The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools.
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The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools.

Posted By: Jackson Roberts , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ,

Tandem mass spectrometry (MS/MS) is often used within the identification of peptides and proteins. Typical <em>proteomic</em> experiments depend on algorithms corresponding to SEQUEST and MASCOT to match hundreds of tandem mass spectra towards the theoretical fragment ion spectra of peptides in a database. The chances that these spectrum-to-sequence assignments are appropriate may be decided by statistical <em>software program</em> corresponding to PeptideProphet or by estimations based mostly on reverse or decoy databases. Nonetheless, most of the <em>software program</em> functions that assign possibilities for MS/MS spectra to sequence matches have been developed utilizing coaching knowledge units from <em>3D</em> ion-trap mass spectrometers.

Given the number of forms of mass spectrometers which have turn out to be commercially out there over the past 5 years, we sought to generate a knowledge set of reference knowledge protecting a number of instrumentation platforms to facilitate each the refinement of present computational approaches and the event of novel <em>software program</em> instruments. We analyzed the proteolytic peptides in a mix of tryptic digests of 18 proteins, named the “ISB commonplace protein combine”, utilizing eight completely different mass spectrometers. These embody linear and <em>3D</em> ion traps, two quadrupole time-of-flight platforms (qq-TOF), and two MALDI-TOF-TOF platforms. The ensuing knowledge set, which has been named the Commonplace Protein Combine Database, consists of over 1.1 million spectra in 150+ replicate runs on the mass spectrometers.

We have now developed a software program device known as MassSorter for administrating and analyzing knowledge from peptide mass fingerprinting experiments on proteins with recognized amino acid sequences. It’s meant for small scale mass spectrometry laboratories which can be occupied with posttranslational modifications of recognized proteins. A number of experiments may be in contrast concurrently, and the matched and unmatched peak values are clearly indicated. The hits may be sorted in accordance with m/z values (default) or in accordance with the sequence of the protein. Filters outlined by the consumer can mark autolytic protease peaks and different contaminating peaks (keratins, proteins co-migrating with the protein of curiosity, and so on.).

Comparative analysis of two two-dimensional gel electrophoresis picture evaluation software program functions utilizing synovial fluids from sufferers with joint illness.

The <em>proteomic</em> composition of synovial fluid (SF) might maintain clues to understanding the molecular foundation of arthritis. Nonetheless, the extremely viscous nature and <em>proteomic</em> complexity of SF current a problem when analyzing outcomes obtained by two-dimensional gel electrophoresis (2D-GE). A number of <em>software program</em> functions can be found for analyzing 2D-GE photos. Regardless of inherent strengths and weaknesses, no comparability between these functions has been reported utilizing SF or any human fluid specimens. We evaluated two widespread <em>software program</em> packages–PDQuest and Progenesis Workstation–for spot detection, matching, and quantitation of 2D-GE photos of SF from 4 sufferers with arthritic illness.

Initially, complete 2D-gel photos have been analyzed for spot detection, which recommended that PDQuest is extra constant than Progenesis; nevertheless, PDQuest appeared to require extra consumer intervention than Progenesis. Subsequently, two small areas (spots nicely resolved and spots not nicely resolved) have been chosen from every gel picture, which have been analyzed by the <em>software program</em> for spot detection, matching, quantity, and backbone. These analyses counsel that each instruments can quantify well-resolved spots comparatively constantly when put next with guide spot detection (the “gold commonplace”).

The “<em>3D</em> viewer” possibility supplied by each instruments permits appropriate spot identification and matching. The strengths and weaknesses of those laptop instruments can present steerage within the selection of a specific workstation for figuring out biomarkers of arthritis. Unmatched peaks may be additional analyzed for surprising modifications by searches towards a neighborhood model of the UniMod database. They will also be analyzed for surprising cleavages, a extremely helpful characteristic for proteins that bear maturation by proteolytic cleavage, creating new N- or C-terminals.

