Global Proteomic Profiling - Bioproximity LLC

Features LFQ Assays Plasma Assays Exosome Assays Specifications

Identify and quantify thousands of proteins in a fast, 20 minute assay, in almost any protein-containing sample
Assess differences in protein and peptide abundance between samples
Measure changes in isoforms and post-translational modifications
All assays performed on a Thermo Q-Exactive HF-X Orbitrap mass spectrometer
Pricing from $225, no minimums
Typical turnaround: next week for gel-based samples, the following week for other sample types
Choose from our growing list of available add-on reports for statistical tests of change, taxonomic classification and more

Animation of Q-Exactive Orbitrap mass analyzer performing MS/MS. Image courtesy of Thermo Scientific. More info

Global proteomic analysis and profiling assays allow you to ID and accurately measure hundreds to thousands of proteins in nearly any sample type which contains protein. Via our online data portal you receive a list of all proteins identified, with quantitative measurements presented across all of your samples, to easily assess differences. From there you can drill down to the peptide level to assess changes in peptide abundance, including post-translational modifications. You can even view the actual tandem mass spectra used to identify each peptide. All of the data presented online is easily downloaded.

We have leveraged the incredible speed (up to 40 sequencing events per second) and sensitivity of Thermo's newest mass spectrometer, the Q-Exactive HF-X, to offer unprecedented pricing starting at just $225 to profile up to 500 proteins. Max pricing is under $1000 - profile in excess of 6,000 proteins for only $875.

$225

pricing to profile up to 500 proteins

You can test your samples at our lowest price point and then make a decision about which is the best assay for you, based on your samples.

We tell you how many proteins you would be able to profile in a different assay. No more wondering if your sample quality is good. This makes it easy to test out different conditions and prep methods for your samples.

40%

increase in unique identifications via APD algorithm

Our global proteomic analysis and profiling assays take advantage of the latest data processing methods to generate the highest quality data. Quantitation is performed by the "label-free quantitation" (LFQ) method in wide use across the industry. This method uses the "MS1" peptide peak area measurement to determine peptide abundance. The high mass accuracy (sub-5 ppm) and high mass resolution (60,000) enabled by the Orbitrap analyzer allow accurate measurements to made even in the presence of hundreds of co-eluting peptides.

The new advanced peak determination (APD) algorithm, found only in the HF-X model of the Q-Exactive line, enables almost full utilization of the instrument's sequencing capacity by improved annotation of the MS1 peaks, leading to a 40% increase in unique identifications vs. the previous instrument model (Q-Exactive HF). Multiple search algorithms (Comet and Tandem) are used for peptide identification. A spectral library is created for each individual project and searched to improve identification rates. Finally, a match-between-runs algorithm is used to impute identifications based on accurate mass and retention time values.

Standard Label-Free Quantitative Proteome Profiling Assays

These assays are appropriate for a wide range of samples types, see the assay descriptions for commonly used samples. Standard sample preparation is included with these assays, including protein extraction from standard sample types. For specialized sample type assays and enrichment assays, see the sections below.

Affinity-Enriched Proteome Profiling
- Assay:
  LFQ Profiling, Top 500
- ID and Quantify: Up to 500 protein groups (redundant isoforms do not count to this total)
- Specifications: UPLC-MS/MS, 25 cm column, up to 45,000 sequencing events
- Suggested sample types: Affinity-enriched and other minimally complex samples
In-gel $225 Non-gel $275
Sub-cellular Proteome Profiling
- Assay:
  LFQ Profiling, Top 2,000
- ID and Quantify: Up to 2,000 protein groups (redundant isoforms do not count to this total)
- Specifications: UPLC-MS/MS, 25 cm column, up to 45,000 sequencing events
- Suggested sample types: Sub-cellular fractionations, mitochondria, exosomes, microparticles, some prokaryotes
In-gel $325 Non-gel $375

Prokaryotic Proteome Profiling
- Assay:
  LFQ Profiling, Top 4,000
- ID and Quantify: Up to 4,000 protein groups (redundant isoforms do not count to this total)
- Specifications: UPLC-MS/MS, 25 cm column, up to 45,000 sequencing events
- Suggested sample types: Prokaryotes, some eukaryotes (yeast), some biofluids (saliva, urine)
In-gel $425 Non-gel $475
Eukaryotic Proteome Profiling
- Assay:
  LFQ Profiling, Unlimited
- ID and Quantify: All detectable protein groupss
- Specifications: UPLC-MS/MS, 50 cm column, up to 215,000 sequencing events
- Suggested sample types: Eukaryotes, microbiomes
Get for $875

