 days DAL00910 55

GC-MS TQ Operator


C6EA13 300/320 TQ series Training part of Instrument purchase

3 days 3 days

DAL00905 DAL00901

57

C6EA23 EVOQ TQ series Training part of Instrument purchase

3 days 3 days

DAL00905 DAL00901

58


S6AA01 GC-MS TQ 1 day DAL00908 59

S6AA03 GC-MS TQ 3 days DAL00910 59

LC-MS TQ Operator


C7EA13 EVOQ series Training part of Instrument purchase

3 days 3 days

DAL00905 DAL00901

61


S7AA01 LC-MS TQ 1 day DAL00908 62

S7AA03 LC-MS TQ 3 days DAL00910 62

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The training courses (Order Number DAL00901) are part of the instrument purchase and cannot be ordered independently from the instrument. All trainings provided (One training course from the list below) with the instrument purchase can also be ordered as standalone trainings (please just look for the corresponding training order number). The location at the on-site trainings indi-cates where Bruker has local trainers available. An ordered on-site training can be provided any-where on the world. Bruker reserves the right to convert an ordered on-site training into an in-house training in case of war, civil war, political instability, the risk of terrorist activity or natu-ral disasters which pose a significant threat for Bruker employees. In this case Bruker will carry the costs for traveling in economy class to the Bruker training center providing the training as well as lodging costs for a maximum of three training participants. Travel costs of accompanying persons not participating in the training cannot be covered.

For the local availability please refer to the training center codes. We currently operate training centers in Beijing/China (BEI), Billerica/USA (BIL), Bremen/Germany (BRE), Coventry/UK (COV), Fremont/USA (FRE), Melbourne/Australia (MEL), Champs-sur-Marne/France (PAR), Shanghai/China (SHA), Saol Paulo (SAO) and Yokohama/Japan (YOK).



Register Number


NumberPage

Software Trainings


C9AA11 Metabolite Tools for ESI 1 day DAL00903 64

C9AA21 Metabomolics for ESI-TOF 1 day DAL00903 65

C9AA32 ProteinScape™ 1.5 days DAL00914 66

C9AA41 Label-free Proteomics Quantitation 1 day DAL00903 67

C9AA51 Glycoanalysis using ProteinScape™ and GlycoQuest

1 day DAL00903 68

C9AA61 Multitargetscreening 1 day DAL00903 69

C9AA71 Cohort Profiling using ProfileAnalysis 1 day DAL00903 70

MALDI Operator

Training courses cover the range from instrument control to application driven solution

Essential Operator Training Courses ....................................... 10

Advanced Operator Training Courses ...................................... 16

On site Operator Training Courses .......................................... 28

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C1EP13

LOCATION ............................................. BEI, BIL, BRE, FRE, SHA, YOK

Course TopicsInstrument overviewGeneral introduction to the principles of MALDI-TOF(/TOF) (MALDI ionization, TOF(/TOF) analyzer)

Sample preparationSample requirements (concentration, purity); sample pre-treatment (desalting); matrices of choice and matrix preparation protocols for various types of samples (peptides, proteins, incl. samples modified by f.e. phosphorylation, glycosylation)

Data acquisitionIntroduction to Bruker´s FlexControl software; optimization of most important acquisition method parameters (f.e. laser fluence, shot count per spectrum); automated data acquisi-tion using autoXecutee

Data processingIntroduction to Bruker´s FlexAnalysis software; peak annotation; smoothing; baseline subtrac-tion; recalibation (internal / external); automated processing using FlexAnalysis methodss

Data interpretationIntroduction to Bruker´s Biotools software; protein identification by database search (MASCOT); batchwise database searching using Biotools batch search methods

Instrument maintenanceParticipants are familiarized with all those maintenance operations that are to be done routinely by instrument users.

IntentionThis training course focuses on the basics of practical MALDI-TOF(/TOF) operation in the context of proteomics and protein analysis experiments. The course covers the essentials of sample prep-aration, data acquisition/processing and instrument maintenance, and, thus, will enable novice users getting started with MALDI-TOF(/TOF) analyses of peptides and proteins.

PrerequisiteNo deeper pre-experience is required. However, before attending the training course, participants are encouraged to take part in the user familiarization that is done at customer´s site upon installa-tion of the MALDI-TOF(/TOF) instrument, and to gain some first practical experience over a few weeks.

Duration3 days 3.5 days @ BIL, FRE training center

MALDI-TOF/TOF Essential OperatorTraining Course

Proteomics using BioToolsVersion 5.0

11



Course TopicsInstrument overviewGeneral introduction to the principles of MALDI- TOF(/TOF) (MALDI ionization, TOF(/TOF) analyzer)

Sample preparationSample requirements (concentration, purity); sample pre-treatment (desalting); matrices of choice and matrix preparation protocols for various types of samples (peptides, proteins, incl. samples modified by f.e. phosphorylation, glycosylation)

Data acquisitionIntroduction to Bruker´s FlexControl software; optimization of most important acquisition method parameters (f.e. laser fluence, shot count per spectrum); automated data acquisi-tion using autoXecute

Data processingIntroduction to Bruker´s FlexAnalysis software; peak annotation; smoothing; baseline subtrac-tion; recalibation (internal / external); automated processing using FlexAnalysis methods

Data interpretationIntroduction to Bruker´s ProteinScape™ pro-teomics database system; administrative oper-ations in ProteinScape™ (f.e. user manage-ment); structured archiving of proteomics data; protein identification by database search (MASCOT); batchwise database searching using ProteinScape™ search methods; report-ing of results


IntentionThis training course focuses on the basics of practical MALDI-TOF(/TOF) operation in the context of proteomics and protein analysis experiments. The course covers the essentials of sample prep-aration, data acquisition/processing and instrument maintenance, and, thus, will enable novice users getting started with MALDI-TOF(/TOF) analyses of peptides and proteins.

PrerequisiteNo deeper pre-experience is required. However, before attending the training course, participants are encouraged to take part in the user familiarization that is done at customer´s site upon installa-tion of the MALDI-TOF(/TOF) instrument, and to gain some first practical experience over a few weeks.

Duration3.5 days

Proteomics using ProteinScape™Version 2.0


C1EP24

12


C1EC12

LOCATION .......................... BEI, BIL, BRE, COV, FRE, MEL, SAO, YOK

Course TopicsObjectiveThe objective of this training is to consolidate the knowledge that the operators have obtained during the first few weeks of operating the instrument.After the Training, you will be able to undertake sample preparation, to operate the software necessary for microorganism measurement, and to interpret the results reports.Furthermore, you will be able to train new col-leagues based on your acquired knowledge and the sample preparation protocols. You will be able to induct them in sample preparation and MALDI Biotyper software. (only valid for RUO)

Content• Introductory Presentation on the theoretical

basics (optional)• Handling and storageof chemicals, HCCA

Matrix and Bruker Bacterial Test Standard• MBT Sepsityper Kit• Usage of reusaeable target plates and

disposable target plates• Sample preparation procedures: Direct

Transfer Method, extended Direct Transfer Method, Formic Acid Extraction Method

• Target plate cleaning procedure• Briefing MALDI Biotyper Compass Software:

Interpretation and evaluation of MALDI Biotyper results and consistency

• Calibration / Validation of the instrument• trouble shooting

ParticipantsAll lab members who will potentially work with the MALDI Biotyper are invited to the introductory presentation (optional).All those who attended the familiarization during installation are invited to the following training. The number of participants should not exceed 4 people.

Duration1 day to be run approximately two weeks after installation

MALDI Essential OperatorTraining Course

MALDI Biotyper non IVDVersion 1.0

13


LOCATION ................................................... BRE, COV, FRE, MEL, YOK

Course TopicsObjectiveThe objective of the training is to deepen the knowledge that the operators have obtained during the first few weeks of operating the instrument.After the MALDI Biotyper IVD Training, you will be able to undertake sample preparation, to operate the IVD MALDI Biotyper Software and to interpret the results reports.

ContentThe scope of training course is based on the user manual delivered with the IVD MALDI Biotyper• Recapitulation of familiarization• Calibration of the Instrument• Briefing IVD MALDI Biotyper Compass

manual:– Handling and storage of chemicals

(IVD Matrix preparation, IVD BTS etc.)– IVD Sample preparation: Direct Transfer

Method, extended Direct Transfer Method, Formic Acid Extraction Method

– Validation / QC position– MALDI Target Plate Cleaning Procedure– MBT Sepsityper IVD Kit– Usage of reusaeable target plates and

disposable target plates– Identification via IVD Compass– Interpretation and evaluation of IVD

MALDI Biotyper Compass results and consistency

• Results interpretation

ParticipantsThe number of participants should not exceed 4 people.

Duration1 day to be run approximately two weeks after installation

MALDI Biotyper IVDVersion 1.0

MALDI Essential OperatorTraining Course

C1EC21

14


C1EI12


Course TopicsDay 1:• Introduction to MALDI mass spectrometry• Concepts of MALDI Imaging• Sample preparation

(Considerations redarding requirements to, transportation and storage of good quality tissue samples)

• Cryosectioning (Introduction and hands-on training)

• Matrix deposition (Matrix selection guidelines, basics of Bruker ImagePrep instrument operation)

• MALDI-TOF instrument operation - basics (Introduction to flexControl software, method optimization for MALDI Imaging)

• Image acquisition (Introduction to flexImaging software and automatic image data acquisition)

Day 2:• flexImaging software training

(Guided tour of all program features, including hands-on training)

• ImagePrep training (Hands-on training, including troubleshoo-ting and method development guidelines)

• Introduction to histology (Hands-on H&E staining, co-registration of images and introduction to virtual microscopy)

• Batch acquisition of multiple MALDI images• Instrument maintenance

IntentionThis course is intended for beginners in the field of MALDI Imaging and will provide a compre-hensive introduction to the entire workflow. The course is focused on the mass spectrometric analysis of tissue sections using Bruker MALDI-TOF hard- and software.

