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Technische Universität München

FAQs

GENERAL

PUBLISHING COLLABORATIVE PROJECTS

USER FEES

PROTEOMICS

SCOPE OF PROTEOMICS ANALYSIS
SAMPLE PREPARATION PROTEOMICS
DATA ANALYSIS PROTEOMICS

ANSWERS

How are projects selected/accepted at the BayBioMS core facility?

All scientific projects supported and carried out at the BayBioMS are of collaborative nature. We do not do provide any measurements on the basis “data-for-money”.

We support and consult all our projects from start to end, which means:

  • We provide you a letter of support for the mass spectrometric measurements of your grant applications and generally consult you in all mass-spec related points of your grant applications.

  • We discuss and optimize with you the experimental design of your project.

  • We setup and optimize with you the mass spectrometric sample preparation workflow for your project, which will be carried out either at the collaboration site or at the BayBioMS, or both.

  • We perform the mass spectrometric measurements on our high-end mass spectrometers located at the BayBioMS.

  • We perform the first-level bioinformatics data analysis of your data.

  • We support and discuss with you the biological interpretation of the quantitative mass spectrometric data you receive (second-level bioinformatics data analysis)

  • We support you in your manuscript preparation and publication process

Due to the collaborative nature of all our projects, our collaboration partners acknowledge that the involved scientists from the BayBioMS will be co-authors on publications arising from the joint project (see more information below).

Further, our collaboration partners acknowledge that a mass spectrometric measurements fee will be charged according to DFG guidelines (see more information below).

How do you select projects to be supported by the BayBioMS?

The decision if a given project will be carried out in collaboration with the BayBioMS is done through at least one initial kick-off meeting. In this meeting all involved scientists discuss motivation, aim, scope and feasibility of a given project and decide together if, when and how a collaboration will be started.

In case we do get more project applications than we can handle, priority will be given to internal TUM projects over external projects, and priority will be given according to scientific excellence and project feasibility.

How do you prioritize samples for mass spectrometric measurements?

Prioritization of mass spectrometric measurements for projects that have been accepted for collaboration is done on a first-come first-serve basis.

We try to have our instruments running 24/7. For that reason, we sometimes prioritize smaller or larger projects during vacation times or weekends

How should I deliver my samples?

Before you bring us (personally) or ship us (by mail) your samples, please make sure that we have agreed on accepting your samples. In case of shipment, please make sure you inform us about the exact shipment date (maybe including tracking number) by email.

Importantly, always provide us your samples under appropriate conditions (sufficient amounts of dry ice or ice, clear and solvent-safe labelling of all vials, etc.) and carry our shipment rather at the beginning of the week (Monday) to avoid too long delivery times.

Our shipment address:

  • Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS)
    Technical University of Munich (TUM)
    2.Stock, Raum 09
    Gregor-Mendel-Strasse 4,
    85354 Freising

Which information do I need to provide for my project and samples?

For every new project, our collaboration partners need to fill in a Project Information document to provide us project specific information, including collaborator information, project description, motivation, applied workflow and sample descriptions.

Further, for each project our collaboration partners need to fill in a Collaboration Agreement document, in which he/she provides financial information and acknowledges co-author ship in potential publications arising from the collaborative work.

Finally, for each sample a Sample Description Table needs to be filled out. In this table we ask for sample specific information, including sample name, concentration, volume and a statement if the sample is safe according to German Biostoffverordnung (BioStoffV), the German Gentechnikgesetz (GenTG) and the German Infektionsschutzgesetz (IfSG).

How can I contact the BayBioMS facility?

General E-Mail
baybioms[at]tum.de

Section Metabolomics
Dr. Karin Kleigrewe
Tel: +49 8161 71 6130
E-Mail: karin.kleigrewe@tum.de

Section Proteomics
Dr. Christina Ludwig
Tel: +49 8161 71 6199
E-Mail: tina.ludwig[at]tum.de

Section Bioinformatics
Miriam Abele
Tel: +49 8161 71 6128
E-mail: m.abele[at]tum.de

Which mass spectrometric and bioinformatic devices are used at BayBioMS?

