Services
PRI offers a number of mass spectrometry-based services.
Global proteome profiling
Global proteome profiling provides an unbiased, comprehensive analysis of protein expression across the entire proteome. This approach enables quantitative comparison between conditions, identification of regulated pathways, and discovery of potential biomarkers. It is well suited for cell lines, tissues, and other complex biological samples.
Label-free proteomics is typically the method of choice for global proteome profiling, offering robust and scalable quantification across larger sample cohorts. For smaller studies (up to 18 samples), we offer tandem mass tag (TMT) labeling, which provides enhanced quantitative precision, improved specificity, and reduced missing values across samples.
Samples can be provided as tissue, cell pellets, or protein extracts. A minimum of ~20–50 µg total protein per sample is recommended for standard workflows. However, protocols can be adapted to lower amounts if needed.
Cells should be washed with PBS prior to pelleting to ensure optimal sample quality. Lysate samples may contain common detergents (e.g. SDS, Triton, NP-40); please provide the exact buffer composition when submitting lysates.
Tissue
- 2–5 mg tissue in 150 µL Eppendorf TwinTec skirted PCR plate
- 5–50 mg tissue (upper limit 50 mg) in 2 mL Eppendorf tubes (up to 48 samples; for larger sample sets, please discuss the optimal sample collection strategy with PRI)
Cell pellets
- 100,000 – 5 million cells, pelleted in a 1.5 mL Eppendorf tube
Cell / Tissue lysates
- Lysates in 1.5 mL Eppendorf tubes, adjusted to a consistent protein concentration (e.g. 2 mg/mL)
- For more than 24 samples, submit in a 150 µL Eppendorf TwinTec PCR plate or a 0.5 mL Eppendorf Protein LoBind Deepwell Plate, sealed with a dry ice–resistant, easy-to-peel foil. PRI can advise on suitable sealing options.
In the Service Details screen, please fill in all mandatory fields.
Number of samples must match the number of samples delivered to PRI, and the number of rows in the sample table.
Please include all necessary sample information required for statistical analysis such as sample grouping as well as the required comparisons (e.g., ko vs wt). For any additional information on the experiment please use the comment section.
Please enter the sample information in the sample table. Samples can be added via the + Add Samples button, or by using the export / import tool. Following columns need to be filled in:
- Analytical Sample ID: please use alphanumeric entries with a consecutive number at the end (e.g., S1, S2, S3, …)
- If statistical analysis is requested, please fill in the Grouping column. Groupings should reflect the replicate groups used for statistical analysis (e.g., ko, wt).
- For samples provided in 96-well plates or Evotip boxes, please define Plate Id, Plate Position, Volume, and – if applicable – Concentration. Only registered plate Ids can be selected, and you can obtain a list of valid plate IDs together with barcoded label stickers from PRI.
- All other columns are optional
Plasma / Serum / CSF
We offer multiple options for the analysis of body fluid samples, including plasma, serum, and cerebrospinal fluid (CSF). These approaches differ primarily in proteome depth, sensitivity, and associated costs.
Samples can be analyzed directly (neat), following depletion of the top 14 most abundant proteins, or using nanoparticle-based enrichment (Seer technology) for deep proteome coverage. PRI staff can advise on the most suitable strategy based on your specific research question.
PRI supports projects ranging from small-scale studies to large cohorts of up to 10,000 samples, leveraging a highly automated sample preparation pipeline.
Samples should be submitted in 0.75 mL Micronic hybrid external thread screw cap tubes, sealed with either screw caps or push caps.
For requests of up to 384 samples, samples can alternatively be provided in 96-well Eppendorf TwinTec 150 µL skirted PCR plate, sealed with a dry ice–resistant, easy-to-peel foil. PRI can advise on suitable sealing options.
Minimum input volumes
- Neat analysis: 50 µL (Micronic tubes or TwinTec plates)
- Top14 depletion: 100 µL (Micronic tubes or TwinTec plates)
- Seer (nanoparticle enrichment): 150 µL (Micronic tubes only)
In the Service Details screen, please fill in all mandatory fields.