PrerequisiteNo detailed knowledge in mass spectrometry and/or histology is required to attend the course. Basic familiarity with Bruker MALDI-TOF instruments and a general understanding of the MALDI imaging concept would be helpful. A substantial part of the course will be conducted in a level 2 biosafety lab. This essential operator training will always also encompass an additional day of training on statistical analysis (C1AI21) so that the total duration of the essential training is 3 days!

Duration2 days 1 day @ BIL, FRE training center


MALDI ImagingVersion 1.0

15



Course TopicsInstrument overviewGeneral introduction to the principles of MALDI- TOF(/TOF) (MALDI ionization, TOF(/TOF) ana-lyzer)

Sample preparationSample requirements (concentration, purity); matrices of choice and matrix preparation proto-cols for various types of samples (in particular: synthetic polymers; further compound classes will be treated on demand)

Data acquisitionIntroduction to Bruker´s FlexControl software; optimization of most important acquisition method parameters (f.e. laser fluence, shot count per spectrum); automated data acquisition using autoXecute

Data processingIntroduction to Bruker´s FlexAnalysis software; peak annotation; smoothing; baseline subtrac-tion; recalibation (internal / external); automated processing using FlexAnalysis methods

Data interpretationIntroduction to Bruker´s Polytools software; determination of end groups, number average molecular weight (Mn), weight average molec-ular weight (Mw) and polydispersity of syn-thetic polymer samples


IntentionThis training course focuses on the basics of practical MALDI-TOF(/TOF) operation in the context of polymer & synthetic chemicals analysis. The course covers the essentials of sample prepara-tion, data acquisition/processing and instrument maintenance, and, thus, will enable novice users getting started with MALDI-TOF(/TOF) analyses synthetic polymers and further classes of organic and inorganic compounds.

PrerequisiteNo deeper MALDI-TOF(/TOF) pre-experience is required. However, before attending the training course, participants are encouraged to take part in the user familiarization that is done at customer´s site upon installation of the MALDI-TOF(/TOF) instrument, and to gain some first practical experience over a few weeks.

Duration3 days

Polymers & Synthetic ChemistryVersion 4.0


C1ES13

16


C1AP12


Course TopicsNano-LC separation / fraction spotting:Introduction to Bruker´s Hystar software: – nano-LC method setup – optimization of fraction spotting, including

automated MALDI matrix preparation.

MALDI-TOF/TOF data acquisition & processingIntroduction to Bruker´s WARP-LC software: – setup of a WARP-LC method for automated

MS and non-redundant, automated MS/MS data acquisition

– familiarization with the workflow of relative protein quantitation based on Stable Isotope Labeling (SILE, for example iTRAQ, SILAC)

Data interpretationAnalysis of LC-MALDI-MS/MS data using Bruker´s ProteinScape™ proteomics database software (including SILE quantitation)

IntentionThis training course addresses users of Bruker MALDI-TOF/TOF instruments who want to expand into the field of LC-MALDI coupling. The course covers essential aspects of nanoLC separation, fraction spotting and MALDI-TOF/TOF analysis of rather complex peptide mixtures.

PrerequisiteParticipants should have attended a MALDI-TOF(/TOF) Essential Operator Training Course to get familiar with the basics of MALDI-TOF/TOF.

Duration1.5 days

MALDI-TOF/TOF Advanced Operator Training Course

LC-MALDIVersion 5.0

17


LOCATION ........................... BEI, BIL, BRE, COV, FRE, SAO, SHA, YOK

Course TopicsObjectiveTo consolidate basic knowledge of the software programs in order to create custom database entries.

Content • Sample Preparation methods• Briefing Compass Software• Calibration procedure (manual and automatic)• Setting up and starting a measurement (manual and automatic)• AutoXecute method: use and application• Adjustment and optimization of the various parameters• AutoX-Run-Editor• Meaning and explanation of Calibration control• Spectra Interpretation, spectra profile• Creation of custom database entries, Dendrogram creation

ParticipantsThe MALDI Biotyper Advanced Operator Training is an extension of the MALDI Biotyper Essential Training. The number of participants should not exceed 3 people.

Requirements• Previous knowledge of the safe and secure handling of chemicals, the Bruker Bacterial Test

Standard and the HCCA Matrix.• Previous knowledge of the different sample preparation methods (Direct Transfer, Extended

Direct Transfer, Formic Acid Extraction).• Calibration (manual and automatic)• Results Interpretation

• Basic knowledge of MALDI Biotyper and MALDI Biotyper AutomationControl

Duration1 day and requires to have attended the essential operator training.

Database entry creationVersion 1.0

MALDI Advanced Operator Training Course

C1AC11

18


LOCATION .................................................... BIL, BRE, FRE, MEL, SAO

Course TopicsObjectiveThe objective of the training is to learn how to prepare positive blood cultures using the MALDI Sepsityper Kit.

Content• Introductory Presentation on the theoretical basics (optional)• Handling and storage of Chemicals, HCCA Matrix and Bruker Bacterial Test Standard• Preparation of positive blood cultures using the MALDI Sepsityper Kit• Usage of reusable Target plates and disposable Target plates• Briefing MALDI Biotyper Compass Software with Sepsityper module• Interpretation and evaluation of MALDI Biotyper Compass results with the Sepsityper module• Calibration

ParticipantsThe training is an extension of the MALDI Biotyper Training. The number of participants should not exceed 4 people.

Requirements• Previous knowledge of the safe and secure handling of chemicals, the Bruker Bacterial Test

Standard and the HCCA Matrix

• Calibration (manual and automatic)


• Basic knowledge of MALDI Biotyper and MALDI Biotyper Automation Control

Duration1 day

MALDI Biotyper Sample PreparationVersion 1.0


C1AC21

19


C1AC31

LOCATION .................................................................... BRE, MEL, SAO

Course TopicsObjectiveThe objective of the training is to learn how to perform the sample preparation according to the Bruker SOP.

Content• Introductory Presentation on the theoretical basics • Handling and storage of Chemicals, HCCA Matrix and Bruker Bacterial Test Standard• Sample preparation from solid and liquid media• Mycobacteria Extraction (MycoEX) Method• Usage of reusable Target plates and disposable Target plates• Briefing MALDI Biotyper Compass Software• Interpretation and evaluation of MALDI Biotyper Compass• Calibration

ParticipantsThe training is an extension of to the MALDI Biotyper Essential Training. The number of participants should not exceed 4 people.

Requirements• Previous knowledge of the safe and secure handling of chemicals, the Bruker Bacterial

Test Standard and the HCCA Matrix• Calibration (manual and automatic)• Results interpretation• Basic knowledge of MALDI Biotyper and MALDI Biotyper Automation Control

Duration1 day


MALDI Biotyper Mycobacteria IdentificationVersion 1.0

20


LOCATION .................................................................... BRE, MEL, SAO

Course TopicsObjectiveThe objective of the training is to learn how to perform the sample preparation according to the Bruker SOP.

Content• Introductory Presentation on the theoretical basics • Handling and storage of Chemicals, HCCA Matrix and Bruker Bacterial Test Standard• 3 Step workflow / Sample preparation from solid and liquid media (Direct Transfer Method,

Formic Acid Extraction Method, Broth cultivation)• Usage of reusable Target plates and disposable Target plates• Briefing MALDI Biotyper Compass Software• Interpretation and evaluation of MALDI Biotyper Compass• Calibration

ParticipantsThe training is an extension of to the MALDI Biotyper Essential Training. The number of participants should not exceed 4 people.

Requirements• Previous knowledge of the safe and secure handling of chemicals, the Bruker Bacterial

Test Standard and the HCCA Matrix

• Calibration (manual and automatic)


• Basic knowledge of MALDI Biotyper and MALDI Biotyper Automation Control

Duration1 day

MALDI Biotyper Filamentous Funghi IdentificationVersion 1.0


C1AC41

21


LOCATION ............................................................................. BRE, MEL

Course TopicsInstrument overviewGeneral introduction to the principles of MALDI-TOF (MALDI ionization, TOF analyzer)

Sample preparation• Handling and storage of the chemicals and

HCCA Matrix and Bruker Bacterial Test Standard

• Formic Acid Extraction method• Calibration procedure

Software• Short introduction to Bruker´s FlexControl

software• Optimization of dedicated flexControl

methods prior to the measurement to ensure high quality spectra

• Setting up the AutoXecute Run editor• FlexAnalysis software to assess spectra

quality and detect peak shifts• MALDI Biotyper software• Date analysis using the Gel-like view• PCA analysis• Preparation of an excel table is used to

assist in visualizing dedicated peaks for strain typing

IntentionThe advanced MALDI Biotyper strain typing training course will cover the essentials of MALDI-TOF theory and practical training and provide the knowledge for the use of the MALDI Biotyper system for strain typing applications.