Complete understanding of organic techniques requires environment friendly and systematic assimilation of high-throughput datasets within the context of the present data base. A significant limitation within the area of <em>proteomics</em> is the dearth of an acceptable <em>software program</em> platform that may synthesize numerous experimental datasets within the context of the present data base. Right here, we describe a <em>software program</em> platform, termed PROTEOME-<em>3D</em>, that makes use of three important options for systematic evaluation of <em>proteomics</em> knowledge:

creation of a scalable, queryable, personalized database for recognized proteins from revealed literature; graphical instruments for displaying proteome landscapes and developments from a number of large-scale experiments; and interactive knowledge evaluation that facilitates identification of essential networks and pathways. Thus, PROTEOME-<em>3D</em> provides a standardized platform to research high-throughput experimental datasets for the identification of essential gamers in co-regulated pathways and mobile processes.

The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools.

pdb-care (PDB carbohydrate residue verify): a program to help annotation of advanced carbohydrate buildings in PDB information.

Carbohydrates are concerned in quite a lot of basic organic processes and pathological conditions. They due to this fact have a big pharmaceutical and diagnostic potential. Information of the <em>3D</em> construction of glycans is a prerequisite for a whole understanding of their organic capabilities. The biggest supply of biomolecular <em>3D</em> buildings is the Protein Knowledge Financial institution. Nonetheless, about 30% of all 1663 PDB entries (model September 2003) containing carbohydrates comprise errors in glycan description. Sadly, no <em>software program</em> is at present out there which aligns the <em>3D</em> info with the reported assignments. It’s the intention of this work to fill this hole.

Control Magnetic Beads
M1302-1
EUR 98

Protein A Magnetic Beads
6507-1
EUR 262

Protein G Magnetic Beads
6517-1
EUR 262

Protein L Magnetic Beads
6537-1
EUR 294

Anti-Flag magnetic beads
B26101 1 mL
EUR 483
Description: Anti-Flag magnetic beads is based on hydroxyl magnetic beads covalently coupling with mouse IgG1 monoclonal antibody. It is recommended to use for co-immunoprecipitation and protein purification.

Anti-Flag magnetic beads
B26102 5 mL
EUR 1452
Description: Anti-Flag magnetic beads is based on hydroxyl magnetic beads covalently coupling with mouse IgG1 monoclonal antibody. It is recommended to use for co-immunoprecipitation and protein purification.

Anti-HA magnetic beads
B26201 1 mL
EUR 483
Description: Anti-HA magnetic beads kit is based on hydroxyl magnetic beads covalently coupling with high quality mouse IgG2b monoclonal antibody, used for co-immunoprecipitation and protein purification.

Anti-HA magnetic beads
B26202 5 mL
EUR 1452
Description: Anti-HA magnetic beads kit is based on hydroxyl magnetic beads covalently coupling with high quality mouse IgG2b monoclonal antibody, used for co-immunoprecipitation and protein purification.

Anti-Myc magnetic beads
B26301 1 mL
EUR 483
Description: Anti-Myc magnetic beads kit is based on hydroxyl magnetic beads covalently coupling with mouse IgG1 monoclonal antibody.it is recommended to use for co-immunoprecipitation and protein purification.

Anti-Myc magnetic beads
B26302 5 mL
EUR 1452
Description: Anti-Myc magnetic beads kit is based on hydroxyl magnetic beads covalently coupling with mouse IgG1 monoclonal antibody.it is recommended to use for co-immunoprecipitation and protein purification.

