understanding life - biognosys · peptides and fragment ions are recorded, targeted proteomics...

Understanding lifeWITH BIOGNOSYS TOOLS FOR BLOOD PROTEOMICS

Innovative services and products for highly multiplexed protein discovery and quantification to help you understand the biological processes that shape life.

n Absolute quantification of up to 100 human plasma proteins in a single measurement n Unbeatable specificity and precision n Requires as little as 10 µl of plasma n Actionable results in less than 48 hours n Suitable for high-throughput & large sample cohorts

A new standard for clinical research, biomarker discovery and development of companion diagnostics

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Protein extraction, digestion and clean-up

LC separation & MS data acquisition

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Assay matching& multiplexed quantification

precursor selection fragmentation mass analyzerprecursor ionscell/tissue sample protein extraction split to peptides peptide separation & ionization MS2 spectrum quantification

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collision cell Orbitrap

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precursor selection fragmentation mass analyzerprecursor ionscell/tissue sample protein extraction split to peptides peptide separation & ionization MS2 spectrum

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precursor selection fragmentation transition selectionprecursor ionscell/tissue sample protein extraction split to peptides peptide separation & ionizationselected transition

ion currents quantification

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collision cell Q3

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precursor selection fragmentation mass analyzerprecursor ionscell/tissue sample protein extraction split to peptides peptide separation & ionization MS2 spectrum quantification

m/z

time


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precursor selection fragmentation mass analyzerprecursor ionscell/tissue sample protein extraction split to peptides peptide separation & ionization MS2 spectrum

m/z


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precursor selection fragmentation transition selectionprecursor ionscell/tissue sample protein extraction split to peptides peptide separation & ionizationselected transition

ion currents quantification

time

quantification

time

collision cell Q3

BIOGNOSYS BLOODPROTEOMICS TECHNOLOGY

n Multiple Reaction Monitoring (MRM) is a well-established method for targeted proteomics and is performed on triple quadrupole mass spectrometers.

n Parallel Reaction Monitoring (PRM) it is a novel variant of MRM and was introduced recently. PRM is performed on the latest generation of high-resolution mass spectrometric instruments.

Proteins are the functional units of all living organisms. The entire set of proteins making-up a given biological system is referred to as its proteome. As all functional units are represented by the proteome, its characterization enables linking a phenotype to molecular events. Proteomics aims at understanding the proteome by enabling the unbiased and large-scale study of proteins.

Blood is the most frequently used biological

sample in clinical research and routine

laboratory diagnostics. Quantitative levels

of blood proteins reflect the health status

of single organs and the body as a whole.

Changes in composition of proteins and/or

their quantities in the blood can be correlated

to disease onset or therapy response. Often

the relative changes in protein concentrations

to each other are the key indicator of a certain

condition. Only monitoring the levels of

major blood proteins simultaneously makes

it possible to recognize the “Big Picture” and

explain pathological processes going on in the

body.

Today monitoring of blood proteins is

mainly performed by immunoassays.

However, immunoassays have several

limitations like lack of specificity, low

multiplexing ability, and its expensive

development for new protein targets. These

challenges can be overcome by using targeted

proteomics, a mass spectrometry based

method that allows absolute quantification

of more than 100 proteins analyzed in high-

throughput mode in thousands of samples.

Biognosys Blood Proteomics tools are based on targeted proteomics, a mass spectrometry technology that targets specific peptides in a complex mixture and determines their presence and quantity.

Targeted proteomics relies on two main approaches: In contrast to data independent acquisition where all peptides and fragment ions are recorded, targeted proteomics limits the number of peptides that will be monitored and only focuses on those peptides during acquisition to achieve the highest sensitivity and throughput for hundreds or thousands of

n Assay development and set-up where a collection of assays (also called transition or inclusion lists) is built and optimized for the proteins of interest. These assays are later used in the next step.

n Data acquisition is performed on triple quadrupole (MRM) or high-resolution mass spectrometric instruments (PRM). In both approaches an upfront quadrupole is used to isolate the targeted precursor ions from the assay list followed by a collision cell where product ions (transitions) are generated.

n Data analysis is historically a limitation in high-throughput analysis of multiplexed MRM and PRM runs and a significant manual input is required with available tools. Biognosys overcomes these challenges with its proprietary software SpectroDive that enables extremely fast analysis of large datasets.