PrerequisiteMALDI Biotyper Basic Training

Duration1.5 days

MALDI Biotyper Strain Typing CourseVersion 1.0


C1AC62

22


Course TopicsObjectiveHow to operate the compass STAR-BL module necessary for ß-lactamase activity

Sample preparationSample preparation with STAR-BL Kit

Content• Handling and storage of Chemicals (incuba-

tion buffer, HCCA Matrix, BrukerBacterial Test Standard, Antibiotic Calibration Stan-dard (ACS), MBT STAR-BL Matrix, MBT STAR-BL Matrix solvent, Antibiotic)

• Specific sample preparation method for STAR-BL with MBT STAR-BL IMI Kit

• Method optimization and instrument tuning for STAR-BL Module

• Briefing MALDI Biotyper Compass Software and STAR-BL module including MBT STAR-BL Calibration with Bruker Bacterial Test Standard and Antibiotic Calibration Standard in flexControl

• Interpretation and evaluation of MALDI Biotyper STAR-BL results

The MALDI Biotyper Selective Testing of Antibiotic Resistance beta- lactamase (MBT STAR-BL Module) hydrolyzation assay is a mass spectrometry- (MS-) based tool for the rapid detection of ß-lactamase activity in microbial cultures.

The MBT STAR- BL Module is a part of the MBT Compass solution, and providesseamless workflow integration, fast procedures, and conclusive automated reporting

ParticipantsThe number of participants should not exceed 3 people

Duration1 day

STAR-BL Module


C1AC71

LOCATION ....................................................................................... BRE

23


Course TopicsObjectiveThe objective of the training is to learn how to prepare positive blood cultures using the MBT Sepsityper IVD Kit.

Content• Introductory Presentation on the theoretical

basics• Handling and storage of the MBT Sepsityper

IVD Kit• Preparation of positive blood cultures using

the MBT Sepsityper IVD Kit• Formic Acid Extraction Method• Calibration with IVD Bruker Bacterial Test

Standard• Briefing MALDI Biotyper Compass Software

with Sepsityper module (Optional)• Interpretation and evaluation of the results

ParticipantsThe training is an extension of the MALDI Biotyper Training. The number of participants should not exceed 4 people.

Requirements• Previous knowledge of the safe and secure handling of chemicals, the IVD Bruker Bacterial

Test Standard, the IVD HCCA Matrix and calibration• IVD Results interpretation• Basic knowledge of MALDI Biotyper Software

DurationApproximately 1 day

MALDI Biotyper Sepsityper IVD


C1AC81

LOCATION ....................................................................................... BRE

24


C1AI11

LOCATION ............................................................................. BRE, MEL

Course Topics• Introduction to targeted small molecule imaging• Strategies for developing a drug imaging workflow using model compounds

(Establishing sample preparation, detection limit, fragmentation pattern and Selected Reaction Monitoring (SRM) transitions)

• ImagePrep method: specific modifications for small molecule analysis• Setup of MALDI-SRM and -MS/MS imaging measurements using flexControl and flexImaging

software• Hands-on data acquisition using tissue homogenates spiked with model compounds• Visit to the Bruker FTMS laboratory; discussion of small molecule imaging performed on

solariX series instruments

IntentionDedicated add-on course focusing on the targeted analysis of small molecules in tissues using MALDI Imaging. The main focus of the course will be on monitoring exogenous small molecules (i.e. drug imaging).

PrerequisiteParticipants must have a solid understanding of the MALDI Imaging workflow using Bruker instrumentation, including sample preparation and handling, data acquisition using flexControl and flexImaging. Ideally, participants should have attended in advance a MALDI Essential training course MALDI Imaging (#C1EI12).Part of the course will be conducted in a level 2 biosafety lab.

Duration1 day. Some time will be reserved to discuss the participants’ applications in detail.


Small molecule ImagingVersion 2.0

25



Course TopicsStatistical analysis of MALDI-TOF data for the detection of potential biomarkers• Mean based and median based statistics• Reported p-values and CV• Receiver-operating characteristic (ROC)

Unsupervised feature extraction from MALDI Imaging datasetsFundamentals and practical application of Principal Component Analysis (PCA)

Semi-supervised feature extraction from MALDI Imaging datasetsFundamentals and practical application of hierarchical clustering

Multivariate classification of clinical proteomics and/or imaging datasets• How to set up statistical models for the

classification of datasets?• Cross-validation, external validation and

classification• Outlier detection• Interpretation of class images

ApplicationsSpecific customer requests regarding statistical data analysis will be discussed if time permits.

IntentionThis course is intended for users of Bruker MALDI-TOF(/TOF) systems who want to enter the field of statistical analysis of MALDI profiling data originating from various workflows, for exam-ple MALDI imaging, clinical proteomics profiling, and others.

PrerequisiteAttendees should have a basic knowledge of how to operate a Bruker MALDI-TOF(/TOF) mass spectrometer with at least several weeks of practical experience. Ideally, participants have attended a MALDI-TOF(/TOF) Essential Operator Training course.

Duration1 day

Statistical data analysisVersion 2.0


C1AI21

26


C1AI31

LOCATION ............................................................................... BIL, BRE

Course Topics• Introduction to the “ImageID” workflow• Strategies for protein identification applicable to MALDI Imaging• Using the ImagePrep for trypsin deposition and matrix application after on-tissue digestion

(hands-on)• Acquisition and processing of peptide imaging data using flexControl, flexAnalysis and

flexImaging• Matching MALDI Imaging and LC-MS/MS data using the ImageID software tool

IntentionDedicated add-on course focusing on a combined bottom-up spatial proteomics workflow called “ImageID” consisting of

– enzymatic treatment of tissue sections using the ImagePrep– subsequent generation of MALDI images of the resulting peptides from the digested tissue– identification of the imaged peptides by LC-MS/MS analysis of an adjacent enzyme treated

tissue section

PrerequisiteParticipants must have a solid understanding of the MALDI Imaging workflow using Bruker instrumentation, including sample preparation and handling as well as data acquisition using flexControl and flexImaging. Idealy, attendees should have participated in a three-day basic training course MALDI Imaging (#C1EI12). In addition, participants should have basic knowledge of classical bottum-up proteomics (e.g. LC-MS/MS based peptide/protein ID workflows).



ImageIDVersion 2.0

27


LOCATION .................................................... BEI, BRE, FRE, SHA, YOK

Course TopicsThe training course will cover essential aspects of polymer data analysis when using Polytools, such as

– analysis of end groups– determination of further key features of polymers, such as number average molecular

weight (Mn), weight average molecular weight (Mw) and polydispersity

IntentionThis training course addresses users of Bruker MALDI-TOF(/TOF) instruments working in the field of synthetic polymer analysis. The course focuses on Bruker´s Polytools software and how to use it for the in-depth analysis of MS and MS/MS data obtained from polymer samples.

PrerequisiteParticipants should have a basic knowledge of mass spectrometry based workflows applied to polymer analysis.

Duration1 day

PolytoolsVersion 4.0


C1AS11

28


S1AA01S1AA02S1AA03S1AA04S1AA05

LOCATION .................. BEI, BIL, BRE, COV, FRE, PAR, SAO, SHA, YOK

Course OutlineAs these training courses are specifically tailored according to our customer’s requirements, a general course outline cannot be provided. This depends on instrument, topics to be covered as well as duration of the course and will be discussed with the Bruker application specialist in advance of the training course. Check for language availability.

IntentionThis course is intended as an individual training course tailored for the specific needs of our customers. The course will be held on-site of the customer using his installed instrumentation. This ensures that all applications trained during the course will for sure be applicable on the local installation. The number of customers trained during this training is defined by the custom-er’s requirements. However, for practical and didactical reasons, groups should not get larger than 5-6 trainees.

PrerequisitePrerequisites depend on the actual training course content and should be discussed with the responsible application specialist from bruker in advance of the training.

DurationDepends on the requirements1, 2, 3, 4 or 5 days

MALDI OperatorOn Site Training Course

GeneralVersion 1.0

ESI Ion Trap Operator





29

30


C2EL13

LOCATION .......................................... BIL, BRE, COV, MAD, PAR, YOK

Course TopicsIntroductionTheory of the ion trap mass spectrometry and atmospheric pressure ionization (API) tech-niques.

Atmospheric pressure ionization (API) Electrospray Ionization (ESI) and alternative API techniques (IonBooster/APCI/APPI), ionization efficiency, direct infusion and HPLC-ESI-MS coupling.

Calibration and tuningCalibration (e.g. detector, scan modes), tuning of the ion transfer with special focus on small molecules, positive/negative switching.

Ion trap and MS(n) operationScan modes, resolution and speed, scan range, Ion Charge Control (ICC), MS(n) capabilities of the ion trap, isolation and fragmentation options, Manual MS(n), MRM and data dependent MS(n) with intelligent precursor ion selection.

Method handling and data acquisition Method handling in trapControl™, Hystar™ and DataAnalysis™. Set-up and accomplishment of HPLC MS(n) analyses.

Data analysisGeneral data processing in DataAnalysis™, chromatogram trace definitions and MS(n) spectra extraction, FindCompounds algor-thims, basic introduction to library search applications, QuantAnalysis™ software.

MaintenanceGood working conditions (solvents, containers, nitrogen etc.), cleaning of the ion source.