Anti-HA Magnetic Beads
HY-K0201 1 mL
EUR 279

Protein A Magnetic Beads
HY-K0203 1 mL
EUR 124

Protein G Magnetic Beads
HY-K0204 5 mL
EUR 371

Anti-Flag Magnetic Beads
HY-K0207 1 mL
EUR 475

Protein A/G Magnetic Beads
6527-1
EUR 294

Protein A/G Magnetic Beads
HY-K0202 1 mL
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Anti-c-Myc Magnetic Beads
HY-K0206 5 mL
EUR 1140

Magnetic Beads (DNA) 30 mL
P920-30 NULL
EUR 0

Magnetic Beads (DNA) 450 mL
P920-450 NULL
EUR 0

Magnetic Beads (DNA) 5 mL
P920-5 NULL
EUR 0

Magnetic Beads (DNA) 60 mL
P920-60 NULL
EUR 0

Magnetic Beads for DNA Purification
M1502-5 5 ml
EUR 277

Protein A/G/L Magnetic Beads
6547-1
EUR 338

Protein A/G Magnetic Beads for IP
B23201 1 ml
EUR 132
Description: Protein A/G Magnetic Beads for immunoprecipitation (IP) are based on a biological nanosurface technology (S-TEC). Protein A/G coats the surface of super paramagnetic microspheres with high coating density up to 9.3 × 10^13 molecules/cm2. Compared to similar immune magnetic beads, our Protein A/G beads display much more antibody binding sites therefore using less magnetic beads per reaction and ultimately achiving greater cost-efficiency. Non-specific binding is reduced to an absolute low eliminating any detectable interference with your IP assays. The large, specific surface area of the beads greatly shortens the adsorption time and achieves complete antibody/antigen adsorption process in 10 minutes and complete total purification and precipitation in just 30 minutes. This product can be used on a wide variety of samples, such as in cell lysates, supernatants collected from cell secretion, serum, ascites, and other immune antigens.

Protein A/G Magnetic Beads for IP
B23202 5 ml
EUR 465
Description: Protein A/G Magnetic Beads for immunoprecipitation (IP) are based on a biological nanosurface technology (S-TEC). Protein A/G coats the surface of super paramagnetic microspheres with high coating density up to 9.3 × 10^13 molecules/cm2. Compared to similar immune magnetic beads, our Protein A/G beads display much more antibody binding sites therefore using less magnetic beads per reaction and ultimately achiving greater cost-efficiency. Non-specific binding is reduced to an absolute low eliminating any detectable interference with your IP assays. The large, specific surface area of the beads greatly shortens the adsorption time and achieves complete antibody/antigen adsorption process in 10 minutes and complete total purification and precipitation in just 30 minutes. This product can be used on a wide variety of samples, such as in cell lysates, supernatants collected from cell secretion, serum, ascites, and other immune antigens.

FFPE Tissue DNA Extraction Kit - Magnetic Beads
K5011450 1 kit
EUR 256

Magnetic Beads-conjugated Mouse anti DDDDK-Tag mAb
AE037 50 ul
EUR 176

Trypsin, Recombinant, Proteomics grade
P1228-1000
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Trypsin, Recombinant, Proteomics grade
P1228-10000
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Trypsin, Recombinant, Proteomics grade
P1228-5000
EUR 615

Human Complement Component 4 (C4) ELISA Kit
DLR-C4-Hu-48T 48T
EUR 479
  • Should the Human Complement Component 4 (C4) ELISA Kit is proven to show malperformance, you will receive a refund or a free replacement.
Description: A sandwich quantitative ELISA assay kit for detection of Human Complement Component 4 (C4) in samples from serum, plasma, tissue homogenates, cell lysates, cell culture supernates or other biological fluids.

Human Complement Component 4 (C4) ELISA Kit
DLR-C4-Hu-96T 96T
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  • Should the Human Complement Component 4 (C4) ELISA Kit is proven to show malperformance, you will receive a refund or a free replacement.
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Mouse Complement Component 4 (C4) ELISA Kit
DLR-C4-Mu-48T 48T
EUR 489
  • Should the Mouse Complement Component 4 (C4) ELISA Kit is proven to show malperformance, you will receive a refund or a free replacement.
Description: A sandwich quantitative ELISA assay kit for detection of Mouse Complement Component 4 (C4) in samples from serum, plasma or other biological fluids.