Number of samples’ must match the number of samples delivered to PRI, and the number of rows in the sample table.
Please include all necessary sample information required for statistical analysis such as sample grouping as well as the required comparisons (e.g., treatment vs control). For any additional information on the experiment, please use the comment section.
Please enter sample information in the sample table.
- Analytical Sample ID can either represent the sample id (key cath) of the biobank, or an experiment specific id (S1, S2,…. Sx).
- Subject ID should contain the pseudonymized subject identifier.
- Biological Sample ID is optional and can be used for any additional information (e.g. timepoint 1 and 2)
- Tube label represents the barcode id in case barcodes tubes are used
- For samples provided in 96-well plates, please define Plate Id, Plate Position, and Only registered plate Ids can be selected, and you can obtain a list of valid plate IDs together with barcoded label stickers from PRI.
FFPE tissue analysis
We support the analysis of FFPE tissue provided as either punches or sections (scrolls). While the required input depends on the size and composition of the tissue, in most cases 1–2 sections of 10 µm thickness are sufficient for robust proteomic analysis.
Samples do not need to be deparaffinized prior to submission. Macrodissection can be used to enrich for regions of interest. For microdissection-based approaches, please refer to the section on spatial proteomics.
Samples should be submitted in 2 mL Eppendorf tubes or in 96-well Eppendorf TwinTec 150 µL skirted PCR plate, depending on sample size. Please consult with PRI to determine the optimal sampling strategy.
- Analytical Sample ID either represents the sample id (key cath) of the biobank, or an experiment specific id (S1, S2,…. Sx).
- Subject ID should contain the pseudonymized subject identifier.
- Biological Sample ID is optional and can be used for any additional information (e.g. timepoint 1 and 2)
Global PTM analysis
PRI currently offers global analysis of phosphorylation (Ser/Thr/Tyr; STY), lysine acetylation, and lysine ubiquitylation. Analysis of additional PTM types can be requested and will be evaluated on a per-project basis.
For phosphorylation analysis, both data-independent acquisition (DIA) and tandem mass tag (TMT) workflows are available.
Samples can be provided as tissue, cell pellets, or protein extracts. A minimum of ~20–50 µg total protein per sample is recommended for standard workflows; protocols can be adapted to lower amounts if needed.
Cells should be washed with PBS prior to pelleting to ensure optimal sample quality. Lysate samples may contain common detergents (e.g. SDS, Triton, NP-40), as well as protease and phosphatase inhibitors; please provide the exact buffer composition when submitting lysates.
Tissue
- 2–5 mg tissue in 150 µL Eppendorf TwinTec skirted PCR plate
- 5–50 mg tissue (upper limit 50 mg) in 2 mL Eppendorf tubes (up to 48 samples; for larger sample sets, please discuss the optimal sample collection strategy with PRI)
Cell pellets
- 500,000 – 5 million cells, pelleted in a 1.5 mL Eppendorf tube
Cell / Tissue lysates
- Lysates in 1.5 mL Eppendorf tubes, adjusted to a consistent protein concentration (e.g. 2 mg/mL)
- For more than 24 samples, submit in a 150 µL Eppendorf TwinTec PCR plate or a 0.5 mL Eppendorf Protein LoBind Deepwell Plate, sealed with a dry ice–resistant, easy-to-peel foil. PRI can advise on suitable sealing options.
In the Service Details screen, please fill in all mandatory fields.
Number of samples must match the number of samples delivered to PRI, and the number of rows in the samples table.
Please include all necessary sample information required for statistical analysis such as sample grouping as well as the required comparisons (e.g., treatment vs control). For any additional information on the experiment please use the comment section.
Please enter sample information in the sample table.
- Analytical Sample ID: Please use alphanumeric entries with a consecutive number at the end (e.g., S1, S2, S3, …)
- If statistical analysis is requested, please fill in the Grouping column. Groupings should reflect the replicate groups used for statistical analysis (e.g., ko, wt).
- Biological Sample ID is optional can be used for any additional information or internal sample ids.