ApplicationsSmall molecule analysis using LC-MS(n). Specific requirements of the customer with respect to the focus of this course will be discussed.

IntentionThis training course is intended for novice Bruker ion trap users without significant prior experi-ence in data acquisition, data analysis and instrument maintenance. The course covers all impor-tant aspects of ion trap operation and data processing as well as application relevant HPLC aspects but does not substitute an explicit HPLC training.

PrerequisiteDue to the familiarization during system installation, attendees should have a basic knowledge of the ion trap mass spectrometer with several weeks of practical experience with the instrument and software.

DurationThe duration of the course is 2.5 daysPlease note: This training does not replace a dedicated HPLC training!

Ion Trap Essential Operator Training Course

Low Molecular Weight ApplicationsVersion 1.0

31


LOCATION ....................................................................... BIL, BRE, PAR

IntentionIntroduction to the standard Toxtyper screening workflow. The training course allows new users of the Toxtyper to start immediately with their samples, therefore the training course should be scheduled right after installation. In addition to the workflow routine maintenance of the instru-mental set up is trained.

PrerequisiteAttendees should have a basic knowledge of LCMS coupling and the analysis of toxicologic or forensic samples.

DurationThe duration of the course is 2 days.

Toxtyper Routine WorkflowsVersion 1.0

Toxtyper Essential OperatorTraining Course

C2ET12

Course TopicsIntroductionIntroduction to the HPLC hardware including the software ”Chromeleon” and a brief intro-duction to the ion trap hardware. General fea-tures of the Compass OpenAccess software also explained.

Toxtyper Workflow Based on the Toxtyper user tutorial the Tox-typer workflow is trained. This includes LCMS system setup, quality control samples, result interpretation based on real life samples and standby conditions.

Routine Toxtyper Ion Trap Performance TestsWeekly recommended maintenance tests of the system are trained: ESI source mainte-nance, detector check, and Toxtyper specific automatic system tests.

Toxtyper Ion Trap CalibrationsAfter a brief introduction to the trapControl software calibrations of detector, scan calibra-tion and isolation/fragmentation are discussed.

TroubleshootingInformation is provided on what to do in case of error messages.

Additional Topics on RequestAs add-ons more information on ESI and ion trap mass spectrometry can be given. Besides that administrator options for Compass OpenAccess are another option.

32


C2EP13

LOCATION ............................................ BIL, BRE, COV, FRE, PAR, YOK

Course TopicsIntroductionTheory of the ion trap mass spectrometry and electrospray ionization.

Atmospheric pressure ionization (API) Electrospray Ionization (ESI) and nano ESI oper-ation, ionization efficiency, direct infusion and HPLC-ESI-MS coupling.

Calibration and tuningCalibration (e.g. detector, scan modes), tuning of the ion transfer with special focus on pro-teomics samples.

Ion trap and MS(n) operationScan modes, resolution and speed, scan range, Ion Charge Control (ICC), MS(n) capabilities of the ion trap, isolation and fragmentation options, data dependent MS(n) with intelligent precursor ion selection.

Method handling and data acquisition Method handling in trapControl™, Hystar™ and DataAnalysis™. Set-up and accomplishment of HPLC MS(n) analyses.

Data analysisGeneral data processing in DataAnalysis™, file export options, basics of BioTools™ / Protein-Scape™ software, protein identification via database search, automation.


ApplicationsWorkflow for protein identification by data dependent LC-MS(n) analysis of tryptic digests. Specific requirements of the customer with respect to the focus of this course will be discussed.

IntentionThis training course is intended for novice Bruker ion trap users without significant prior experi-ence in data acquisition, data analysis and instrument maintenance. The course covers all impor-tant aspects of ion trap operation and data processing as well as application relevant HPLC aspects but does not substitute an explicit HPLC training.

PrerequisiteDue to the familiarization during system installation, attendees should have a basic knowledge of the ion trap mass spectrometer with several weeks of practical experience with the instrument and software.

DurationThe duration of the course is 3 days.Please note: This training does not replace a dedicated HPLC training!

Ion Trap Essential Operator Training Course

ProteomicsVersion 1.0

33


LOCATION ....................................................................... BIL, BRE, PAR

IntentionIntroduction to custom Toxtyper screening workflows using the Toxtyper custom library. Introduction of new compounds to the custom library will be shown by a dedicated workflow.

PrerequisiteAttendees should be familiar with the Toxtyper system and the standard screening workflow and therefore should have attended the “Toxtyper Essential Operator Training Course”.


Use of Toxtyper Custom LibrariesVersion 1.0

Toxtyper Advanced Operator Training Course

C2AA12

Course TopicsIntroduction to Administrator Options in Compass OpenAccessIntroduction to the web interface of Compass OpenAccess and the administrator options. Discussion of the administration of methods.

Overview of Expert Software Modules Compass OpenAccess will be closed and the system will be re-started using the standard expert software. Following software modules will be activated and introduced to the user: HPLC-MS software HyStar, ion trap software trapControl, DataAnalysis software, and Library Editor.

Modulation of the Toxtyper Workflow and Introduction of new CompoundsBased on the Toxtyper administrator tutorial the systematic modulation from the standard Toxtyper workflow to Toxtyper “custom” will be discussed. All features of the correspond-ing expert software necessary for the custom workflow will be trained in detail.

Test of Custom Toxtyper MethodThe system will be switched back to operation under Compass OpenAccess and test runs are performed to test the new build custom library.

More Features in Compass OpenAccess Handling of large sample lists, introduction to user management and statistics.

Additional Topics on RequestIn agreement with the participants.

34


C2AA21

LOCATION ................................. BIL, BRE, COV, FRE, MAD, PAR, YOK

Course TopicsTuningOptimization of API source parameters and tuning of the ion transfer for highest sensitivity.

Optimization of MS / MS parameters Adjustment of isolation window, fragmentation amplitude and cut-off, Enhanced Fragmentation, SmartFrag.

LC-MS/MS method set-up for QuantificationUse of external or internal and smartMRM (Compass 1.7) calibration standards, Manual MS(n) and/or MRM acquisition mode with or w/o time segments, adjustment of scan mode, scan range and spectral averaging.

Data acquisition Set-up of calibration curve and sample analysis in HyStar™ sample table.

Data AnalysisGeneral data processing in DataAnalysis™, Quantification workflow in the QuantAnalysis™ software, external versus internal calibration, reintegration of chromatograms, weighting of calibration curves, removal of outliers.

ApplicationsSmall molecule quantification workflow from start to result. Specific requirements with respect to the focus of this course will be discussed

IntentionFor users familiar with Bruker ion trap systems who want to deepen their knowledge in the use of Bruker ion traps for quantitative applications. The course covers all relevant aspects of quanti-tation on the ion trap including tuning for highest sensitivity, MS/MS optimization as well as application relevant HPLC aspects and the use of the QuantAnalysis™ software.

PrerequisiteParticipants should have attended an Ion Trap Essential Operator Training Course “Low Molecular Weight Applications”.

DurationThe duration of the course is 1 dayPlease note: This training does not replace a dedicated HPLC training!

Ion Trap Advanced Operator Training Course

Small Molecule QuantitationVersion 1.0

35



IntentionFor users familiar with Bruker ion trap ETD systems who want to start with ETD analyses.

PrerequisiteParticipants should have attended an Ion Trap Essential Operator Training Course “Proteomics Applications”.

DurationThe duration of the course is 1 day

Peptide Analysis using ETDVersion 1.0

Ion Trap Advanced Operator Training Course

C2AA31

Course TopicsIntroduction to Electron Transfer Dissocia-tion (ETD) and Proton Transfer Reaction (PTR)Principles of ETD, ETD fragmentation mecha-nism, differences between ETD and CID, nCI source configuration and function.

ETD and PTR operationOverview on ETD software features, tuning of nCI source parameters for ETD and PTR operation.

ETD acquisition modesManual and data dependent ETD, alternating CID-ETD analysis, neutral loss triggered ETD (PTMScan™), SmartDecomposition for bottom-up analysis of post-translational modifications (PTMs).

Data analysisData processing in DataAnalysis™, file export options.

BioTools™ (ProteinScape™) Handling of ETD data in BioTools™ / Protein-Scape™.

ApplicationsAnalysis of phosphopeptides by data dependent LC-MS(n) using CID and ETD. Specific require-ments with respect to the focus of this course will be discussed.

36


C2AA41


Course TopicsIntroduction to Electron Transfer Dissocia-tion (ETD) and Proton Transfer Reaction (PTR)Principles of ETD and PTR, PTR operation, nCI source configuration and function.

ETD and PTR operation Overview over ETD and PTR software features, tuning of nCI source parameters for ETD and PTR operation.

ETD-PTR analysisETD-PTR top-down sequencing capabilities for small and medium size proteins.

Data AnalysisData processing in DataAnalysis™, file export options.

BioTools™ (ProteinScape™) Handling of ETD-PTR data in BioTools™/ ProteinScape™.

ApplicationsETD-PTR top-down sequencing of a small protein. Specific requirements with respect to the focus of this course will be discussed.

IntentionFor users familiar with Bruker ion trap ETD systems who want to start with ETD-PTR analyses.