Metabolomics

  • TripleTOF 6600 (Sciex)

  • QTrap 5500 (Sciex)

  • GCMS-TQ8040 (Shimadzu)

 

Proteomics

  • Orbitrap Fusion Lumos Tribrid equipped with nano-flow LC (Ultimate 3000 nano) (Thermo)

  • Q-Exactive HFX equipped with nano-flow LC (Ultimate 3000 nano) (Thermo)

  • Exploris 480 equipped with micro-flow LC (Ultimate 3000 cap) (Thermo)

 

Metabolomics and Proteomics

  • MALDI ultrafleXtreme (Bruker)

  • MALDI microflex LT/SH

 

Bioinformatics

  • 100 TB Storage System (NetApp)

  • Serververbund (Dell/Megware)

  • Serververbund (IBM/Lenovo)

  • OmicsDB (IBM/Lenovo)

What is a typical turnaround time for my project?

This depends on your project, the amount of samples and the complexity of the sample preparation and data analysis. Furthermore, it depends on the current sample load of the core facility. Samples are analysed on a first-come, first-serve basis. For a typical project, the turnaround time would amount to 4-8 weeks.

How can I check the status of my samples?

We will contact you once your samples are processed. If you have any urgent matter please contact us by email.

Do you offer any proteomics, metabolomics or bioinformatics teaching?

On our website you find self-reliant teaching options, including videos, webinars and tutorials for download:

https://www.baybioms.tum.de/teaching/

Further, we organize twice per semester an “Advanced Mass Spectrometry Seminar”, in which our collaboration partners present their scientific work, and in which we provide information on basic workflows used in our facility:

https://www.baybioms.tum.de/teaching/advanced-mass-spectrometry-seminar/

We regularly organize proteomic and metabolomics courses, workshops and conferences. Check out the news section on our website for up-to-date information:

https://www.baybioms.tum.de/

Can you guarantee that my sample will work?

No, we cannot guarantee you that the mass spectrometric results will provide you the information you are looking for. However, if you consult us prior to your sample preparation we will go through all sample preparation and measurement steps and discuss with you potential issues and optimal workflows.

Prior to running the entire study, we usually set up a pilot study to ensure that your samples are processed and measured in the right way, and that we can provide you the high quality data that you need to answer your specific biological question.

What type of quality control does the BayBioMS perform?

We monitor the quality of each of our proteomic mass spectrometers on a daily basis by measuring a commercial standard sample (Pierce™ HeLa Protein Digest www.thermofisher.com/order/catalog/product/88328) before and after each project. For large projects with a high number of samples, we also measure the Pierce HeLa standard sample in between the project samples. In this way, we can optimally control the performance of our mass spectrometers.

Additionally, we perform project-specific quality checks for all measured mass spectrometric data files in each project. We check the number and intensity distributions of detected proteins/peptides/PTMs, the clustering of biological or technical replicates, labelling efficiencies, etc.

Co-authorship

As we operate all our projects on a collaborative basis, co-authorship on manuscripts that entail data generated with us, and to which we have provided intellectual input, is justified. We are happy to provide you help and advice during your paper writing process.

Please use the following sentence in your publications when referring to us:

"Proteomic/Metabolomics analysis was performed at the Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS) of the Technical University of Munich (TUM), a registered research infrastructure of the Deutsche Forschungsgemeinschaft (DFG, RI-00010)".

Do I need to upload the proteomic raw data into a public repository?

Yes, for every proteomic publication that uses mass spectrometric data generated in our facility, the corresponding data files (raw files, results tables and database) must be uploaded to a public repository PRIDE. The corresponding link must be provided within the “data availability section” of your manuscript.

We are happy to take care about the upload and to provide you the required PXD identifier number (and reviewer account details). Please contact us as soon as you are planning to write or have written a manuscript. After submission of all data files to Pride it usually takes 2 to 5 working days until the PXD identifier number will be available for your project.

The following sentence should be added to the data availability section in your manuscript:

“The proteomics raw data, MaxQuant search results and used protein sequence database(s) have been deposited with the ProteomeXchange Consortium via the PRIDE partner repository and can be accessed using the data set identifier PXD000000”.

What is the user fee that I have to pay?

In agreement with published DFG rates (DFG = Deutsche Forschungsgemeinschaft) for mass spectrometric measurements we charge:

40 €/h MS time without data analysis

75 €/h MS time including basic data analysis

100 €/h MS time including complex bioinformatic analysis or sample preparation

http://www.dfg.de/formulare/55_04/55_04_de.pdf

These costs cover consumables for sample preparation and mass spectrometers.