MULTIPLE REACTION MONITORING (MRM)

PARALLEL REACTION MONITORING (PRM)

samples. Targeted proteomics allows absolute quantification of the proteins of interest by including stable isotope labled standard peptides (SIS peptides) in the analysis. Targeted proteomics is based on three essential parts:

targeted proteomics technology

We offer various MRM and PRM Panel kits including customized solutions that can be transferred to your laboratory or analyzed in our state-of-the-art facility.”

ASSAY MATCHING &MULTIPLEXED QUANTIFICATION

LC SEPARATION & MS DATA ACQUISITION

PROTEIN EXTRACTION, DIGESTION & CLEAN-UP

PlasmaDive™ reference peptides

A set of 100 heavy labelled SIS peptides with corresponding MRM or PRM assays combined in one multiplexed, scheduled method. Each peptide represents a human plasma protein, with almost half of the panel’s proteins being considered a putative cancer, cardio-vascular or metabolic biomarker. Available for 48 or 96 samples.

PlasmaDeepDive™ reference peptides

A set of 100 heavy labelled SIS pepA set of 100 heavy labelled SIS peptides with corresponding MRM or PRM assays combined in one multiplexed, scheduled method, specifically designed to monitor protein levels in depleted plasma or serum. It includes 16 peptides corresponding to the typically depleted proteins to monitor the depletion quality, 9 housekeeping proteins for normalization and consequently high reproducibility of the results, and 75 proteins that represent relevant targets for biomarker screening. Available for 48 or 96 samples.

Sample Preparation Kit Pro

A high-throughput all-in-one sample preparation kit for mass spectrometry proteomics. It enables processing of 96 cell culture or plasma samples in parallel for all mass spectrometry proteomics workflows (SRM/MRM, PRM, HRM/DIA, DDA).

SpectroDive™

Professional software for setting up, signal processing and analysis of MRM and PRM measurements. Smartest peak picking algorithms enable extremely fast analysis of large datasets.

PlasmaDeepDive™ multiplexed assay panel

A complete workflow consisting of sample preparation kit, stable isotope labeled standard (SIS) reference peptides and the corresponding assay panel and SpectroDive™ software. Everything you need for quantifying 100 proteins per depleted human plasma sample in one box!

PlasmaDive™ multiplexed assay panel

A complete workflow consisting of sample preparation kit, stable isotope labeled standard (SIS) reference peptides and the corresponding assay panel and SpectroDive™ software. Everything you need for quantifying 100 proteins per human plasma sample in one box!

Available in 2 sizes: n 48 – for 48 samples n 96 – for 96 samples

Available in 2 sizes: n 48 – for 48 samples n 96 – for 96 samples

BLOOD PROTEOMICS TOOLSBiognosys is the leading proteomics company providing products and services for the highly multiplexed quantification of proteins in any species and any biological matrix. Biognosys’ team of interdisciplinary scientists has developed PlasmaDive™ and PlasmaDeepDive™ solutions for the absolute quantification of human plasma with targeted proteomics mass spectrometry technology. With PlasmaDive™ or PlasmaDeepDive™ multiplexed quantification panels the user gets a complete workflow consisting of sample

preparation kit, stable isotope labeled standard (SIS) reference peptides and the corresponding assay panel and SpectroDive™ – Biognosys proprietary software for the analysis of targeted proteomics data sets acquired with multiple reaction monitoring (MRM) or parallel reaction monitoring (PRM). However, each component of the complete panel is also available as a separate product in case you are looking to upgrade your existing blood proteomics workflows.

PlasmaDive™ Multiplexed Assey Panel contains:

n Reagents and optimized protocol for reproducible sample preparation n Stable isotope standards for accurate quantitation n iRT Standard for transfer to virtually any LC setup n MS Method for optimized measurements n SpectroDive software for data analysis

PlasmaDeepDive™ Multiplexed Assey Panel contains:

n Reagents and optimized protocol for reproducible sample preparation n Stable isotope standards for accurate quantitation n iRT Standard for transfer to virtually any LC setup n MS Method for optimized measurements n SpectroDive software for data analysis

Available in 3 sizes:

n Mini - for 20 samples with 3 month SpectroDive license n 48 – for 48 samples with 6 month SpectroDive license n 96 – for 96 samples with 12 month SpectroDive license