Mouse Complement Component 4 (C4) ELISA Kit
DLR-C4-Mu-96T 96T
EUR 635
  • Should the Mouse Complement Component 4 (C4) ELISA Kit is proven to show malperformance, you will receive a refund or a free replacement.
Description: A sandwich quantitative ELISA assay kit for detection of Mouse Complement Component 4 (C4) in samples from serum, plasma or other biological fluids.

Rat Complement Component 4 (C4) ELISA Kit
DLR-C4-Ra-48T 48T
EUR 508
  • Should the Rat Complement Component 4 (C4) ELISA Kit is proven to show malperformance, you will receive a refund or a free replacement.
Description: A sandwich quantitative ELISA assay kit for detection of Rat Complement Component 4 (C4) in samples from serum, plasma, tissue homogenates, cell lysates, cell culture supernates or other biological fluids.

Rat Complement Component 4 (C4) ELISA Kit
DLR-C4-Ra-96T 96T
EUR 661
  • Should the Rat Complement Component 4 (C4) ELISA Kit is proven to show malperformance, you will receive a refund or a free replacement.
Description: A sandwich quantitative ELISA assay kit for detection of Rat Complement Component 4 (C4) in samples from serum, plasma, tissue homogenates, cell lysates, cell culture supernates or other biological fluids.

Human Complement Component 4 (C4) ELISA Kit
RDR-C4-Hu-48Tests 48 Tests
EUR 500

Human Complement Component 4 (C4) ELISA Kit
RDR-C4-Hu-96Tests 96 Tests
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Mouse Complement Component 4 (C4) ELISA Kit
RDR-C4-Mu-48Tests 48 Tests
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Mouse Complement Component 4 (C4) ELISA Kit
RDR-C4-Mu-96Tests 96 Tests
EUR 709

Human Complement Component 4 (C4) ELISA Kit
RD-C4-Hu-48Tests 48 Tests
EUR 478

Human Complement Component 4 (C4) ELISA Kit
RD-C4-Hu-96Tests 96 Tests
EUR 662

Mouse Complement Component 4 (C4) ELISA Kit
RD-C4-Mu-48Tests 48 Tests
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Mouse Complement Component 4 (C4) ELISA Kit
RD-C4-Mu-96Tests 96 Tests
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D1131-01 1 PC
EUR 238.13
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Bulk Beads
D1131-10 1 PC
EUR 410.39
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Bulk Beads
D1132-01TP 1 PC
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D1132-05TP 1 PC
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D1132-10TP 1 PC
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D1132-15TP 1 PC
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D1132-30TP 1 PC
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D1132-60 1 PC
EUR 241.61
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D1133-28 1 PC
EUR 93.71
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Latex Beads
abx291003-1L 1 L
EUR 2332
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RNA Beads
20-abx298002
  • EUR 217.00
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  • EUR 1386.00
  • 1 ml
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Exorose Beads
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EXOB-25 25 ml
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EXOB-250 250 ml
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Streptavidin-Sepharose Beads
6565-10
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6568-300
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Refill Glass Beads
B1201-BEAD 1 PC
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7925-1
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7926-1
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7927-1
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7927-25
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7927-5
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Immobilized Catalase Beads
7931-1
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Calmodulin-Sepharose Beads
7934-1
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Calmodulin-Sepharose Beads
7934-10
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Calmodulin-Sepharose Beads
7934-5
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V5 agarose beads
AE029-100ul 100 ul Ask for price

V5 agarose beads
AE029-200ul 200 ul
EUR 228

V5 agarose beads
AE029-20ul 20 ul Ask for price

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Glass Beads 0.1mm
GB01 1pack
EUR 108
Description: Glass beads. 0.1mm. 1 lb. Non-sterile.

Glass Beads 0.5mm
GB05 1pack
EUR 103
Description: Glass beads. 0.5mm. 1 lb. Non-sterile.

Glass Beads 1.0mm
GB10 1pack
EUR 103
Description: Glass beads. 1.0mm. 1 lb. Non-sterile.