All files avilable in csv or web view

Grouped proteins and peptides data

Parcoords data presentation

Plasma Proteome Profiling

Plasma/Serum Label-Free Quantitative Proteome Profiling Assays
- Assay:
  Non-depleted Plasma/Serum Proteome Profiling
- ID and Quantify: Up to 500 protein groups (redundant isoforms do not count to this total)
- Specifications: UPLC-MS/MS, 25 cm column, up to 45,000 sequencing events
- Sample: At least 5 uL of plasma or serum
Get for $425
Depleted Plasma/Serum Proteome Profiling
- Assay:
  Depleted Plasma LFQ Profiling, Top 2,000
- ID and Quantify: Up to 2,000 protein groups (redundant isoforms do not count to this total)
- Specifications: Agilent MARS depletion (human top 14, mouse top 3) UPLC-MS/MS, 25 cm column, up to 45,000 sequencing events
- Sample: 50 uL plasma or serum from human or mouse
Get for $525

Plasma Microparticle Proteome Profiling

Assay:
Plasma Microparticle LFQ Profiling, Top 4,000
ID and Quantify: Up to 4,000 protein groups (redundant isoforms do not count to this total)
Specifications: UPLC-MS/MS, 25 cm column, up to 45,000 sequencing events
Sample: 5 mL frozen plasma

Get for $525

Exosome Enrichment and Label-Free Quantitative Proteome Profiling Assays

Media and Biofluid Exosome Enrichment and Proteome Profiling

Assay:
Exosome Enrichment, Media or Biofluid, LFQ Profiling, Top 4,000
ID and Quantify: Up to 4,000 protein groups (redundant isoforms do not count to this total)
Specifications: UPLC-MS/MS, 25 cm column, up to 45,000 sequencing events
Sample: 10 mL cell culture media (exosome depleted!), 5 mL urine, saliva or CSF
Requirements: 10 mL of cell culture media, saliva or urine, 5 mL plasma

Get for $525

Plasma/Serum and Ascites Exosome Enrichment and Proteome Profiling

Assay:
Exosome Enrichment, Plasma or Ascites, LFQ Profiling, Top 4,000
ID and Quantify: Up to 4,000 protein groups (redundant isoforms do not count to this total)
Specifications: UPLC-MS/MS, 25 cm column, up to 45,000 sequencing events
Samples: 250 uL plasma, serum or ascites fluid

Get for $525

MS/MS spectra annotated with fragment ions

Sample Requirements

See each assay for assay-specific requirements, in general samples should:

contain at least 10 micrograms of total protein, 30 micrograms is ideal
be free of contaminants such as detergents or protease inhibitors, please let us know if this is not the case
ideally be less than 100 uL in volume, but no greater than 1.5 mL, a handling charge applies to larger volumes

Workflow

Protein extraction and cleanup
Enzymatic digestion with sequencing-grade trypsin
SPE of the digest
UPLC-MS/MS
UPLC - Thermo Easy-nLC 1200 fitted with a heated Easy-Spray column of 25 or 50 cm length
MS/MS - Thermo Q-Exactive HF-X quadrupole-Orbitrap mass spectrometer
Peptide identification with Comet and Tandem, spectral library searching and match-between-runs
Quantitation via MS1 peak are measurement
Data securely stored and accessible for one year with our basic plan

Deliverables

All data is hosted and delivered using our web-based data portal
View data reports online or download as Excel files
Data reports include:

– proteins identified, with intensity values for each sample
– proteins grouped by common peptide identifications, to allow isoform discrimination
– tandem MS spectrum viewer: see fragment ion assignments for all identified peptides

Download raw data files (mzML format) and search result files (mzID format) -- available to plus/pro users only

Optional deliverables available at extra cost include a growing number of add-on reports:

Protein LFQ Comparison: fold-change and statistical significance measurements for up to 5 comparisons between any samples or groups of samples in the project
Taxonomy Classification: lowest-common ancestry calculation of discriminative peptides in a sample

Global Proteomic Analysis and Profiling Assays

Standard Label-Free Quantitative Proteome Profiling Assays

Affinity-Enriched Proteome Profiling

LFQ Profiling, Top 500

Sub-cellular Proteome Profiling

LFQ Profiling, Top 2,000

Prokaryotic Proteome Profiling

LFQ Profiling, Top 4,000

Eukaryotic Proteome Profiling

LFQ Profiling, Unlimited

Plasma Proteome Profiling

Plasma/Serum Label-Free Quantitative Proteome Profiling Assays

Non-depleted Plasma/Serum Proteome Profiling

Depleted Plasma/Serum Proteome Profiling

Depleted Plasma LFQ Profiling, Top 2,000

Plasma Microparticle Proteome Profiling

Plasma Microparticle LFQ Profiling, Top 4,000

Exosome Enrichment and Label-Free Quantitative Proteome Profiling Assays

Media and Biofluid Exosome Enrichment and Proteome Profiling

Exosome Enrichment, Media or Biofluid, LFQ Profiling, Top 4,000

Plasma/Serum and Ascites Exosome Enrichment and Proteome Profiling

Exosome Enrichment, Plasma or Ascites, LFQ Profiling, Top 4,000

Sample Requirements

Workflow

Deliverables