Available in 3 sizes:

n Mini - for 20 samples with 3 month SpectroDive license n 48 – for 48 samples with 6 month SpectroDive license n 96 – for 96 samples with 12 month SpectroDive license

Entry Name UniPot ID Description Protein Average Mass [g/mol]

A1AG1_HUMAN P02763 Alpha-1-acid glycoprotein 1 (Orosomucoid-1) 23511,6

A1AG2_HUMAN P19652 Alpha-1-acid glycoprotein 2 (Orosomucoid-2) 23602,6

A1AT_HUMAN P01009 Alpha-1-antitrypsin 46736,6

A1BG_HUMAN P04217 Alpha-1B-glycoprotein 54253,5

A2AP_HUMAN P08697 A lpha-2-antiplasmin (Serpin F2) 54565,8

A2GL_HUMAN P02750 Leucine-rich alpha-2-glycoprotein (LRG) 38177,9

A2MG_HUMAN P01023 Alpha-2-macroglobulin (Alpha-2-M) 163291,2

AACT_HUMAN P01011 Alpha-1-antichymotrypsin (ACT) 47651,0

AFAM_HUMAN P43652 Afamin (Alpha-albumin) 69069,2

ALBU_HUMAN P02768 Serum albumin 69366,7

ALS_HUMAN P35858 Insulin-like growth factor-binding protein complex acid labile subunit

66034,8

AMBP_HUMAN P02760 Protein AMBP 38999,5

ANGT_HUMAN P01019 Angiotensinogen (Serpin A8) 53154,3

ANT3_HUMAN P01008 Antithrombin-III (Serpin C1) 52602,5

APOA1_HUMAN P02647 Apolipoprotein A-I 30777,9

APOA2_HUMAN P02652 Apolipoprotein A-II 11175,0

APOA4_HUMAN P06727 Apolipoprotein A-IV 45399,1

APOB_HUMAN P04114 Apolipoprotein B-100 515605,2

APOC1_HUMAN P02654 Apolipoprotein C-I 9331,9

APOC2_HUMAN P02655 Apolipoprotein C-II 11283,9

APOC3_HUMAN P02656 Apolipoprotein C-III 10852,3

APOD_HUMAN P05090 Apolipoprotein D 21275,6

APOE_HUMAN P02649 Apolipoprotein E 36154,1

APOH_HUMAN P02749 Apolipoprotein H 38298,2

APOL1_HUMAN O14791 Apolipoprotein L1 43974,3

APOM_HUMAN O95445 Apolipoprotein M 21253,3

BTD_HUMAN P43251 Biotinidase 61133,0

C1QA_HUMAN P02745 Complement C1q subcomponent subunit A 26016,6

C1QB_HUMAN P02746 Complement C1q subcomponent subunit B 26721,8

C1QC_HUMAN P02747 Complement C1q subcomponent subunit C 25773,7

C1R_HUMAN P00736 Complement C1r subcomponent 80118,6

C1S_HUMAN P09871 Complement C1s subcomponent 76684,5

C4BPA_HUMAN P04003 C4b-binding protein alpha chain 67033,2

CBG_HUMAN P08185 Corticosteroid-binding globulin (Serpin A6) 45141,0

CD5L_HUMAN O43866 CD5 antigen-like (CT-2) (SP-alpha) 38087,8

CERU_HUMAN P00450 Ceruloplasmin (Ferroxidase) 122205,3

CFAB_HUMAN P00751 Complement factor B 85532,9

CFAH_HUMAN P08603 Complement factor H (H factor 1) 139096,4

CFAI_HUMAN P05156 Complement factor I 65750,3

CHLE_HUMAN P06276 Cholinesterase (EC 3.1.1.8) 68418,1

CLUS_HUMAN P10909 Clusterin (Aging-associated gene 4 protein) (Apoli-poprotein J)

