SpectroDive

NEXT GENERATION TARGETED PROTEOMICS

Integration of Ready-Made Panels Improved Workflow for Custom Panels

FEATURES BENEFITSFull automation Publication-ready results with minimum effort

High throughput More samples, more meaningful results without the need of manual revision

Optimized scheduling Increase your number of targets with High-Precision iRT Calibration assisted scheduling

Powered by Pulsar Fast and scalable library generation for a library-based panel generation

Custom-made panels Easy and intuitive panel generation wizard

PQ500 supportNative support for our ready-made panel for the absolute quantification of more than 500 human plasma proteins

Better user experience Setup wizards, comprehensive plots and reports, list of candidates ready to export

Seamless pipeline From panel generation to biological interpretation in one application

Novel targeted proteomics workflows can be highly multiplexed, allowing for parallel quantification of hundreds of proteins. This requires new approaches for the development and handling of optimized assay panels.

Targeted proteomics is the best analytical approach when a selected set of proteins needs to be quantified with high sensitivity, quantitative accuracy, and reproducibility. Previously, most applications used only small assay panels, limited to tens of proteins. The main reasons for under-using the multiplexing capabilities of modern PRM and MRM are manual assay generation methods that are suitable for single proteins, but not hundreds.

Biognosys offers two solutions to turn tar-geted proteomics into a highly multiplexed technology: Ready-made assay panels that don’t need any development, and a simpli-fied workflow for generation of large custom panels; both supported by the latest version of SpectroDive.

With routine investigations of plasma samples in mind, Biognosys developed PQ500: a ready-made kit including stable isotope standards for the targeted analysis of more than 500 proteins for human plasma profiling. Integration of PQ500 into SpectroDive provides researchers with a largely expanded panel of proteins.

With the latest version of SpectroDive, Biognosys has introduced a workflow for quick set-up of optimized custom-made panels. With the panel set-up wizard, users can quickly assemble an optimized assay panel from the peptides that are most suited for quantification.

Additional features of SpectroDive include:

• MS1 support for PRM: Improved confidence in peak picking by using MS1 information

• MaxQuant.Live support: Analysis of MaxQuant.Live acquired data; inclusion list export in MaxQuant.Live compatible format

• False discovery rate control: Increased confidence in peptide identification, specifically in larger panels

• Pulsar integration: Fast and scalable library generation with Biognosys’ embedded search engine

• Easier assay panel generation: Intuitive and automated selection of the best suited peptides for any target protein assay

Supported Instruments

• Thermo Scientific™ Q Exactive™ Series• Thermo Scientific™ Orbitrap Fusion™ Series• Thermo Scientific™ TSQ™ Series • SCIEX TripleTOF® Series• SCIEX Triple Quad Series• SCIEX QTRAP Series• SCIEX API Series• Agilent 6400 Series• Waters Xevo® TQ-S

Minimum System Requirements

• Windows 7 x64• Intel Core™ CPU 2.7 GHz (quad core)

or similar• 500 GB of free HDD space• 16 GB of RAM memory• .NET Framework 4.7

IMPROVING MULTIPLEXING FOR TARGETED PROTEOMICS

«We use SpectroDive™ 9.0 to perform highly multiplexed tar-geted proteomics experiments. The High-Precision iRT concept expedites our newly introduced ″global targeting″ approach based on MaxQuant.Live, which enables targeted proteomics with thousands of peptides.»

Florian Meier, Max Planck Institute of Biochemistry, Martinsried, Germany (Matthias Mann Group)

Subset PQ500 (160 peptides) Full PQ500 (1'600 peptides)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