PrerequisiteParticipants should have attended an Ion Trap Basic Operator Training Course “Proteomics Appli-cations” as well as an Advanced Operator training course “Peptide Analysis using ETD” (C2AG32)

DurationThe duration of the course is 0.5 days

Ion Trap Advanced OperatorTraining Course

Top down analysis using ETD/PTRVersion 1.0

37


LOCATION ........................ BIL, BRE, COV, FRE, MAD, PAR, SAO, YOK


PrerequisitePrerequisites depend on the actual training course content and should be discussed with the responsible application specialist from bruker in advance of the training.

DurationDepends on the requirements

GeneralVersion 1.0

Ion Trap Operator On Site Training Course

S2AA01 S2AA02 S2AA03 S2AA04 S2AA05

Course OutlineAs these training courses are specifically tailored according to our customer’s requirements, a general course outline cannot be provided. This depends on instrument, topics to be covered as well as duration of the course and will be discussed with the Bruker application specialist in advance of the training course.

ESI-TOF Operator





38

39


LOCATION .......................................................... BRE, MAD, PAR, YOK

IntentionThis course is intended for novice Bruker micrOTOF users without significant prior experience in data acquisition and/or instrument maintenance. This course covers all important aspects of micrOTOF operation as well as application relevant HPLC aspects but does not substitute an explicit HPLC training.

PrerequisiteDue to the familiarization during system installation, attendees should have a basic knowledge of the micrOTOF mass spectrometer with several weeks of experience with the instrument and the software.

DurationThe duration of the course is 2.5 days.Please note: This training does not replace a dedicated HPLC training!

Low Molecular Weight MicroTOFVersion 3.0

ESI-TOF Essential OperatorTraining Course

C3EL13

Course TopicsInstrument overviewInstrument geometry, theory of the orthogonal time of flight system, accurate mass measure-ment

Atmospheric pressure ionization (API)ESI, APCI, APPI, ionization efficiency, positive and negative ion mode ionization, direct infusion, electrolyte and buffer requirements for MS- coupling of separation instruments like HPLC or UPLC

Tuning and optimization of the micrOTOF Calibration and tuning of the micrOTOF, ioniza-tion modes, ion transfer, tuning for high sensi-tivity and high mass accuracy, cycle- and trigger-times

Data acquisitionMass range, mass accuracy, data acquisition, internal and external mass calibration, HPLC control using Hystar software

Data analysisGeneral data processing and evaluation with DataAnalysis, SmartFormula3D and quantifica-tion using QuantAnalysis software, basic intro-duction of the LibaryEditor and ReportDesigner

MaintenanceGeneral Maintenance of the micrOTOF, source maintenance, and methods of cleaning

ApplicationsSpecific requirements of the customer with respect to the focus of this course will be discussed.

40


C3EL23


Course TopicsInstrument overviewInstrument geometry, theory of the orthogonal time of flight system, accurate mass measure-ment, MS/MS-capabilities of the instrument.

Atmospheric pressure ionization (API) ESI, APCI, APPI, ionization efficiency, positive and negative ion mode ionization, direct infusion, electrolyte and buffer requirements for MS- coupling of separation instruments like HPLC or UPLC

Tuning and optimization of the QTOFCalibration and tuning of the QTOF, ionization modes, ion transfer, tuning for high sensitivity and high mass accuracy, cycle- and trigger-times

Data acquisitionResolution (focus / non-focus mode), mass range, mass accuracy, data acquisition, speed

internal and external mass calibration, HPLC control using Hystar software

MS/MS-capabilitiesIsolation, fragmentation, Auto-MS/MS, MRM, intelligent precursor selection

Data analysisGeneral data processing and evaluation with DataAnalysis, SmartFormula and quantification using QuantAnalysis software, basic introduc-tion of the LibraryEditor and ReportDesigner

MaintenanceGeneral Maintenance of the QTOF, source maintenance, including dismantling and meth-ods of cleaning


IntentionThis course is intended for novice Bruker QTOF users without significant prior experience in data acquisition and/or instrument maintenance. This course covers all important aspects of QTOF operation as well as application relevant HPLC aspects but does not substitute an explicit HPLC training.

PrerequisiteDue to the familiarization during system installation, attendees should have a basic knowledge of the QTOF mass spectrometer with several weeks of experience with the instrument and the software.

DurationThe duration of the course is 2.5 days.Please note: This training does not replace a dedicated HPLC training!

ESI-TOF Essential Operator Training Course

Low Molecular Weight ESI-QTOF SeriesVersion 3.0

41


LOCATION ..................................................................... BRE, PAR, YOK

IntentionThis course is intended for novice Bruker micrOTOF users without significant prior experience in data acquisition and/or instrument maintenance. This course covers all important aspects of micrOTOF operation as well as application relevant HPLC aspects but does not substitute an explicit HPLC training.

PrerequisiteDue to the familiarization during system installation, attendees should have a basic knowledge of the micrOTOF mass spectrometer with several weeks of experience with the instrument and the software.

DurationThe duration of the course is 2.5 days. Please note: This training does not replace a dedicated HPLC training!

Proteomics MicroTOFVersion 3.0

ESI-TOF Essential OperatorTraining Course

C3EP13

Course TopicsInstrument overviewInstrument geometry, theory of the micrOTOF, accurate mass, IS-CID MS2-capabilities

Atmospheric pressure ionization (API) ESI operation, ionization efficiency, direct infu-sion, coupling to separation instruments: LC, nano-LC

Tuning and optimization of the QTOFCalibration and tuning of the micrOTOF, ioniza-tion mode, ion transfer, tuning for high sensi-tivity/high resolution or wide mass range

Data acquisitionCalibration, HyStar control

Data analysisGeneral data processing, accurate mass, reca-libration, deconvolution (also MaxEnt), peaklist generation and export

Database searchingFile export options, basics of BioTools software, database search

General MaintenanceSource maintenance, including dismantling and methods of cleaning


42


C3EP23

LOCATION ................................... BIL, BRE, COV, FRE, PAR, SAO, YOK

Course TopicsInstrument overviewInstrument geometry, theory of the Bruker QTOF systems, accurate mass, MS2-capabilities

Data acquisition Resolution, calibration. HPLC control using Hystar software

Tuning and optimization of the maXis Calibration and tuning of the QTOF system, ionization mode, ion transfer, tuning for high sensitivity/high resolution or wide mass range.

MS/MS-experimentsIsolation, fragmentation, Auto-MS2, MRM experiments, intelligent precursor ion selection

Atmospheric pressure ionization (API)ESI operation, ionization efficiency, direct infu-sion, coupling to separation instruments: LC, nano-LC

Data AnalysisGeneral data processing, accurate mass, recalibration, deconvolution (including MaxEnt), peaklist generation and export

Database searchingFile export options, basics of BioTools and ProteinScape™ software, database search

General MaintenanceSource maintenance, including dismantling and methods of cleaning

ApplicationsSpecific requirements of the customer with respect to focus of this course will be dis-cussed.

IntentionThis course is intended for novice Bruker QTOF users without significant prior experience in data acquisition and / or instrument maintenance. This course covers all important aspects of QTOF system operation as well as application relevant HPLC aspects but does not substitute an explicit HPLC training.

PrerequisiteDue to the familiarization during system installation, attendees should have a basic knowledge of the ESI-QTOF mass spectrometer with several weeks of experience with the instrument and the software.

DurationThe duration of the course is 3 days.Please note: This training does not replace a dedicated HPLC training!


Proteomics Applications ESI-QTOF seriesVersion 1.0

43



IntentionThis course is intended for novice users of the Bruker Screener solutions like e.g. Pesticide-Screener or ToxScreener without significant prior experience in data acquisition and / or instrument maintenance. This course covers all important aspects of QTOF operation as well as application relevant HPLC aspects but does not substitute an explicit HPLC training.

PrerequisiteDue to the familiarization during system installation, attendees should have a basic knowledge of the screener solution.

DurationThe duration of the course is 2.5 days. Please note: This training does not replace a dedicated HPLC training!

Bruker Screener SolutionsVersion 1.0


C3ES13

Course TopicsInstrument overviewInstrument geometry, theory of the orthogonal time of flight system, accurate mass measure-ment, MS/MS-capabilities of the instrument.

Atmospheric pressure ionization (API) ESI, APCI, APPI, ionization efficiency, positive and negative ion mode ionization, direct infusion, electrolyte and buffer requirements for MS coupling of separation instruments like HPLC or UPLC.

Tuning and Maintenance of the QTOFCalibration and tuning of the QTOF, general maintenance of the QTOF, source maintenance, including dismantling and methods of cleaning.

Data acquisitionSetup of screening and quantitation experiments and discussion of the general workflow settings.

Data analysisGeneral data processing and evaluation includ-ing automation using TASQ setup of customized databases.


44



IntentionFor users familiar with Bruker ESI TOF systems which want to deepen their knowledge in its use for quantification applications. The course covers all relevant aspects of quantition on ESI TOF-including application relevant HPLC aspects and the operation of QuantAnalysis software.

PrerequisiteAttendees should have attended a ESI TOF Essential Operator Training course “Low molecular weight applications”.

DurationThe duration of the course is 1 day. Please note: This training does not replace a dedicated HPLC training!