52494,7

CO2_HUMAN P06681 Complement C2 83268,0


CO4A_HUMAN P0C0L4 Complement C4-A 192785,7


CO8A_HUMAN P07357 Complement component C8 alpha chain 65163,3

CO9_HUMAN P02748 Complement component C9 63173,4

CXCL7_HUMAN P02775 Platelet basic protein (C-X-C motif chemokine 7) 13894,2

F13A_HUMAN P00488 Coagulation factor XIII A chain 83267,4

F13B_HUMAN P05160 Coagulation factor XIII B chain 75510,7

FA10_HUMAN P00742 Coagulation factor X 54731,7

FA9_HUMAN P00740 Coagulation factor IX 51778,5

FBLN1_HUMAN P23142 Fibulin-1 77214,1

FETUA_HUMAN P02765 Alpha-2-HS-glycoprotein 39324,7

FETUB_HUMAN Q9UGM5 Fetuin-B 42055,0

FIBA_HUMAN P02671 Fibrinogen alpha chain 94973,1

FIBG_HUMAN P02679 Fibrinogen gamma chain 51511,7

FINC_HUMAN P02751 Fibronectin (FN) 262624,7

GELS_HUMAN P06396 Gelsolin (Actin-depolymerizing factor) 85697,6

GPX3_HUMAN P22352 Glutathione peroxidase 3 25552,4

HBB_HUMAN P68871 Hemoglobin subunit beta 15998,4

HBD_HUMAN P02042 Hemoglobin subunit delta (Delta-globin) 16055,5

HEMO_HUMAN P02790 Hemopexin (Beta-1B-glycoprotein) 51676,4

HEP2_HUMAN P05546 Heparin cofactor 2 57070,7

HPT_HUMAN P00738 Haptoglobin 45205,3

HPTR_HUMAN P00739 Haptoglobin-related protein 39029,6

HRG_HUMAN P04196 Histidine-rich glycoprotein 59578,3

IC1_HUMAN P05155 Plasma protease C1 inhibitor 55154,3

IGHA1_HUMAN P01876 Ig alpha-1 chain C region 37654,7

IGHA2_HUMAN P01877 Ig alpha-2 chain C region 36526,3

IGHG1_HUMAN P01857 Ig gamma-1 chain C region 36105,9

IGHG2_HUMAN P01859 Ig gamma-2 chain C region 35900,7

IGHG3_HUMAN P01860 Ig gamma-3 chain C region (HDC) 41287,0

IGHM_HUMAN P01871 Ig mu chain C region 49306,6

IPSP_HUMAN P05154 Plasma serine protease inhibitor 45674,8

ITIH1_HUMAN P19827 Inter-alpha-trypsin inhibitor heavy chain H1 101389,3

ITIH2_HUMAN P19823 Inter-alpha-trypsin inhibitor heavy chain H2 106463,6

ITIH4_HUMAN Q14624 Inter-alpha-trypsin inhibitor heavy chain H4 103357,6

KAIN_HUMAN P29622 Kallistatin (Kallikrein inhibitor) 48542,0

KLKB1_HUMAN P03952 Plasma kallikrein 71369,8

KNG1_HUMAN P01042 Kininogen-1 71957,4

PEDF_HUMAN P36955 Pigment epithelium-derived factor (PEDF) 46312,2

PGRP2_HUMAN Q96PD5 N-acetylmuramoyl-L-alanine amidase 62217,1

PLF4_HUMAN P02776 Platelet factor 4 (Oncostatin-A) 10844,9

PLMN_HUMAN P00747 Plasminogen 90569,1

PON1_HUMAN P27169 Serum paraoxonase 39731,4

PRG4_HUMAN Q92954 Proteoglycan 4 151077,2

RET4_HUMAN P02753 Retinol-binding protein 4 23010,0

SAA4_HUMAN P35542 Serum amyloid A-4 protein 14746,7

SEPP1_HUMAN P49908 Selenoprotein P 43173,7

SHBG_HUMAN P04278 Sex hormone-binding globulin 43779,2

TETN_HUMAN P05452 Tetranectin 22536,8

THBG_HUMAN P05543 Thyroxine-binding globulin (Serpin A7) 46324,6

THRB_HUMAN P00734 Prothrombin 70036,9

TRFE_HUMAN P02787 Serotransferrin 77064,0

TTHY_HUMAN P02766 Transthyretin 15887,0

VTDB_HUMAN P02774 Vitamin D-binding protein 52963,7

VTNC_HUMAN P04004 Vitronectin 54305,6

VWF_HUMAN P04275 von Willebrand factor 309264,9

ZA2G_HUMAN P25311 Zinc-alpha-2-glycoprotein 34258,7

Entry Name UniPot ID Description Group

ADIPO_HUMAN Q15848 Adiponectin Target

ALS_HUMAN P35858 Insulin-like growth factor-binding protein complex acid labile subunit