Other expenditures e.g. for stable isotopes and reference molecules (like TMT labelling reagents, heavy synthetic peptides, standards, etc.) must be purchased by our collaboration partners or will be added to the price per sample.

TUM internal collaborations are not subject to taxes. For external collaborators, we are required to add a surcharge of 25% and 19% VAT to all costs.

We note that the above rates are subsidized by the TUM and are far below market prices for similar types of analysis.

Example: Most proteomic samples are measured by us with 1 hour MS time including basic data analysis. For such projects (typically carried out label-free) each sample cost 50 Euro for TUM internal projects. As we also run a blank after each sample to clean the LC-MS system with 30 minutes MS time and without data analysis, 12.50 Euro for each blank measurement must be taken into account as well.

Do you offer discounts for large sets of samples?

No, we do not offer any type of discount. Our fees are already heavily subsidized by TUM.

How to generate funding for my MS measurements?

We note that the above stated DFG rates for MS measurements are eligible for additional funding. For most grant agencies, these costs can be applied for on top of normal consumable costs. For more details, see: http://www.dfg.de/formulare/55_04/55_04_de.pdf

Interesting additional grant options, specifically for research projects with a proteomics focus, are for example:

These European grants offer financial support for mass spectrometric measurements (and potentially also money for visiting scientist) for research carried out within the European Union.

Do you support analysis of post-translationally modified (PTM) proteins?

Yes, we have setup a proteomic workflow based on IMAC (immobilized metal affinity chromatography) to specifically enrich phosphopeptides from proteomic samples. Enrichment of other PTM-types need to be carried out by our collaborators, but can also be measured and analysed by us.

We also analyse purified protein samples without an additional PTM-enrichment step. PTMs such as phosphorylation, acetylation, methylation or ubiquination can maybe be detected in purified protein samples (like for example Co-IP samples) without a specific enrichment. However, in complex samples a PTM-enrichment strategy is required.

Can you identify the specific amino acid that carries a post-translational modification (PTM)?

Yes, with mass spectrometry it is possible to assign within a given peptide sequence the exact amino acid position of a PTM. However, it depends on the quality of the spectrum, the detected fragment ions of a given phosphopeptide (whether they are site-determining or not) and the PTM-type if such a PTM-site assignment is successful and confident. In a typical phosphoproteomic analysis, usually around 60% of the identified S, T and Y- phosphorylation sites can be assigned to a specific amino acid position with high confidence.

Can you measure intact proteins at the BayBioMS?

No, we do not offer this service. The liquid-chromatography and mass spectrometry setups that we use are optimized for the measurements of peptides. Therefore, we do not offer measurements of intact proteins (top-down proteomics).

Can you quantify proteins by stable isotope labelling?

Yes, we can analyse samples that entail heavy isotopes, for example introduced by TMT-labeling, di-methyl labelling, 15N-labeling, SILAC labelling or by a heavy peptide or heavy protein spike-in. Be aware, SILAC labelling will have to be performed during cell growth in the laboratory of our collaborators.

Do you offer a workflow based on TMT-labeling at the BayBioMS?

Yes, we provide an optimized workflow of isobaric peptide labelling using TMT11plex. This workflow is carried out on peptide-level and is typically followed by a high-PH-reverse phase peptide fractionation step.

How do I exactly prepare my samples for LC-MS analysis?

The exact workflow really depends on your sample type, your specific research question and the agreed sample handover point to us. Please contacting us and we will discuss all the details of sample preparation with you in the kick-off meeting(s).

What is the minimum amount of protein required for MS analysis?

  • Label-free quantitative proteomics: 15 µg
  • Label-free deep fractionation proteomics: 150 µg
  • TMT quantitative proteomics: 15 µg
  • Phospho-proteomics (as well as other PTMs): 500 µg – 1 mg
  • Micro-flow label-free proteomics: 100 µg
  • Micro-flow deep fractionation proteomics: 500 µg – 1 mg

Concentrations in the range of 0.5 – 5 µg/µl are ideal.

Which type of proteomic samples can I send you?

We are able to analyse a wide range of protein-containing samples from various organisms and origins:

  • Cell pellets and tissues from human, bacterial, fungi, animal or plant origin. We generally request to provide us snap frozen cell pellets (please provide estimated cell numbers or tissue weight and to store samples at -80°C prior to analysis).

