Due to recent changes to US-international importation guidelines,  we ask all customers shipping from outside of the US to ensure that all shipping invoices total $0, and to email info@seqcenter.com for additional guidance regarding shipping documentation before sending samples. Customs delays are now extremely common, and taking much longer than before to resolve.

Illumina Protein Prep

Proteomic insights bridge the gap between genotype and phenotype, providing a real-time snapshot of cellular activity between healthy and disease states. The Illumina Protein Prep is an innovative aptamer-based assay leveraging the scalability of NGS technology to deliver a high-throughput, high-accuracy solution and maximize protein identification and quantification per sample. Useful in biomarker discovery, complex disease risk assessment, and precision therapeutics, NGS-based proteomics add an important piece to the cell state puzzle.

Leveraging our extensive experience with Illumina technology, SeqCenter is now offering the Illumina Protein Prep solution which uses a streamlined end-to-end workflow starting with human plasma or serum samples that are generated into sequencing-ready libraries. This proteomics assay can detect over 9000 unique protein measurements, and combining this service with our genomics and transcriptomics offerings enables secondary and tertiary analysis for combined modality studies.

To ensure quality protein abundance, it is crucial to follow the Illumina Protein Prep sample collection and general processing guidelines. Please see the “Submission Considerations” section below for more details.

Submission Requirements:

  • Samples must be pre-processed human serum or plasma with EDTA, aliquoted as follows:
    • 70 µL for each sample
    • In Thermo Scientific Matrix 0.64 mL ScrewTop Tubes with barcodes (3744BR)
    • See the IPP Recommendations section for more information
  • Submissions must be sent in a Matrix rack. Sample type must be uniform within each rack.
  • Grouping and comparison information must be submitted with each order.

What You Will Receive:

  • Proteomics aptamer counts in .adat file format
  • Comparative analysis
  • Materials and methods summary
  • Data shared via Globus within 2 weeks

Packages & Pricing

Sequencing Package Price
42 Sample Block
$550.00 per sample		 $23.100.00
85 Sample Block
$500.00 per sample		 $42,500.00
170 Sample Block
$475.00 per sample		 $80,750.00
425 Sample Block
$450.00 per sample		 $191,250.00

Submission Considerations

Sample degradation begins as soon as the blood is drawn. Similar to when working with RNA, temperature has a large impact on the sample performance for this assay, meaning that the resulting data will be greatly affected by the number of freeze-thaw cycles and handling time.

To ensure high quality data, please adhere to the following guidelines and recommendations for sample collection and pre-processing, provided by Illumina.

Guidelines for Sample Collection

  • Temperature considerations:
    • Ideally, complete processing and freezing of plasma and serum samples within 2 hours of collection.
    • If a freeze-thaw cycle must be introduced between collection and processing, store at -80°C. Thaw and process samples in batches to minimize the amount of time any given sample is not frozen.
    • Up to 3 freeze-thaw cycles are permitted. (Creating multiple one-use aliquots during pre-processing is recommended.)
    • Avoid extended thaw time (2 hours maximum.)
    • Samples must be transported on dry ice.
  • Use only unexpired collection tubes.
    • Whole blood specimens for plasma samples must be collected in EDTA blood collection tubes.
      • Do not freeze whole blood specimens.
      • Performance is not guaranteed for samples collected using other collection tubes.
    • Avoid adding anticoagulant to serum samples
  • If collecting more than one sample type, follow the collection order specified in the guidelines provided by the tube manufacturer.
  • Treat all samples as if they are potentially infectious agents, including when assessing transportation regulations.

General Processing Guidelines for Both Sample Types

  • Proper processing of the collected samples is critical.
  • Do not chill collection tubes before processing.
  • For tubes that have minimum and maximum fill lines, follow the fill guidelines indicated.
  • Hemolyzed samples (colored pink to red) can prevent accurate biomarker detection. If only hemolyzed samples are available, please contact SeqCenter.
  • If you will be processing more volume than required for a single use, separate it into multiple aliquots, so that each aliquot is single-use.
  • Perform all steps at room temperature, but avoid leaving sample at room temperature longer than the procedure requires.
  • If samples have been frozen:
    • Thaw and process samples in batches to minimize the amount of time any given sample is not frozen.
    • Avoid multiple freeze-thaw cycles.
  • All long term storage must be at -80°C.
  • Refer to the sample-type specific guidelines below.
  • Processing plasma samples within 30 minutes of collection is recommended.
  • Before centrifugation, invert a minimum of 5 times to ensure that EDTA and blood are well mixed.
  • Plasma samples do not need to clot before placing on the centrifuge.
  • Centrifuge collection tubes at room temperature at 2200 × g (RCF) for 15 minutes. This speed optimizes the removal of all cellular contents and platelets from samples. Standard centrifugation of 1300 × g for 10 minutes provides comparable results.
    • Observe separation of blood cells and plasma, with a pale yellow plasma layer on top.
    • Hemolyzed samples (plasma colored pink to red) can prevent accurate biomarker detection.
  • Aliquot plasma samples immediately into barcoded Matrix screw-top tubes. Place into a matrix rack.
  • Aliquot only the plasma layer. To avoid disturbing the buffy coat, leave a residual of plasma and avoid the cell layer.
  • Store aliquoted samples in a -80°C freezer. Storage effects at -20°C have not been evaluated for the Illumina Protein Prep assay.
  • Avoid multiple freeze-thaw cycles and extended thaw time (2 hours maximum.) Up to 3 cycles are permitted.
  • Allow serum to clot for 60–90 min at room temperature before placing on the centrifuge.
  • Centrifuge collection tubes at room temperature at 2200 × g (RCF) for 15 minutes. This speed optimizes the removal of all cellular contents and platelets from samples. Standard centrifugation of 1300 × g for 10 minutes provides comparable results.
    • Observe separation of blood cells and serum, with a pale yellow serum layer on top.
    • Hemolyzed samples (serum colored pink to red) can prevent accurate biomarker detection.
  • Aliquot serum samples within 30 min of centrifugation into barcoded Matrix screw-top tubes. Place into a matrix rack.
  • Aliquot only the serum layer.
  • Store aliquoted samples in a -80°C freezer. Storage effects at -20°C have not been evaluated for the Illumina Protein Prep assay.
  • Avoid multiple freeze-thaw cycles of serum samples and extended thaw time (2 hours maximum). Up to 3 freeze-thaw cycles are permitted.