Target

BDNF_HUMAN P23560 Brain-derived neurotrophic factor Target

C1RL_HUMAN Q9NZP8 Complement C1r subcomponent-like protein Target

CAD13_HUMAN P55290 Cadherin-13 Target

CADH5_HUMAN P33151 Cadherin-5 (CD144) Target

CBPB2_HUMAN Q96IY4 Carboxypeptidase B2 Target

CD14_HUMAN P08571 Monocyte differentiation antigen CD14 Target

CH3L1_HUMAN P36222 Chitinase-3-like protein 1 Target

CHL1_HUMAN O00533 Neural cell adhesion molecule L1-like protein Target

CNDP1_HUMAN Q96KN2 Beta-Ala-His dipeptidase Target

CNTF_HUMAN P26441 Ciliary neurotrophic factor Target

CO4B_HUMAN P0C0L5 Complement C4-B Target

CRAC1_HUMAN Q9NQ79 Cartilage acidic protein 1 Target

CRF_HUMAN P06850 Corticoliberin Target

CXCL7_HUMAN P02775 Platelet basic protein Target

CYTC_HUMAN P01034 Cystatin-C Target

DIAC_HUMAN Q01459 Di-N-acetylchitobiase Target

DOPO_HUMAN P09172 Dopamine beta-hydroxylase Target

EGFR_HUMAN P00533 Epidermal growth factor receptor Target

ENOG_HUMAN P09104 Gamma-enolase Target

FA11_HUMAN P03951 Coagulation factor XI Target

FBLN3_HUMAN Q12805 EGF-containing fibulin-like extracellular matrix protein 1 Target