Small Molecule QuantitationVersion 1.0

ESI-TOF Advanced OperatorTraining Course

C3AA11

Course TopicsInstrument overviewTheory of the orthogonal time of flight system in summary, specific features in ESI-TOF oper-ation for quantification

Atmospheric pressure ionization (API) ESI, APCI, APPI, ionization efficiency, positive and negative ion mode ionization, electrolyte and buffer requirements for MS-coupling of separation instruments like HPLC, UPLC, or CE with focus on quantitation and reproducibility

QuantitationGeneral quantitation strategies, relative and absolute quantitation, external versus internal standard calibration, isotopic labeled stan-dards, standard deviation

Data acquisitionSetup of quantitation experiments, use of time segments for optimization on different ana-lytes

Tuning and optimization of the ESI-TOF Calibration and tuning for high sensitivity ion transfer

Data analysisGeneral data processing and evaluation with DataAnalysis and QuantAnalysis, automation using available scripts


45


C3AA21

LOCATION ....................................................................................... BRE

Course TopicsCoupling GC-APCI source to ESI-TOF instrumentMounting the GC-APCI source, advise on GC-APCI specific source parameters

Instrument calibrationIntroduction how to calibrate the instrument when using a GC-APCI source

Data acquisitionHow to set up a Hystar sequence table in combination with CTC autosampler, GC-APCI specific method setup in OTOFcontrol, data acquisition

Data analysisGC-APCI-MS specific data processing and evaluation with DataAnalysis

ApplicationsSpecific requirements of the customer with respect to the focus of this course can be discussed

IntentionFor users familiar with Bruker ESI-TOF systems which want to successfully use the GC-APCI ion source. The course covers all relevant aspects of operating the GC-APCI ion source.

PrerequisiteAttendees should have attended a Essential Operator Training course “Low molecular weight applications”.

DurationThe duration of the course is half a day.Please note: This course does not substitute an explicit GC training!


GC-APCI SourceVersion 1.0

46


LOCATION ............................................... please ask for local availability

IntentionFor users familiar with the Bruker maXis UHR-QTOF system and which want to successfully use the ETD option for top-down protein analysis.

PrerequisiteAttendees should have a previous knowledge of ESI mass spectrometry with several weeks of experience with the instrument and the software and should have previously attended an Essential Operator Training course “Proteomics applications” (C3EP33).

DurationThe duration of the course is 1.5 days.

Electron Transfer Dissociation on maXis ETD systemsVersion 1.0

ESI-(Q)TOF Series Advanced Operator Training Course

C3AA31

Course TopicsIntroduction to Electron Transfer Dissociation (ETD)Principles of ETD, nCI source configuration and function.

Performance check and tuning ETD performance check, tuning of the system

ETD-MS/MS data acquisitionMultiple Reaction Monitoring (MRM-) based ETD-MS/MS data acquisition for top-down analysis and auto-MS/MS based ETD-MS/MS data acquisition for peptide analysis.

Data analysis including database searchingGeneral data processing in DataAnalysis (spec-tra processing, peak detection and annotation), file export to BioTools, basics of BioTools soft-ware, protein identification via database search (MASCOT and MS-BLAST).

ApplicationsIf time permits, specific requirements of the customer with respect to the focus of this course will be discussed.

47


LOCATION ....................................................................................... BRE

IntentionFor users familiar with Bruker ESI-MS systems which want to successfully use the BioPharma-Compass software for the analysis of recombinant proteins.

PrerequisiteThis course is only offered as on-site training course as it includes customer specific method adaptation. Attendees should have a basic knowledge of ESI mass spectrometry (micrOTOF(-Q), compact, impact or maXis series) with several weeks of experience with the instrument and the software and should have previously attended an Essential Operator Training course “Proteomics applications”.


BioPharmaCompass SoftwareVersion 1.0

ESI-(Q)TOF Series Advanced Operator Training Course

C3AP42

Course TopicsIntroductionIntroduction to BioPharma Compass top-level functionalities and introduction of the main workflows which are supported

Administrative Tasks Basic administrative tasks include user-, station-, workflow- and method management. After these tasks have been completed we can start to use the system.

AutomationBioPharma Compass is a “turn-key” solution, meaning that the whole process of acquiring data, analysis of data, report generation and result storage is executed without the need of user intervention. In this section it is explained how this automation is implemented. The Workflow and Method concept is discussed; samples will be submitted, measured and analyzed. Finally the available tools for inspect-ing results are customized and used.

Reprocessing and ValidationThe functionality for reprocessing of acquired data sets and validation of obtained results are discussed.

Workflows in DetailDetails of the Intact Protein Workflow, Protein Digest Workflow, Glycan Workflow and Library Search Workflow are presented.

Tips and Tricks, TroubleshootingA step-by-step approach will be presented for situations in which unexpected behavior is observed.

48


S3AA01 S3AA02 S3AA03 S3AA04 S3AA05

LOCATION ....... BEI, BIL, BRE, COV, FRE, MAD, PAR, SAO, SHA, YOK

Course OutlineAs these training courses are specifically tailored according to our customer’s requirements, a general course outline cannot be provided. This depends on instrument, topics to be covered as well as duration of the course and will be discussed with the Bruker application specialist in advance of the training course. Check for language availability.

IntentionThis course is intended as an individual training course tailored for the specific needs of our cus-tomers. The course will be held on-site of the customer using his installed instrumentation. This ensures that all applications trained during the course will for sure be applicable on the local installation. The number of customers trained during this training is defined by the customer’s requirements. However, for practical and didactical reasons, groups should not get larger than 5-6 trainees.

PrerequisitePrerequisites depend on the actual training course content and should be discussed with the responsible application specialist from Bruker in advance of the training.

DurationDepends on the requirements 1, 2, 3, 4 or 5 days

ESI-TOF Operator On Site Training Course

GeneralVersion 1.0

FT-ICR-MS Operator




49

50


LOCATION ................................................................................ BIL, BRE

IntentionThis training course is intended for novice Bruker solariX series users without significant prior experience in data acquisition, data analysis and instrument handling. The course covers all important aspects of data acquisition and data processing for proteomics applications as well as application relevant HPLC aspects for proteomics applications but does not substitute an explicit HPLC training.

PrerequisiteDue to the familiarization during system installation, attendees should have a basic knowledge of the solariX series FTMS mass spectrometer with several weeks of practical experience with the instrument and DataAnalysis software.

DurationThe duration of the course is 3 or 5 days, depending on the actual instrument configuration. Please note: This training does not replace a dedicated HPLC training!

Proteomics ApplicationsVersion 1.0

solariX series FTMS Essential Operator Training Course

C4EP15

Course TopicsIntroductionTheory of the solariX series mass spectro-meter and electrospray ionization and MALDI.

Atmospheric pressure ionization (API) Electrospray Ionization (ESI) and nano ESI operation, ionization efficiency, direct infusion and HPLC-ESI-MS coupling.

Calibration and tuningCalibration, tuning of the ion source, ion trans-fer and ICR cell with special focus on pro-teomics samples.

MS operationResolution, speed, scan range, method han-dling, quadrupole isolation and fragmentation options like CID, ECD and ETD, data depen-dent MS/MS parameters.

Method handling and data acquisition Method handling in ftmsControl, Hystar™ and DataAnalysis™. Set-up and accomplishment of HPLC MS/MS analyses.

Data analysis including database searchingGeneral data processing in DataAnalysis™, file export options, basics of BioTools™/ Protein-Scape™ software, protein identification via database search, automation.


ApplicationsWorkflow for protein identification by data dependent LC-MS/MS analysis of tryptic digests. Specific requirements of the customer with respect to the focus of this course will be discussed.

51


C4EL15

LOCATION ................................................................................ BIL, BRE

Course TopicsIntroductionTheory of the solariX series mass spectrom-eter and atmospheric pressure ionization (API) techniques and MALDI.

Atmospheric pressure ionization (API) and MALDIElectrospray Ionization (ESI) and other API tech-niques (APCI/APPI) as well as MALDI, ionization efficiency, flow injection (FI), direct infusion and HPLC-ESI-MS coupling.

Calibration and tuningCalibration, tuning of the ion source, ion trans-fer and ICR cell with special focus on small molecules, positive / negative switching.

MS operationResolution, speed, scan range, method han-dling, CASI, quadrupole isolation and fragmen-tation options.

Method handling and data acquisition Method handling in ftmsControl, Hystar™ and DataAnalysis™. Set-up and accomplishment of HPLC MS analyses.

Data analysisGeneral data processing in DataAnalysis™, pro-cessing of single spectra generated by MALDI and ESI/APCI/APPI infusion or FI experiments, smart formula calculation, chromatogram trace definitions, FindCompounds algorithms.


ApplicationsSmall molecule analysis using MALDI, ESI / APCI / APPI FI or infusion experiments as well as LC-MS. Specific requirements of the cus-tomer with respect to the focus of this course will be discussed.

IntentionThis training course is intended for novice Bruker solariX series users without significant prior experience in data acquisition, data analysis and instrument handling. The course covers all important aspects of data acquisition and data processing for proteomics applications as well as application relevant HPLC aspects for metabolomics and other small molecule applications but does not substitute an explicit HPLC training.

PrerequisiteDue to the familiarization during system installation, attendees should have a basic knowledge of the solariX series FTMS mass spectrometer with several weeks of practical experience with the instrument and DataAnalysis software.