Attention, in case you work with cells or tissue that require S2 safety-level, please be aware that you need to inactive your sample prior to shipment to us. Please contact us to discuss further details

  • Cellular lysates from human, bacterial, fungi, animal or plant cells = cellular proteins in-solution

  • Extracellular or secreted proteins (taken from the medium, extracellular vesicles, wash-fluids, etc.) = proteins in-solution taken from extracellular matrices

  • Purified proteins in solution (for example purified by affinity purification or other methods)

  • Purified protein complexes in solution (for example purified by co-immunoprecipitation, BioID, TurboID etc.)

  • Clinically relevant human samples = blood (plasma or serum), urine, CSF, biopsies or stool

  • Coomassie-Blue stained protein gel bands

Attention, avoid silver staining

  • Proteins in (processed) food samples (beer, vegetables, bread, etc.)

  • etc.

For all protein samples provided to us in solution/buffer, please check out in what buffer composition you should ideally send us your sample (see below)

In what buffer should I send my sample?

If you provide us your samples on protein-level, protein digestion and peptide clean-up will be carried out by us. The proteins should ideally be delivered in an aqueous buffer system at rather “neutral” pH.
Typically used buffers in proteomics are:

  •     Tris, pH range 7.0 - 9.0
  •     HEPES, pH range 7.2 - 8.2
  •     Ammonium bicarbonate NH4HCO3, pH range 7.0 – 8.0

Usually these buffers are used at concentrations between 50-100 mM.
Further Additives
Next to the buffering molecule, further additives can be added to the lysis buffer that improve solubility and stability of proteins (but at the same time denature them, i.e. the proteins are no longer in their native folded structure. If native fold and protein activity is required, other lysis buffers should be used). Typical denaturing additives in proteomics are detergents such as

  •     8M Urea
  •     2% sodium deoxycholate (SDC)
  •     2% sodium dodecylsulfate (SDS)

They help solubilizing poorly soluable proteins, but they also require good sample clean-up protocols, as the sample needs to be detergent free for mass spectrometry.
Further, reducing agents, such as

  •     1 mM DTT (Dithiothreitol)
  •     5 mM TCEP (Tris(2-carboxyethyl)phosphine)

are frequently added, because they help to reduce oxidation damage and denature proteins through the cleave of disulfide bridges.
Other typical additives in lysis buffers are

  •     protease inhibitors (to prevent unspecific cleavage of proteins)
  •     phosphatase inhibitors (to prevent phosphorylation changes)
  •     metal chelators (like EDTA, to bind metal ions)
  •     salts (to maintain ionic strength of the buffer)

A typical cell lysis buffer used in proteomics is:

  •     8 M Urea
  •     100 mM NH4HCO3
  •     1 mM DTT
  •     (5 mM EDTA)
  •     pH 8.0

A nice overview of lysis buffers for proteins can be found here:
www.embl.de/pepcore/pepcore_services/protein_purification/extraction_clarification/lysis_buffer_additives/index.html
If you provide us your samples on peptide-level (so protein digestion and peptide clean-up has happened at your laboratory), ideally send us your peptides completely dry (so we can re-suspend them in an MS-suitable solvent) or provide them to us in highly pure water (ideally MS-grade) with maximally 2% acetonitrile and 0.1% formic acid. For micro-flow samples 0 % acetonitrile is required.
Importantly, please share your specific buffer composition with us! Then we can make an informed decision and advise you accordingly.

Which are buffer additives that I strictly avoid for proteomics analysis?

Detergents, such as NP-40 or Triton X-100 are generally problematic and should be avoided completely. Also avoid usage of glycerine if possible.

Metal salts (Na+, K+, and phosphate), such as sodium chloride affect the electron spray ionisation and must therefore be removed in the last peptide-cleaning step of all sample.

A nice overview solvents and caveats for LC-MS is given here:

https://www.waters.com/waters/en_US/Solvents-and-Caveats-for-LC-MS/nav.htm?cid=10091173&locale=en_US

Why do I have Polyethylene glycol PEG contamination in my sample?

Strong contaminations with Polyethylene glycols (PEGs) can be a big issue in mass spectrometry. They will negatively impact your data and are super hard to get rid of. We have observed that a frequent source of PEGs are filters and membranes used during sample preparation, for example 0.2 or 0.45 µm filters or MWCO filters. Depending on the company, those filters and membranes can be heavily contaminated with PEG. Please avoid using such filters if possible, or contact us to discuss specific companies.

I see many keratins in my list of proteins. Where do they come from?