- For samples provided in 96-well plates, please define Plate Id, Plate Position, Volume, and – if applicable – Concentration. Only registered plate Ids can be selected, and you can obtain a list of valid plate IDs together with barcoded label stickers from PRI.
Protein Interaction Analysis
PRI offers guidance and support for the study of a wide range of intracellular interactions, enabling the characterization of molecular networks and functional protein complexes. Supported applications include:
- Protein–protein interactions (e.g. co-immunoprecipitation, proximity labeling)
- PTM–protein interactions (e.g. peptide pulldown assays)
- Domain–protein interactions (e.g. tagged deletion constructs)
- RNA–protein interactions (e.g. ChIRP-MS)
- DNA–protein interactions (e.g. DNA probe pulldown, ChIP-MS)
Samples are delivered as washed beads (magnetic or agarose). Following the regular washes of the enrichment experiment, beads need to be washed twice with detergent-free buffer (e.g., TBS or PBS). Please change the tube to a fresh 1.5 mL Eppendorf tube with the last wash. Remove the last wash buffer before freezing the beads or bringing them to the PRI on ice.
Pulldowns should be performed in at least triplicates per group, which are essential for robust quantitative analysis. Replicates should be processed in parallel on the same day to minimize technical variability. Input lysates can be derived either from the same extract or from biological replicate samples.
In the Service Details screen, please fill in all mandatory fields.
Number of samples must match the number of samples delivered to PRI, and the number of rows in the Request Samples table.
Please include all necessary sample information required for statistical analysis such as sample grouping as well as the required comparisons (e.g., bait vs control). For any additional information on the experiment please use the comment section.
Please enter sample information in the sample table.
- Analytical Sample ID: Please use alphanumeric entries with a consecutive number at the end (e.g., S1, S2, S3, …)
- If statistical analysis is requested, please fill in the Grouping column. Groupings should reflect the replicate groups used for statistical analysis (e.g., bait, control).
- Biological Sample ID is optional and can be used for any additional information or internal sample ids.
- All other columns are optional
Gel Band ID
PRI offers streamlined analysis of gel-bands from Coomassie stained SDS-PAGE gels using a fully automated sample preparation platform.
Gel Bands should be provided in barcoded Micronic 0.75 mL hybrid tubes (can be obtained at PRI). When cutting the band, please remove as much of the surrounding gel as possible and chop up the band in cubes of about 2 mm edge length.
Please also acquire a picture of the gel before cutting the gel and upload the picture with marked bands into the comment section of the request form.
In the Service Details screen, please fill in all mandatory fields.
Number of samples must match the number of samples delivered to PRI, and the number of rows in the samples table.
Please enter the sample information in the sample table.
You can generate new samples with the + Sample button, or via using the download / upload function and adding new rows (with empty id) to the template file.
The following columns need to be filled in:
- Analytical Sample ID: Please use alphanumeric entries with a consecutive number at the end (e.g., S1, S2, S3, …)
- Tube label refers to the barcode indicated on the tube (e.g., 4055436968)
- Sample type should contain the term ‘gel band’
- Taxa ID should contain the Uniprot taxa id of the organism (e.g., 9606)
- Biological Sample ID is optional and can be used for any additional information or internal sample ids (e.g., Band1).
- All other columns are usually not relevant for this service type
Peptide Mapping
This request type covers the analysis of non-complex samples, when the aim is to identify individual proteins.
Samples are submitted in solution. Please indicate the exact buffer composition and discuss about potential compatibility issues beforehand.
In the Service Details screen, please fill in all mandatory fields.
Number of samples must match the number of samples delivered to PRI, and the number of rows in the samples table.
Please enter the sample information in the sample table.
The following columns need to be filled in:
- Analytical Sample ID: Please use alphanumeric entries with a consecutive number at the end (e.g., S1, S2, S3, …)
- Taxa ID should contain the Uniprot taxa id of the organism
- Biological Sample ID is optional and can be used for any additional information or internal sample ids (e.g., sample1).
- All other columns are usually not relevant for this service type