Biognosys PlasmaDive Mini Manual

Second Edition, Version 2.03

April 2017

© Biognosys AG, Switzerland

PlasmaDive™ Mini

Human Plasma Assay Panel for MRM or PRM analysis

MANUAL

Second Edition, Version 2.03

April 2017

PlasmaDive™ Mini Manual, © Biognosys AG, Switzerland

Page 2 of 22

Table of Contents

PlasmaDive™ Mini Assay Panel Components ........................................................... 3

Storage and Quality Control of PlasmaDive™ Mini Kit ............................................... 3

Use Limitations ........................................................................................................... 3

Product Warranty and Satisfaction Guarantee ........................................................... 4

Technical Assistance .................................................................................................. 4

Safety Information ...................................................................................................... 4

Introduction: PlasmaDive™ Mini Assay Panel at a Glance ......................................... 5

Important Notes before Start ...................................................................................... 7

Sample Requirements ................................................................................................ 7

SpectroDive™ Software and PlasmaDive™ Mini Panel Plug-in ................................. 8

Additionally Required Laboratory Equipment and Consumables ................................ 9

Additionally Required Reagents, Solvents and Solutions ........................................... 9

Sample Preparation Procedure & LC-MRM/PRM Analysis....................................... 10

Report Columns Description ..................................................................................... 18

Troubleshooting Guide ............................................................................................. 19

Trademarks & Limited License Agreement ............................................................... 22

Second Edition, Version 2.03

April 2017

PlasmaDive™ Mini Manual, © Biognosys AG, Switzerland

Page 3 of 22

PlasmaDive™ Mini Assay Panel Components

PlasmaDive™ Mini Kit

Part No: Ki-3012
Sufficient for analysis of 20 samples

Reference
Peptide Mix

1x 1.1 ml tube, black cap

Alkylation
Solution

1x 10 ml tube, yellow cap

Reduction
Stock
Solution

1x 0.5 ml tube, orange cap
LC Solution

1x 10 ml tube, clear cap

10x Dilution
Buffer

1x 10 ml tube, green cap

Denature
Buffer

1x 10 ml tube, violet cap

Dissolution
Buffer

1x 2.0 ml tube, light blue cap

MicroSpin™
C18
columns

20x C18 columns with the adapter collars
PlasmaDive™ Mini MRM and

PRM Panel Plug-ins

Available upon request at

[e-mail]

PlasmaDive™ Mini Panel Manual

Available at

www.biognosys.com/shop/plasmadive-mini

Storage and Quality Control of PlasmaDive™ Mini Kit

Immediately after receiving the kit store:

 Reference Peptide Mix at -20°C
 Reduction Stock Solution and Alkylation Solution at +4°C and protected from light
 All other components should be stored dry at room temperature (15–25°C)

In accordance with Biognosys’ Quality Management System, each lot of the kit is tested
against predetermined specifications to ensure consistent product quality.

Use Limitations

PlasmaDive™ Mini Assay Panel is intended for mass spectrometry proteomics
applications and research use only. This product is not intended for the diagnostic,
prevention, or treatment of a disease. All due care and attention should be exercised
in the handling of the products.

Second Edition, Version 2.03

April 2017

PlasmaDive™ Mini Manual, © Biognosys AG, Switzerland

Page 4 of 22

Product Warranty and Satisfaction Guarantee

Biognosys guarantees the performance of the product when following the instructions
and protocols described in this product manual. However, the user must determine the
suitability of the product for its particular use. Should the product fail to perform
satisfactorily due to any reason other than misuse, Biognosys will replace it free of
charge. Biognosys reserves the right to change, alter, or modify any product to
enhance its performance and design.

If you have questions about product specifications or performance, please contact us
at [e-mail]. We also encourage you to contact us if you have any
suggestions for improving product performance or for its use in new applications and
techniques.

Technical Assistance

Our Technical Department is composed of experienced scientists with extensive
practical and theoretical expertise in proteomic technologies and bioinformatics. If you
have any questions or experience any difficulties with PlasmaDive™ Mini Assay Panel
please do not hesitate to contact us at [e-mail], call [phone]
or visit www.biognosys.com/shop/plasmadive-mini.

Safety Information

When working with chemicals, always wear a suitable lab coat, disposable gloves, and
protective goggles. For more information, please consult the material safety data sheet
(MSDS) available online in convenient and compact PDF format at

www.biognosys.com/shop/plasmadive-mini.

The following risk and safety phrases apply to components of PlasmaDive™ Mini Kit.
10X Dilution Buffer: Harmful if swallowed.
Alkylation Solution: Toxic if swallowed, may cause allergy or asthma symptoms or

breathing difficulties if inhaled, may cause an allergic skin reaction, may cause long
lasting harmful effects to aquatic life.