Keratins come from the skin or your hair. They are typically found in every sample and filtered out during data analysis as ‘potential contaminants’.

How long will you keep my data files stored?

We store all acquired files and analysed data on our servers for a minimum 10 years.

Can I have the raw data?

Yes. We provide you the raw data upon request.

Next to my samples, what else do I need to provide for the data analysis step?

For every mass spectrometric analysis, a protein fasta file is required. If you are working with a non-model organism, it is extremely helpful if you provide us with a protein fasta file, either from a public database (like NCBI or uniprot) or a self-sequenced and annotated fasta file. If there is none available, please let us know in the kick-off meeting and we can discuss the possible options for you data analysis.

Further, it is helpful if you provide us any information regarding your interest in the occurrence of post-translational modifications on proteins, or weather for your project it is important to differentiate between specific protein isoforms, etc.

Additionally, please also give us the sample information important for data analysis. Usually, we need to compare the proteins abundance of samples from two or more different groups. To do so, we would need to know which samples belong to which group. If would be great if the information is already available in the Sample Description Table.

Why can you only work with samples from organisms that have a sequenced genome?

The way how we identify peptides and proteins in our MS data is by matching the acquired MS spectra to an organism-specific protein sequence database (this is a theoretical proteome database file in a format called “fasta”, which typically can be downloaded from public databases such as NCBI, RefSeq, etc.). We cannot detect any peptides and proteins that are not represented in the underlying protein database (fasta file) that we use to analyse your data.

Alternative mass spectrometric analysis methods exist, that allow analysing MS data WITHOUT a protein sequence database, called de-novo sequencing. However, these analysis methods are way less sensitive and specific than analyses based on protein database-searching. We do not offer de-novo-sequencing analyses at the BayBioMS.

How do you communicate the results of a large-scale MS experiment?

The communication of the results is one of the most important parts of every project. Depending on the project and on your prior proteomic knowledge we communicate the results in one or more meetings (Zoom of physical). In this meeting we will show and explain you what we did with your samples and go with you through the result table(s).

Further, we have developed an online interface called MQCruncher, which allows the users to visualize mass spectrometric data and explore it in detail without further programming knowledge. For every project a unique passcode will be provided.

MQCruncher Proteomics:
http://10.195.4.22:8080/app/mqc_collab

The link above can be accessed via an internal IP address from an academic institute in the Munich area, e.g. TUM or LUM. You can connect to the internal network using VPN first then access the MQCruncher, the VPN can be downloaded from:
https://doku.lrz.de/display/PUBLIC/VPN+-+AnyConnect

If you want to connect from an external IP address, please contact Miriam Abele for more information.

Miriam Abele
Tel: +49 8161 71 6128
E-mail: m.abele@tum.de

How many replicates do I need to do?

Golden rule: The more, the better ;). The absolute minimal number of replicates required to do any statistics on our data is 3 (ideally biological and not just technical replicates). However, depending on your sample type, your experimental workflow or your biological question larger or smaller variations might be expectable and therefore maybe more or less replicates might be required. In the project kick-off meeting such points will be discussed.

I got the Proteingroups.txt MaxQuant output from you. Where can I find information about the meaning of the individual columns?

www.coxdocs.org/doku.php

How many proteins (proteingroups) can I expect from my samples?

This depends of course on a lot of factors, for example:

  • Your organism of interest (bacteria or human?)

  • Your sample type (full cell lysate or plasma a Co-IP?)

  • Your sample preparation workflow (with fractionation or without fractionation?)

  • Your measurement time per sample (30 minutes gradient or 2 hour gradient?).

For example, for a bacterial full cellular lysate measured with an one hour gradient in single shot DDA proteomics we can typically detect 50% of the theoretical proteome (of all the proteins provided in the protein database/fasta file).

For example, for a human full cellular lysate measured with an one hour gradient in single shot DDA proteomics we can typically detect around 3500 human proteins (proteingroups).

Why some proteins are not detected?

Please keep in mind, MS-based proteomics will not detect all proteins in your samples. Proteins will escape detection for many reasons, just name a few:

  •     if they are too low abundant,
  •     if they do not generate suitable peptides with the used protease,
  •     if they only generate peptides with a bad MS-response factor,
  •     if they only generate PTM-carrying peptides that we do not cover in our data analysis

Therefore, if a protein is not detected, it does not mean it does not exist in your samples.

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