GFAP_HUMAN P14136 Glial fibrillary acidic protein Target

GP1BA_HUMAN P07359 Platelet glycoprotein Ib alpha chain Target

GPV_HUMAN P40197 Platelet glycoprotein V (CD42d) Target

GRP75_HUMAN P38646 Stress-70 protein, mitochondrial Target

GRP78_HUMAN P11021 78 kDa glucose-regulated protein Target

HGFA_HUMAN Q04756 Hepatocyte growth factor activator Target

HS12A_HUMAN O43301 Heat shock 70 kDa protein 12A Target

HS71L_HUMAN P34931 Heat shock 70 kDa protein 1-like Target

HS74L_HUMAN O95757 Heat shock 70 kDa protein 4L Target

HSP71_HUMAN P08107 Heat shock 70 kDa protein 1A/1B Target

HSP74_HUMAN P34932 Heat shock 70 kDa protein 4 Target

HSP76_HUMAN P17066 Heat shock 70 kDa protein 6 Target

HSP7C_HUMAN P11142 Heat shock cognate 71 kDa protein Target

HSP7E_HUMAN Q0VDF9 Heat shock 70 kDa protein 14 Target

IBP2_HUMAN P18065 Insulin-like growth factor-binding protein 2 Target

IBP3_HUMAN P17936 Insulin-like growth factor-binding protein 3 Target

IDHC_HUMAN O75874 Isocitrate dehydrogenase [NADP] cytoplasmic Target

IGF1_HUMAN P05019 Insulin-like growth factor I Target

IGF2_HUMAN P01344 Insulin-like growth factor II Target

IL10_HUMAN P22301 Interleukin-10 Target

IL1AP_HUMAN Q9NPH3 Interleukin-1 receptor accessory protein Target

ITIH3_HUMAN Q06033 Inter-alpha-trypsin inhibitor heavy chain H3 Target

LBP_HUMAN P18428 Lipopolysaccharide-binding protein Target

LDHB_HUMAN P07195 L-lactate dehydrogenase B chain Target

LEP_HUMAN P41159 Leptin Target

LUM_HUMAN P51884 Lumican Target

LYAM1_HUMAN P14151 L-selectin (CD62L) Target

MGMT_HUMAN P16455 Methylated-DNA--protein-cysteine methyltransferase Target

MINP1_HUMAN Q9UNW1 Multiple inositol polyphosphate phosphatase 1 Target

MMP9_HUMAN P14780 Matrix metalloproteinase-9 Target

MMRN1_HUMAN Q13201 Multimerin-1 Target

NCAM1_HUMAN P13591 Neural cell adhesion molecule 1 (CD56) Target

NEBU_HUMAN P20929 Nebulin Target

NEST_HUMAN P48681 Nestin Target

NEUT_HUMAN P30990 Neurotensin/neuromedin N Target

NGF_HUMAN P01138 Beta-nerve growth factor Target

NMB_HUMAN P08949 Neuromedin-B Target

NPY_HUMAN P01303 Pro-neuropeptide Y Target

NRP1_HUMAN O14786 Neuropilin-1 (CD304) Target

P53_HUMAN P04637 Cellular tumor antigen p53 Target

PHLD_HUMAN P80108 Phosphatidylinositol-glycan-specific phospholipase D Target

PROZ_HUMAN P22891 Vitamin K-dependent protein Z Target

PTEN_HUMAN P60484 Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN

Target

PZP_HUMAN P20742 Pregnancy zone protein Target

RETN_HUMAN Q9HD89 Resistin Target

SAMP_HUMAN P02743 Serum amyloid P-component Target

SYPL1_HUMAN Q16563 Synaptophysin-like protein 1 Target

TIMP1_HUMAN P01033 Metalloproteinase inhibitor 1 Target

TKN1_HUMAN P20366 Protachykinin-1 Target

TSP1_HUMAN P07996 Thrombospondin-1 Target

VASN_HUMAN Q6EMK4 Vasorin Target

VWF_HUMAN P04275 von Willebrand factor Target

A1AT_HUMAN P01009 Alpha-1-antitrypsin Depleted protein

A2MG_HUMAN P01023 Alpha-2-macroglobulin Depleted protein

ALBU_HUMAN P02768 Serum albumin Depleted protein

APOA1_HUMAN P02647 Apolipoprotein A-I Depleted protein

APOA2_HUMAN P02652 Apolipoprotein A-II Depleted protein

CO3_HUMAN P01024 Complement C3 Depleted protein

FIBA_HUMAN P02671 Fibrinogen alpha chain Depleted protein

FIBB_HUMAN P02675 Fibrinogen beta chain Depleted protein

FIBG_HUMAN P02679 Fibrinogen gamma chain Depleted protein

HPT_HUMAN P00738 Haptoglobin Depleted protein

IGHA1_HUMAN P01876 Ig alpha-1 chain C region Depleted protein

IGHG1_HUMAN P01857 Ig gamma-1 chain C region Depleted protein

IGHG2_HUMAN P01859 Ig gamma-2 chain C region Depleted protein

IGHM_HUMAN P01871 Ig mu chain C region Depleted protein

TRFE_HUMAN P02787 Serotransferrin (Transferrin) Depleted protein

TTHY_HUMAN P02766 Transthyretin Depleted protein

A1BG_HUMAN P04217 Alpha-1B-glycoprotein QC protein

CERU_HUMAN P00450 Ceruloplasmin QC protein

HEMO_HUMAN P02790 Hemopexin QC protein

IC1_HUMAN P05155 Plasma protease C1 inhibitor QC protein

ITIH2_HUMAN P19823 Inter-alpha-trypsin inhibitor heavy chain H2 QC protein

ITIH4_HUMAN Q14624 Inter-alpha-trypsin inhibitor heavy chain H4 QC protein

KNG1_HUMAN P01042 Kininogen-1 QC protein

VTDB_HUMAN P02774 Vitamin D-binding protein QC protein

VTNC_HUMAN P04004 Vitronectin QC protein

Biognosys PlasmaDive - List of Proteins Scheduled Multiplexed Assay Panel Kit for Human Plasma / Serum

Biognosys PlasmaDeepDive - List of Proteins Scheduled MRM Assay Panel Kit for Depleted Human Plasma / Serum

What is the difference between PlasmaDive™, PlasmaDive™ mini and PlasmaDeepDive™ and PlasmaDeepDive™ mini?PlasmaDive™ and PlasmaDive™ Mini monitor an identical set of 100 proteins levels in human plasma or serum samples with high throughput. Each stable isotope standard peptide represents a human plasma protein, with almost half of the panel’s proteins being considered a putative cancer, cardio-vascular or metabolic biomarker. The difference is only in the number of samples that can be processed. PlasmaDive™ is made for 96 samples and PlasmaDive™ Mini is made for 20 samples.