Dissolution Buffer: Highly flammable liquid and vapour, causes serious eye irritation.
Reduction Stock Solution: Harmful if swallowed, causes skin and eye irritation, may

cause respiratory irritation.

Second Edition, Version 2.03

April 2017

PlasmaDive™ Mini Manual, © Biognosys AG, Switzerland

Page 5 of 22

Introduction: PlasmaDive™ Mini Assay Panel at a Glance

Blood is the most frequently used biological sample in clinical research and routine
laboratory diagnostics. Levels of blood proteins reflect the health status of single
organs and the body as a whole. Changes in composition of proteins 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 possible to
recognize the “Big Picture” and explain pathological processes going on in the body.

The PlasmaDive™ Mini Assay Panel was designed for targeted proteomics
approaches - Multiple Reaction Monitoring (MRM, also called SRM) or Parallel
Reaction Monitoring (PRM) - which focus on quantifying predefined sets of proteins
with high sensitivity and reproducibility. Biognosys is unique in its ability to perform
scheduled highly multiplexed MRM and PRM measurements based on its innovative
iRT concept and its specifically developed signal processing software – SpectroDive™.
Both, iRT and SpectroDive™, are integral parts of Biognosys’ Assay Panels.

The PlasmaDive™ Mini Assay Panel optimally combines 100 peptide MRM or PRM
assays in one scheduled multiplexed method. Each peptide is representative of a
human plasma protein (Table 1). The PlasmaDive™ Mini workflow requires as little as
10 µl of plasma and 48 hours to provide actionable clinically-relevant data.

Table 1. List of proteins quantified with PlasmaDive™ Mini Assay Panel

UniPot ID

Entry Name

Protein Name

P02763

A1AG1_HUMAN

Alpha-1-acid glycoprotein 1 (Orosomucoid-1)

P19652

A1AG2_HUMAN

Alpha-1-acid glycoprotein 2 (Orosomucoid-2)

P01009

A1AT_HUMAN

Alpha-1-antitrypsin

P04217

A1BG_HUMAN

Alpha-1B-glycoprotein

P08697

A2AP_HUMAN

Alpha-2-antiplasmin (Serpin F2)

P02750

A2GL_HUMAN

Leucine-rich alpha-2-glycoprotein (LRG)

P01023

A2MG_HUMAN

Alpha-2-macroglobulin (Alpha-2-M)

P01011

AACT_HUMAN

Alpha-1-antichymotrypsin (ACT)

P43652

AFAM_HUMAN

Afamin (Alpha-albumin)

P02768

ALBU_HUMAN

Serum albumin

P35858

ALS_HUMAN

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

P02760

AMBP_HUMAN

Protein AMBP

P01019

ANGT_HUMAN

Angiotensinogen (Serpin A8)

P01008

ANT3_HUMAN

Antithrombin-III (Serpin C1)

P02647

APOA1_HUMAN

Apolipoprotein A-I

P02652

APOA2_HUMAN

Apolipoprotein A-II

P06727

APOA4_HUMAN

Apolipoprotein A-IV

P04114

APOB_HUMAN

Apolipoprotein B-100

P02654

APOC1_HUMAN

Apolipoprotein C-I

P02655

APOC2_HUMAN

Apolipoprotein C-II

P02656

APOC3_HUMAN

Apolipoprotein C-III

P05090

APOD_HUMAN

Apolipoprotein D

P02649

APOE_HUMAN

Apolipoprotein E

P02749

APOH_HUMAN

Apolipoprotein H

O14791

APOL1_HUMAN

Apolipoprotein L1

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O95445

APOM_HUMAN

Apolipoprotein M

P43251

BTD_HUMAN

Biotinidase

P02745

C1QA_HUMAN

Complement C1q subcomponent subunit A

P02746

C1QB_HUMAN

Complement C1q subcomponent subunit B

P02747

C1QC_HUMAN

Complement C1q subcomponent subunit C

P00736

C1R_HUMAN

Complement C1r subcomponent

P09871

C1S_HUMAN

Complement C1s subcomponent

P04003

C4BPA_HUMAN

C4b-binding protein alpha chain

P08185

CBG_HUMAN

Corticosteroid-binding globulin (Serpin A6)

O43866

CD5L_HUMAN

CD5 antigen-like (CT-2) (SP-alpha)

P00450

CERU_HUMAN

Ceruloplasmin (Ferroxidase)

P00751

CFAB_HUMAN

Complement factor B

P08603

CFAH_HUMAN

Complement factor H (H factor 1)

P05156

CFAI_HUMAN

Complement factor I

P06276

CHLE_HUMAN

Cholinesterase (EC 3.1.1.8)

P10909

CLUS_HUMAN

Clusterin (Aging-associated gene 4 protein)
(Apolipoprotein J)