DurationThe duration of the course is 3 or 5 days, depending on the actual instrument configuration. Please note: This training does not replace a dedicated HPLC training!

solariX series FTMS Essential Operator Training Course

Low Molecular Weight ApplicationsVersion 1.0

52


LOCATION ................................................................BEI, BIL, BRE, YOK




GeneralVersion 1.0

FTMS Operator On Site Training Course

S4AA03 S4AA05


GC Operator




53

54


LOCATION .................................. BEI, BRE, FRE, MAD, PAR, SHA, YOK

IntentionThis course is intended for novice Bruker GC 400 series users without significant prior experi-ence in data acquisition and / or instrument maintenance as well as gas chromatography knowl-edge. This course covers all important aspects of GC operation as well as application relevant aspects according sample introduction and different detectors.

PrerequisiteNo prerequisites necessary.

DurationThe duration of the course is 3 days. Please note: This training does not contain mass spec sections!

GeneralVersion 1.0

GC Essential OperatorTraining Course

C5EA13

Course TopicsInstrument overviewInstrument overview, GC-injectors, injection methods and other sample introduction tech-niques, basic column choice, detectors (ECD, FID, TCD) and hardware familiarization.

Principle of gas chromatographyHistory, theory of (gas) chromatography, choice of carrier gases, influence of parameters, tem-perature, pressure and principles of method development.

Sample IntroductionPrinciple of sample introduction for different applications: split/splitless injection, solvent vent, pressure pulses, less discriminative sample introduction

Advanced inlet techniques (on request) Headspace Injection, ChromatoProbe, cold on column, SPME

Data acquisition Usage of CompassCDS

Optimization of GCCalibration of flow, performance check / troubleshooting

Data analysisGeneral data processing and evaluation Com-passCDS, basic introduction of reporting.

MaintenanceGeneral Maintenance of the GC, its injectors, detectors, columns and accessories.


55


S5AA01 S5AA03

LOCATION ................BEI, BRE, COV, FRE, MAD, PAR, SAO, SHA, YOK





GC Operator On Site Training Course

GeneralVersion 1.0

GC-MS TQ Operator




56

57


C6EA13

LOCATION ......................................... BRE, FRE, MAD, PAR, SHA, YOK

Course TopicsInstrument overviewInstrument overview, GC-injectors, injection methods, theory of the quadrupol systems, MS / MS-capabilities of the quadrupole

Electron impact ionization (EI)Principle of ion formation, ionization efficiency, in source fragmentation

Chemical ionization (CI)Principle of ion formation, ionization efficiency, gases used for ionization, positive and nega-tive ion mode ionization, requirements for laboratory

Advanced inlet techniques (on request)Direct Insertion Probe, ChromatoProbe

Data acquisitionUsage of System Control, Method Builder

Tuning and optimization of the 300/320Calibration and tuning of the instrument, per-formance check / troubleshooting after tuning, ionization modes, scan-, cycle- and dwell-time, fragmentation in Q2

MS / MS-capabilitiesIsolation, fragmentation, MS/MS-method development, (scheduled) MRM

Data analysisGeneral data processing and evaluation with MS Data Review, basic introduction of reporting.

MaintenanceGeneral Maintenance of the GC and the mass spectrometer, source maintenance, including dismantling and methods of cleaning


IntentionThis course is intended for novice Bruker GC-MS TQ users without significant prior experience in data acquisition and/or instrument maintenance. This course covers all important aspects of GC-MS TQ operation as well as application relevant GC aspects but does not substitute an explicit GC training.

PrerequisiteDue to the familiarization during system installation, attendees should have a basic knowledge of the triple quad mass spectrometer with several weeks of experience with the instrument and the software.

DurationThe duration of the course is 3 days.Please note: This training does not replace a dedicated GC training!

GC-MS TQ Essential Operator Training Course

GC-MS 300 / 320 TQ SeriesVersion 1.0

58


LOCATION ............................... BRE, FRE, MAD, PAR, SAO, SHA, YOK

IntentionThis course is intended for novice Bruker EVOQ GC-MS Triple Quadrupole series users without significant prior experience in data acquisition and/or instrument maintenance. This course covers all important aspects of EVOQ TQ operation as well as application relevant GC aspects but does not substitute an explicit GC training.

PrerequisiteDue to the familiarization during system installation, attendees should have a basic knowledge of the triple quad mass spectrometer with several weeks of experience with the instrument and the software.

DurationThe duration of the course is 3 days. Please note: This training does not replace a dedicated GC training!

EVOQ TQVersion 1.0

GC-MS TQ Essential Operator Training Course

C6EA23

Course TopicsInstrument overviewInstrument overview, GC-injectors, injection methods, theory of the quadrupol systems, MS/ MS-capabilities of the quadrupole

Electron impact ionization (EI)Principle of ion formation, ionization efficiency, in source fragmentation

Chemical ionization (CI)Principle of ion formation, ionization efficiency, gases used for ionization, positive and negative ion mode ionization, requirements for laboratory

Advanced inlet techniques (on request)Headspace Injection, ChromatoProbe

Data acquisitionUsage of System Control, Method Builder Tuning and optimization of the EVOQ TQ Cali-bration and tuning of the instrument, perfor-mance check/troubleshooting after tuning, ionization modes, scan-, cycle- and dwell-time, fragmentation in Q2

MS/MS-capabilitiesIsolation, fragmentation, MS/MS-method development, Compound Based Scanning

Data analysisGeneral data processing and evaluation with MS Data Review, basic introduction of report-ing. Introduction to MSWS-Software General data processing in MSWS, using sequences, reprocessing and reports, Advanced automated and manual integration for quantitative analysis. Enhanced peak deconvolution using PACER and efficient reporting by DASH reporting

MaintenanceGeneral Maintenance of the GC and the mass spectrometer, source maintenance, including dismantling and methods of cleaning


59


S6AA01 S6AA03

LOCATION ....................... BRE, COV, FRE, MAD, PAR, SAO, SHA, YOK





GC-MS TQ Operator On Site Training Course

GeneralVersion 1.0

LC-MS TQ Operator




60

61


C7EA13

LOCATION ............................................................BRE, FRE, MAD, PAR

Course TopicsIntroductionFamiliarization with the LC-MS TQ system, principles and practice of LC-MS TQ, QqQ theory and experiments.

Atmospheric pressure ionization (API) Electrospray Ionization (ESI) and Atmospheric Pressure Chemical Ionization (APCI) operation, ionization efficiency, heated ESI characteristics.

Calibration and tuningCalibration, tuning of the ion transfer.

OperationChanging columns, there are not capillary in the EVOQ ESI, changing probes, scan types (specific and universal). Bruker Advance HPLC/UHPLC systems and PAL autosampler operation and troubleshooting.

Method handling and data acquisition Instrument control, creation and running of methods. Set-up and accomplishment of LC MS/MS analyses.

MS/MS-capabilities Isolation, fragmentation, MS/MS-method development, Compound Based Scanning.

Data analysis including efficient reportingIntroduction to MSWS-Software General data processing in MSWS, using sequences, repro-cessing and reports, Advanced automated and manual integration for quantitative analysis. Enhanced peak deconvolution using PACER and efficient reporting by DASH reporting

MaintenanceGood working conditions (solvents, contain-ers, nitrogen etc.), cleaning of the ion source.

ApplicationsIndividual questions and specific requirements with respect to the focus of this course will be discussed.

IntentionFor users who start working with Brukers EVOQ LC-MS Triple Quadrupole Series (EVOQ Qube, EVOQ Elite, EVOQ ER) for the quantitative analysis of small molecules.

PrerequisiteParticipants should have collected a couple of weeks experience with the basic operation of the system after the installation.

DurationThe duration of the course is 3 days

LC-MS TQ Essential Operator Training Course

Small molecule analysisVersion 1.0

62


LOCATION ............................................................BRE, FRE, MAD, PAR

IntentionThis course is intended as an individual training course tailored for the specific needs of our customers. The course will be held on-site of the customer using his installed instrumenta-tion. This ensures that all applications trained during the course will for sure be applicable on the local installation. The number of customers trained during this training is defined by the customer’s requirements. However, for practical and didactical reasons, groups should not get larger than 5-6 trainees.



GeneralVersion 1.0

LC-MS TQ Operator On Site Training Course

S7AA01 S7AA03


Software Trainings


Advanced Operator Training Courses ..................................... 64

63

64


LOCATION ...................BEI, BIL, BRE, COV, FRE, PAR, SAO, SHA, YOK

IntentionFor users familiar with Bruker ESI systems which want to successfully use the MetaboliteTools software.

PrerequisiteAttendees should have a basic knowledge of ESI mass spectrometry with several weeks of experience with the instrument and the software and previously attended a Essential Operator Training course “Low molecular weight applications”.

DurationThe duration of the course will be 1 day, with the course covering all relevant aspects of using of MetaboliteTools software. Individual requirements will be taken into account as far as pos-sible.

Metabolite ToolsVersion 3.0

Advanced Operator Training Course

C9AA11

Course TopicsData acquisitionSetup of metabolomics experiments, data acquisition with the focus on reproducibility between runs

Data analysisGeneral data processing and evaluation with DataAnalysis and MetaboliteTools

MetaboliteTools software• Metabolite Predict: introduction to the

software, manual and automated operation, basic functions of StructureEditor, genera-tion of customized biotransformation rules (advanced)

• Metabolite Detect: introduction to the soft-ware, algorithms, manual and automated operation, relationship to control software, generation of new MS/MS acquisition methods

ApplicationsSpecific requirements of the customer with respect to the focus of this course will be discussed

65


Course TopicsMetabolomicsStatistical Analysis (PCA, T test etc.) or Metabolic Pathway Screening or Metabolites MS/MS spectra library search.