RanBP1 Agarose Beads
STA-421 400 µg
EUR 572
Description: RanBP1 Agarose Beads selectively pull down the active form of Ran. Beads are colored to allow for a visual check. These are the same beads supplied with our Small GTPase Activation Assays. 400 µg.

Sodium hydroxide, Beads
SB6789 500g
EUR 61.01
  • Product category: Biochemicals/Adsorbents/Drying Agents/Adsorbents

Bovine C4/ Complement C4 ELISA Kit
E0044Bo 1 Kit
EUR 717

Rat C4/ Complement C4 ELISA Kit
E1056Ra 1 Kit
EUR 571

C4 Antibody
49604-100ul 100ul
EUR 333

C4 Antibody
49604-50ul 50ul
EUR 239

C4 siRNA
20-abx909861
  • EUR 551.00
  • EUR 732.00
  • 15 nmol
  • 30 nmol
  • Shipped within 5-10 working days.

Calibration Beads for MoFlo
B28479
EUR 289
Description: Please reffer to the technical data sheet for more detail information for this item. Our dedicated team would be happy to assist you via live chat, email or phone.

Size Selection DNA Beads
20-abx298001
  • EUR 217.00
  • EUR 398.00
  • EUR 1386.00
  • 1 ml
  • 5 ml
  • 60 ml
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VAHTS mRNA Capture Beads
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VAHTS DNA Clean Beads
N411-01 5 ml
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VAHTS DNA Clean Beads
N411-02 60 ml
EUR 529

VAHTS DNA Clean Beads
N411-03 450 ml
EUR 2546

VAHTS RNA Clean Beads
N412-01 5 ml
EUR 239

VAHTS RNA Clean Beads
N412-02 40 ml
EUR 413

VAHTS RNA Clean Beads
N412-03 450 ml
EUR 4050

Stainless Steel Beads 0.2mm
SSB02 1pack
EUR 191
Description: Stainless steel beads. 0.2mm. 1 lb. Non-sterile.

Stainless Steel Beads 0.5mm
SSB05 1pack
EUR 191
Description: Stainless steel beads. 0.5mm. 1 lb. Non-sterile.

Stainless Steel Beads 1.6mm
SSB16 1pack
EUR 254
Description: Stainless steel beads. 1.6mm. 1 lb. Non-sterile.

Stainless Steel Beads 2.3mm
SSB23 1pack
EUR 217
Description: Stainless steel beads. 2.3mm. 1 lb. Non-sterile.

Stainless Steel Beads 3.2mm
SSB32 1pack
EUR 184
Description: Stainless steel beads. 3.2mm. 1 lb. Non-sterile.

Stainless Steel Beads 4.8mm
SSB48 1pack
EUR 184
Description: Stainless steel beads. 4.8mm. 1 lb. Non-sterile.

Stainless Steel Beads 6.0mm
SSB60 1pack
EUR 186
Description: Stainless steel beads. 6.0mm. 1 lb. Non-sterile.

PAK1 PBD Agarose Beads
STA-411 400 ?g
EUR 572
Description: PAK1 PBD Agarose Beads selectively pull down the active form of Rac and Cdc42. Beads are colored to allow for a visual check. These are the same beads supplied with our Small GTPase Activation Assays. 400 µg.

Rhotekin RBD Agarose Beads
STA-412 400 ?g
EUR 572
Description: Rhotekin RBD Agarose Beads selectively pull down the active form of Rho. Beads are colored to allow for a visual check. These are the same beads supplied with our Small GTPase Activation Assays. 400 µg.

RalGDS RBD Agarose Beads
STA-418 400 µg
EUR 572
Description: RalGDS RBD Agarose Beads selectively pull down the active form of Rap. Beads are colored to allow for a visual check. These are the same beads supplied with our Small GTPase Activation Assays. 400 µg.

GGA3 PBD Agarose Beads
STA-419 400 µg
EUR 572
Description: GGA3 PBD Agarose Beads selectively pull down the active form of Arf. Beads are colored to allow for a visual check. These are the same beads supplied with our Small GTPase Activation Assays. 400 µg.