P06681

CO2_HUMAN

Complement C2

P01024

CO3_HUMAN

Complement C3

P0C0L4

CO4A_HUMAN

Complement C4-A

P01031

CO5_HUMAN

Complement C5

P07357

CO8A_HUMAN

Complement component C8 alpha chain

P02748

CO9_HUMAN

Complement component C9

P02775

CXCL7_HUMAN

Platelet basic protein (C-X-C motif chemokine 7)

P00488

F13A_HUMAN

Coagulation factor XIII A chain

P05160

F13B_HUMAN

Coagulation factor XIII B chain

P00742

FA10_HUMAN

Coagulation factor X

P00740

FA9_HUMAN

Coagulation factor IX

P23142

FBLN1_HUMAN

Fibulin-1

P02765

FETUA_HUMAN

Alpha-2-HS-glycoprotein

Q9UGM5

FETUB_HUMAN

Fetuin-B

P02671

FIBA_HUMAN

Fibrinogen alpha chain

P02679

FIBG_HUMAN

Fibrinogen gamma chain

P02751

FINC_HUMAN

Fibronectin (FN)

P06396

GELS_HUMAN

Gelsolin (Actin-depolymerizing factor)

P22352

GPX3_HUMAN

Glutathione peroxidase 3

P68871

HBB_HUMAN

Hemoglobin subunit beta

P02042

HBD_HUMAN

Hemoglobin subunit delta (Delta-globin)

P02790

HEMO_HUMAN

Hemopexin (Beta-1B-glycoprotein)

P05546

HEP2_HUMAN

Heparin cofactor 2

P00738

HPT_HUMAN

Haptoglobin

P00739

HPTR_HUMAN

Haptoglobin-related protein

P04196

HRG_HUMAN

Histidine-rich glycoprotein

P05155

IC1_HUMAN

Plasma protease C1 inhibitor

P01876

IGHA1_HUMAN

Ig alpha-1 chain C region

P01877

IGHA2_HUMAN

Ig alpha-2 chain C region

P01857

IGHG1_HUMAN

Ig gamma-1 chain C region

P01859

IGHG2_HUMAN

Ig gamma-2 chain C region

P01860

IGHG3_HUMAN

Ig gamma-3 chain C region (HDC)

P01871

IGHM_HUMAN

Ig mu chain C region

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PlasmaDive™ Mini Manual, © Biognosys AG, Switzerland

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P05154

IPSP_HUMAN

Plasma serine protease inhibitor

P19827

ITIH1_HUMAN

Inter-alpha-trypsin inhibitor heavy chain H1

P19823

ITIH2_HUMAN

Inter-alpha-trypsin inhibitor heavy chain H2

Q14624

ITIH4_HUMAN

Inter-alpha-trypsin inhibitor heavy chain H4

P29622

KAIN_HUMAN

Kallistatin (Kallikrein inhibitor)

P03952

KLKB1_HUMAN

Plasma kallikrein

P01042

KNG1_HUMAN

Kininogen-1

P36955

PEDF_HUMAN

Pigment epithelium-derived factor (PEDF)

Q96PD5

PGRP2_HUMAN

N-acetylmuramoyl-L-alanine amidase

P02776

PLF4_HUMAN

Platelet factor 4 (Oncostatin-A)

P00747

PLMN_HUMAN

Plasminogen

P27169

PON1_HUMAN

Serum paraoxonase

Q92954

PRG4_HUMAN

Proteoglycan 4

P02753

RET4_HUMAN

Retinol-binding protein 4

P35542

SAA4_HUMAN

Serum amyloid A-4 protein

P49908

SEPP1_HUMAN

Selenoprotein P

P04278

SHBG_HUMAN

Sex hormone-binding globulin

P05452

TETN_HUMAN

Tetranectin

P05543

THBG_HUMAN

Thyroxine-binding globulin (Serpin A7)

P00734

THRB_HUMAN

Prothrombin

P02787

TRFE_HUMAN

Serotransferrin

P02766

TTHY_HUMAN

Transthyretin

P02774

VTDB_HUMAN

Vitamin D-binding protein

P04004

VTNC_HUMAN

Vitronectin

P04275

VWF_HUMAN

von Willebrand factor

P25311

ZA2G_HUMAN

Zinc-alpha-2-glycoprotein

Important Notes before Start

Before starting with the sample preparation, read through the steps carefully and make
sure all the required reagents and equipment are available.

Use minimally LC-grade solvents and water throughout the protocol to prepare buffers
and solutions.

The kit components are sufficient for 20 human plasma samples.

Sample Requirements

Human plasma or serum, 10 µl per sample.
Reserve one suitable sample for calibration run. If it is not possible to dedicate one

sample for a calibration run, a separate LC-MS sample for calibration can be prepared
following instructions in Section E of Sample Preparation Procedure & LC-MRM/PRM
Analysis.