Data acquisitionSetup of Metabolomics experiments Design of experiments, quality control samples, reproducibility.

Data analysisGeneral data processing and evaluation using various Metabolomics software solutions.


C9AA21

LOCATION ........ BEI, BIL, BRE, COV, FRE, MAD, PAR, SAO, SHA, YOK

IntentionFor users familiar with Bruker ESI-TOF systems which want to successfully use Bruker Daltonics software solutions for Metabolomics like e.g. PathwayScreener, Profile Analysis or Bruker HMDB Metabolite Library.The course covers all relevant aspects of one of the available software solutions including appli-cation relevant HPLC aspects.

PrerequisiteAttendees should have attended an Essential Operator Training course “Low molecular weight applications”.

DurationThe duration of the course is 1 day. Please note: This course does not substitute an explicit HPLC training!


Metabolomics ApplicationsVersion 1.0

66


C9AA32

LOCATION ..................................... BEI, BIL, BRE, COV, FRE, PAR, YOK

Description of training contentsThe training course will cover the following items:• Download of ProteinScape™ client software• User management• Administrative operations• Setup of structured data projects• Data import• MS and MS/MS analysis by database searching (MASCOT)• Re-processing of database search results• SILE based quantitation workflow• Report generation• Queries

IntentionThis training course addresses users of Bruker mass spectrometry instruments working in the field of proteomic analysis. The course focuses on Bruker´s ProteinScape™ software and how to use it for organizing, analysis and archiving of proteomics and glycomics data.

PrerequisiteParticipants should have a basic knowledge of mass spectrometry based workflows applied to proteomics / protein analysis.

Duration1.5 days


ProteinScape™ including Label based QuantitationVersion 1.0

67


LOCATION ..................................... BEI, BIL, BRE, COV, FRE, PAR, YOK

IntentionDedicated add-on course focusing on the usage of Brukers software solution for label-free untargeted quantitation of proteins and peptides. This course is intended particularly for custom-ers who are familiar with the general use of Bruker ESI-QTOF or ESI-ion trap mass spectrom-eters for proteomics / protein analysis applications, but would like to deepen their knowledge in the capabilities of the ProfileAnalysis and ProteinScape™ software for quantitative and statistical purposes.

PrerequisiteParticipants should have a solid understanding of the typical data acquistion workflows using the Bruker Compass Suite in its recent version, including Hystar, otofControl and DataAnalysis. A general knowlegde of protein biochemistry (e.g gene expression, protein regulation, post-translational modifications, etc.) is also mendatory.


Label-Free Quantitative ProteomicsVersion 1.0


C9AA41

Course TopicsExperimental designBrief discussion of general differences between different label-free quantitation approaches.

Acquisition setupCustomized LC-MS setup for label free untar-geted quantitation.

Data processing• LC-MS data processing via the “Find Mole-

cular Feature” algorithm.• Calculation of peptide quantitation ratios in

ProfileAnalysis using statistical tests.• Generation of scheduled precursor lists• for inclusion or exclusion of precursors for

preferred or restricted fragmentation.• Peak list transfer from ProfileAnalysis to the

ProteinScape™.

Peptide identificationIdentification of peptides based on MS/MS spectra searched against a sequence data-base using ProteinScape™.

Protein quantitationGeneration of a compiled protein list based on all acquired MS/MS spectra of the quantitation experiment and linkage of identified peptides to their regulation ratios using accurate mass and retention time as assignment criteria.Determination of protein regulation, assess-ment of the quantitation statistics, and sum-marization of the statistical analysis of accepted peptides.

68


C9AA51

LOCATION ............................................ BIL, BRE, COV, FRE, SAO, YOK

Course TopicsData handling in ProteinScape™/GlycoQuestImport of glycomics data in the ProteinScape™ database, analysis of oligosaccharide/glycan MS and MS/MS data using the GlycoQuest search engine, analysis of glycopeptide MS/MS data using the classification algorithm in combination with subsequent GlycoQuest search, analysis of ETD-MS/MS spectra obtained from glycopeptides.

Customized glycan databasesGeneration of customized glycan databases

Database searching and reportingSetting up queries and generation of reports

ApplicationsIf time permits, specific requirements with respect to the focus of this course can be discussed.

IntentionFor users familiar with Bruker mass spectrometry systems and the ProteinScape™ software who want to start doing glycan and gylcopeptide analysis using ProteinScape™’s Glycoquest search engine.

PrerequisiteParticipants should have attended an instrument operator training course for proteomics applica-tions as well as an Advanced Operator Training course “ProteinScape™” (C9AG32) or should at least have sound knowledge in working with the ProteinScape™ software.

DurationThe duration of the course is 1 day


Glycoanalysis using ProteinScape™ and GlycoQuestVersion 1.0

69


LOCATION ....... BEI, BIL, BRE, COV, FRE, MAD, PAR, SAO, SHA, YOK

IntentionFor users familiar with Bruker ESI-TOF systems which want to successfully use the TASQ soft-ware for multi-target screening and quantitation. The course covers all relevant aspects of multi-target screening and quantitation including application relevant HPLC aspects and the operation of the TASQ software.

PrerequisiteAttendees should have attended an Essential Operator Training course “Low molecular weight applications”.

DurationThe duration of the course is 1 day. Please note: This course does not substitute an explicit HPLC training!

Multi-target Screening and Quantitation with TASQVersion 1.0

ESI-TOF Advanced Operator Training Course

C9AA61

Course TopicsAtmospheric pressure ionization (API)ESI, positive and negative ion mode ionization, electrolyte and buffer requirements for MS-coupling of separation instruments like HPLC or UPLC with focus on quantitation and repro-ducibility in screening approaches.

ScreeningGeneral screening strategies, differences between Single-, Multiple- and General Unkown Target screening options.

QuantitationGeneral quantitation aspects with regards to calibration, QC samples and unknown samples.

Data acquisitionSetup of screening and quantitation experi-ments.

Data analysisGeneral data processing and evaluation includ-ing automation using TASQ setup of customized databases.


70


C9AA71

LOCATION ................... BEI, BIL, BRE, COV, FRE, PAR, SAO, SHA YOK

Course TopicsIntroductionIntroduction to Metabolomics studies. Discus-sion of the design and setup of a metabolo-mics experiment.

Basics on statistical experiments Introduction to statistical data mining: PCA, T-Test and others.

Data (pre-)processingData handling in DataAnalysis. Feature extrac-tion using peakfinders and automation scripts. Data im- and export.

Statistical models in ProfileAnalysis Discussion of selected advanced models avail-able in PA.

Data qualityDetection and handling of outliers. Evaluation of the data quality.

Method development for targeted MSMS experimentsCreation and use of scheduled precursor lists for the identification of selected target com-pounds.

IntentionThis training is for users of Bruker ESI systems who want to successfully use the ProfileAnalysis Software for statistical analysis or label-free quantitation.

PrerequisiteAttendees should have a basic knowledge of ESI mass spectrometry (micrOTOF(-Q), Compact, Impact(HD), maXis(HD), Amazon series, Solarix series) with several weeks of experience with the instrument and the software. Additionally, they should have attended a Essential Operator Training course “Low molecular weight applications”, previously. Basic knowledge about statis-tics is of advantage.

DurationThe duration of the course is 1 day Please note: This course does not substitute an explicit HPLC training.

ESI-TOF Advanced Operator Training Course

Cohort Profiling using ProfileAnalysisVersion 1.0

71

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Online registration:https://www.bruker.com/service/education-training/training-courses/mass-spectrometry/local-training-centers.html

Registration Form for Training CoursesPlease use one registration per person and training course. Please send this registration form to your regional training center – contact details are provided in the training brochure on page 4.

Training Course

Name Title

Company Department

Street

City Phone

Postal Code Fax

Country Email

Date of arrival Date of departureAccommodation: No Yes Single Room Double Room The travelling and hotel expenses are not included in the training course.Instrument to be trained:

Serial number: Installation date:

Training Course Register Number:

Coupled instrumentation (e.g. LC systems):

Bruker ion-sources connected with the instrument:

Bruker software used with the instrument:

Version No. Build No.

Version No. Build No.

Bruker post processing software used with the instrument:

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Yes, I do have a training confirmation for the above selected training: No.

No, I do not have a training confirmation, yet. Please send me the respective confirmation and charge the training fee. Please refer to our purchase order no.

I agree with the training terms and conditions (page 2). I agree that Bruker Daltonics may store and use the above mentioned data for contacting

me by email with regard to the training and to include me into mailing lists for newsletter distribution. Bruker guarantees that the data will not be distributed to third parties.

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Bruker Daltonik GmbH

Bremen · GermanyPhone +49 (0)421-2205-0 Fax +49 (0)421-2205-103

Bruker Daltonics Inc.

Billerica, MA · USA Phone +1 (978) 663-3660 Fax +1 (978) 667-5993

[email protected] - www.bruker.com

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

Documents

Training Courses 1 - Bruker · Essential Operator Training Courses, In-House C5EA13 General Training part of Instrument purchase 3 days 3 days DAL00905 DAL00901 54 Individual Operator