PlasmaDeepDive™ and PlasmaDeepDive™ Mini multiplexed assay panel target 100 proteins to be measured in one scheduled MRM or PRM experiment. It includes 16 peptides corresponding to the typically depleted proteins in human plasma analysis, which can be used to monitor the depletion quality, 9 housekeeping proteins for normalization and consequently high reproducibility of the results, and 75 proteins that represent relevant targets for biomarker screening. The difference is only in the number of samples that can be processed. PlasmaDeepDive is made for 96 samples and PlasmaDeepDiveMini is made for 20 samples.

What is the dynamic range of PlasmaDive™ and PlasmaDeepDive™ combined?Together the two kits span 6-7 orders of magnitude dynamic range with high precision and reproducibility. Additional information on the targeted proteins and use cases can be found in Science Hub section of the Biognosys website.

Can I measure only a subset of the proteins in each kit?Of course, assays of only a subset of the proteins in one kit can be generated and measured. Thereby the measurement time can be reduced and the sensitivity of the analysis increased.

Can I use the PlasmaDeepDive™ reference peptides with native (not depleted) plasma?

Yes, this is possible. However, sample preparation protocol needs to be updated and you should be aware that some of the analytes in PlasmaDeepDive™ are low abundant proteins and might not be detectable in non-depleted plasma in all conditions. Please contact us for additional information.

Which proteins can be measured with PlasmaDive™ and PlasmaDeepDive™?Please see the list of proteins on the next page.

The following information is for the entire workflow together. The workflow includes the Sample Preparation Kit Pro, Reference Peptides and SpectroDive for the data analysis. The combined workflow enables the generation absolute quantitative information in sample.

Supported Instruments for MRM or PRM measurements:

MRM

n Thermo Scientific™ TSQ™ Series

n AB SCIEX API 4000™

n AB SCIEX Triple Quad™ 5500

n Agilent 6400 Series

PRM

n Thermo Scientific™ Q Exactive™ Series

n Thermo Scientific™ Orbitrap Fusion™ Series

If your instrument is not on the list please contact us at [email protected] to get detailed information on the instruments we support.

TECHNICAL INFORMATION FREQUENTLY ASKED QUESTIONS

Peer-Reviewed Papers

Pechlaner R, Tsimikas S, Yin X, Willeit P, Baig F, Santer P, et al. Very-Low-Density Lipoprotein-Associated Apolipoproteins Predict Cardiovascular Events and Are Lowered by Inhibition of APOC-III. J Am Coll Cardiol. 2017; 69(7):789-800.

Cantonwine DE, Zhang Z, Rosenblatt K, Goudy KS, Doss RC, Ezrin AM, et al. Evaluation of proteomic biomarkers associated with circulating microparticles as an effective means to stratify the risk of spontaneous preterm birth. Am J Obstet Gynecol. 2016; 214(5): 631.e1-631.e11.

Kiseleva OI, Romashova YA, Moskaleva NE, Petushkova NA, Teryaeva NB, Belyaev AY, Lisitsa AV. Plasma preparation to measure FDA-approved protein markers by selected reaction monitoring. Clin Transl Med. 2015; 4(1):32.

ABOUT BIOGNOSYSBiognosys was founded in 2008 as a spin-off from the lab of Prof. Ruedi Aebersold at the ETH Zurich, leading scientist in next-gen proteomics. Biognosys maintains its global presence with offices located in Schlieren, Switzerland and Cambridge, USA. It operates its own state of the art proteomics facility in Switzerland.

OUR PROTEOMICS EXPERTS CLOSE TO YOUFlorian Marty, Director Global Product Support Phone: +41 (0)44 7382045, Email: [email protected]

Fadi Abdi, Director Global Product Sales Phone: +(1) 774 424 8150, Email: [email protected]

WWW.BIOGNOSYS.COM

LET US HELP YOU DO GREAT PROTEOMICS!

If you’re interested in learning more about our blood proteomics tools don’t hesitate to contact us at [email protected]. We would be pleased to schedule a meeting and support you, no commitment from your side. Biognosys blood proteomics tools are also offered as a Service for measurements in our state-of-the-art proteomics facility.

understanding life - biognosys · peptides and fragment ions are recorded, targeted proteomics...

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