SIC1

MCM1

ASH1

SFG1

ACE2

SWI5

IXR1

MBP1

SWI6

MSN2

FKH2

FHL1

NDD1

PDS1

CIN8

NRM1

PLM2

HCM1

TOS4

CLN2

PCL1

CLB5

YOX1

SWI4

GAT1

MSN4

PHD1

−2 −1 0 1 2Value

Color Key

WTR

1.R1

WTR

1.R2

WTR

1.R3

WTR

1.R4

WTR

1.R5

WTR

1.R6

WTR

1.R7

WTR

1.R8

WTR

1.R9

WTR

1.R1

0

WTR

1.R1

1

WTR

1.R1

2

WTR

1.R1

3

WTR

1.R1

4

WTR

1.R1

5

WTR

1.R1

6

WTR

1.R1

7

WTR

1.R1

8

WTR

1.R1

9

WTR

1.R2

0

SIC1

MCM1

ASH1

SFG1

ACE2

SWI5

IXR1

MBP1

SWI6

MSN2

FKH2

FHL1

NDD1

PDS1

CIN8

NRM1

PLM2

HCM1

TOS4

CLN2

PCL1

CLB5

YOX1

SWI4

GAT1

MSN4

PHD1

−2 −1 0 1 2Value

Color Key

0 2-2Z-Score: -1 1 5.48

1.81

5.54

1.86

1 PRM run

Cell Cycle Cell Cycle

1 PRM run

100 PRM runs

100 PRM runs

225.00 234.60

25.2127.85

0

0

-6-8 6 8-4 4-2 20

0

10

4

2

100

50

20

6

8

200

150

30

10

250

Peak Memory Usage

Cancer Plasma StudyOriginal Heatmap Heatmap with SpectroDive

Analysis Time

qVal

ue (-

Log1

0)G

byte

min

utes

Fold Change Cancer / Healthy

CRP

S100A9

S100A8

SAA1

PQ500: A READY-MADE PANEL FOR HUMAN PLASMA Targeted proteomics has been limited by the complexity of developing large customized panels. PQ500 is Biognosys’ ready-made panel that allows for the identification and quantification of more than 500 proteins commonly used for human plasma profiling. SpectroDive is optimized to utilize PQ500 as a large ready-made panel for liquid biopsies.

Human plasma is a widely used matrix in clinical and biological studies. It allows the researcher to gain comprehensive insights into a body’s health status and can easily be collected from patients and healthy individu-als. PQ500 contains more than 800 carefully selected stable-isotope standard (SIS) labeled peptides, corresponding to more than 500 proteins commonly found in human blood plasma. Efficient scheduling workflows in SpectroDive 9.0, together with the optimized PQ500 assay panel, allows the targeted interrogation of patient samples at the level of broadness of a discovery workflow. The figure on the left (top) shows differentially abundant proteins in human plasma detected with the PQ500 panel, including inflammation markers known to be elevated in cancer; e.g. C-reactive protein and protein S100-A9.

SpectroDive includes quality control parame-ters commonly used in discovery proteomics that increase the researcher’s confidence of identifying the correct peaks, such as FDR control and MS1 support for PRM.

Its algorithms are computationally optimized to handle even the largest projects without limitations in assay panel size. The figures on the left demonstrate SpectroDive 9.0 is highly scalable towards experiment size, irrespec-tive of how many peptides are targeted in the panel. In the examples shown, two-hour PRM runs acquired on a high-resolution instrument have been analyzed.

RELIABLE PEAK PICKING WITH CUSTOM PANELS

Recently, Kelliher et al. (2018)1 investigated the role of transcription factors in the periodic expression of genes and the subsequent production of proteins during the cell cycle. In their study, Kelliher et al. used budding yeast Saccharomyces cerevisiae as a model system, and opted for targeted quantitative proteomics to understand transient protein expression patterns over the course of the cell-cycle. The researchers developed custom-made assays for 45 cell cycle proteins and were able to detect 31 unique proteins dynamically expressed during the cell cycle.

To test SpectroDive’s ability to quantify the peptides of interest, Biognosys re-analyzed the published dataset. Using SpectroDive's panel generation functionality and under default factory settings for analysis, we were able to reproduce the identical protein expression pattern over the cell cycle, reaching the same biological interpretation with a minimum amount of time and resources.

Targeted proteomics is known to be the most flexible tool for the quantification of multiple candidate proteins in biological and biomedical applications. Often these assay panels are custom-made to address unique research questions. SpectroDive now supports the optimization of custom panels and subsequent data analysis.

1) Christina M. Kelliher, et al. Layers of regulation of cell-cycle gene expression in the budding yeast Saccharomyces cerevisiae. Molecular Biology of the Cell. 2018, 29, 2644-2655.

Use your panel to analyze your runs with the default factory settings. Get your list of candidates in the Post Analysis Perspective with no further manual revision.

SpectroDive's peak picking is very robust and rarely requires manual adjustments. In the Analysis Perspective, informative overview plots ranging from the individual sample to the entire data set can be used to confirm correctness of peak picking.

SpectroDive's custom panel generation tool is more intuitive and effortless than ever. Generate your panel using a library as a base: follow SpectroDive's wizard to obtain your best fitting panel.

SpectroDive, powered by Pulsar, provides a seamless workflow: use your run files as input to generate a library.Optimize your workflow with library assisted panel generation. Pulsar can search DDA, DIA and PRM (with MS1 information) data.

High-Precision iRT Calibration allows a refined scheduling for increased multiplexing. Ready-made assay panels such as PQ500 benefit the most from this feature.

FROM PANEL REFINEMENT TO BIOLOGICAL INTERPRETATIONSpectroDive takes the hassle from targeted proteomics by offering integrated panel optimization for custom panels, support for ready-made panels, High-Precision iRT Calibration-assisted scheduling and ready-to-publish results without manual revision.

HOW TO GET SPECTRODIVE

If you are interested in learning more about SpectroDive or want to get your free trial license, don’t hesitate to contact us at order@biognosys.com. We would be pleased to schedule a meeting with you and support you in implementing next generation proteomics into your laboratory.

Biognosys is a leader in next generation proteomics, dedicated to transforming the life sciences by making the most advanced proteomics tools available to researchers. Biognosys offers a suite of products and services to decode the proteome and equip researchers from all fields with a deep view of protein expression and quantification in a biological system.

www.biognosys.com