Additional Information

We highly recommend the 2024 study by Stephan Kraemer, et al. for additional insight into aptamer-based project considerations and analyses.

Kraemer, Stephan, Daniel J. Schneider, Clare Paterson, et al. “Crossing the Halfway Point: Aptamer-Based, Highly Multiplexed Assay for the Assessment of the Proteome.” Journal of Proteome Research 23, no. 11 (2024): 4771–88. https://doi.org/10.1021/acs.jproteome.4c00411.

Contact:
91 43rd Street, Ste. 250
Pittsburgh, PA 15201
(878) 227-4915

Services:

About:

Resources:

Full Flowcell:

We offer full flowcell sequencing services for libraries that have been prepared outside of our lab. For each library, we will need to know the loading concentration, phiX spike-in, and run structure. Data is delivered as a complete run folder and can be demultiplexed upon request if a sample sheet is provided.

SARS-CoV-2 Sequencing:

Our SARS-CoV-2 Sequencing services include an assembly on the SARS-CoV-2 reference genome as a scaffold. These packages provide roughly 200Mbp of paired end reads (2×151 bp) as fastq files and the assembly in fasta format.

We require a minimum sample volume of 15 µL of extracted material (or 250µL for VTM samples) and recommend that only samples with Ct values below 35 are sent (because submissions are not measured for viral load before processing). We offer services for both purified RNA and samples in VTM media that require viral RNA extraction. Please see our SARS-CoV-2 Sequencing page for more detailed information.

Microbiome Sequencing:

Please see our Microbiome Sequencing page for package details, including distributables and sample requirements.

Nanopore Sequencing:

Our Oxford Nanopore sequencing packages provide reads equal to the length of input DNA, delivered as a fastq file.

For each sample, we require a minimum volume of 60 µL, and at least 40 ng/µL dsDNA quantified by Qubit or other dye-based method (100 ng/µL by Nanodrop). Variant calling add-on analysis requires an annotated reference file. DNA extraction services are available for only specific categories of microbes.

Please see our DNA Sequencing: Long Read Sequencing page for more detailed information about the package, variant calling analysis, and extraction requirements.

PacBio:

Our PacBio services deliver HiFi reads with an average read length of 8-12kb for standard offerings and up to 25kb for full flowcell runs. All package names are listed by the minimum number of >Q20 reads that will be delivered. Both assembly and annotation are included with all packages.

For each sample, a minimum volume of 60 µL and at least 35 ng/µL dsDNA (quantified by Qubit or other dye-based methods) are required. SeqCenter strongly recommends utilizing our HMW DNA Extraction service for best results; however, we will also accept samples that are shipped on dry ice to avoid DNA integrity issues caused by the shipping process.

Please see our PacBio Sequencing page for more detailed information about our services.

RNA Sequencing:

We offer both rRNA depletion RNA squencing and polyA-tail enrichment mRNA sequencing. Both provide stranded, paired end reads (2x 151bp) as fastq files.

For each sample, we require a minimum volume of 20µL and at least 50ng/µL RNA. We also recommend, but do not require, that samples be DNAse treated and have a RIN score greater than 6. We also offer Basic and Intermediate RNAseq analyses, which require an annotated reference sequence.

Please see our RNA Sequencing page for more detailed information about both our RNA sequencing and analysis packages.

Illumina Sequencing:

The Illumina sequencing packages produce paired end reads (2×151 bp) delivered as fastq files.

For each sample, we require a minimum volume of 30 µL and at least 10 ng/µL dsDNA quantified by Qubit or other dye-based method (20 ng/µL by Nanodrop). Variant calling add-on analysis requires an annotated reference file. DNA extraction services are available for only specific categories of microbes.

Please see our DNA Sequencing: Whole Genome Sequencing page for more detailed information about the package, variant calling analysis, and extraction requirements.

For additional information about variant calling and short read assemblies, please see our Bioinformatics page.

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