RalBP1 PBD Agarose Beads
STA-420 400 µg
EUR 572
Description: RalBP1 RBD Agarose Beads selectively pull down the active form of Ral. Beads are colored to allow for a visual check. These are the same beads supplied with our Small GTPase Activation Assays. 400 µg.

Zirconium Oxide Beads 0.15mm
ZrOB015 1pack
EUR 158
Description: Fused Zirconium Oxide beads . 0.15mm. 1 lb. Non-sterile.

Zirconium Oxide Beads 0.5mm
ZrOB05 1pack
EUR 158
Description: Zirconium Oxide beads . 0.5mm. 1 lb. Non-sterile.

Zirconium Oxide Beads 1.0mm
ZrOB10 1pack
EUR 158
Description: Zirconium Oxide beads . 1.0mm. 1 lb. Non-sterile.

Zirconium Oxide Beads 2.0mm
ZrOB20 1pack
EUR 158
Description: Zirconium Oxide beads . 2.0mm. 1 lb. Non-sterile.

Zirconium Oxide Beads 2.5mm
ZrOB25 1pack
EUR 158
Description: Zirconium Oxide beads . 2.5mm. 1 lb. Non-sterile.

Zirconium Silicate Beads 0.5mm
ZSB05 1pack
EUR 122
Description: Zirconium Silicate beads . 0.5mm. 1 lb. Non-sterile.

Zirconium Silicate Beads 1.0mm
ZSB10 1pack
EUR 122
Description: Zirconium Silicate beads . 1.0mm. 1 lb. Non-sterile.

Magnetic Separator
B23803 2 mL/200 uL/15 mL
EUR 243
Description: This Magnetic Separator is a proprietary machine, supportinga the magnetic beads series of products. A core tenent is the use of a superior magnetic, to ensure that magnetic separation step can be completed in a short time.

Magnetic Stirrer
abx725038-1Unit 1 Unit
EUR 432
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Magnetic Stand
abx799001-1Unit 1 Unit
EUR 258
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Magnetic Stirrer
H3760-SE 1 PC
EUR 101.54
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Magnetic Stirrer
H4000-S-E 1 PC
EUR 81.02
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Magnetic Stand
HY-K0200 200 μL-2 mL-15 mL
EUR 380

Magnetic Separator
MagSep1-1 1/pk
EUR 110

AlbuVoidâ„¢ LC-MS On-Bead For Serum Proteomics
AVB-MS05 5 preps
EUR 379
Description: Albumin Removal Kit

AlbuVoidâ„¢ LC-MS On-Bead For Serum Proteomics
AVB-MS10 10 preps
EUR 521
Description: Albumin Removal Kit

HemoVoidâ„¢ LC-MS On-Bead For Erythrocytes Proteomics
HVB-MS05 5 preps
EUR 379
Description: Hemoglobin Removal Kit

HemoVoidâ„¢ LC-MS On-Bead For Erythrocytes Proteomics
HVB-MS10 10 preps
EUR 521
Description: Hemoglobin Removal Kit

Human Leukotriene C4,LT-C4 ELISA Kit
201-12-1515 96 tests
EUR 440
  • This Leukotriene C4 ELISA kit is validated to work with samples from whole blood, serum, plasma and cell culture supernatant.
Description: A quantitative ELISA kit for measuring Human in samples from biological fluids.

Mouse Apolipoprotein C4 (APO-C4) CLIA Kit
abx195176-96tests 96 tests
EUR 825
  • Shipped within 5-12 working days.

LT-C4/ Rat LT- C4 ELISA Kit
ELA-E0619r 96 Tests
EUR 886

Rat Leukotriene C4,LT-C4 ELISA Kit
CN-01799R1 96T
EUR 455

Monkey Leukotriene C4,LT-C4 ELISA Kit
CN-02241M1 96T
EUR 471

Mouse Leukotriene C4,LT-C4 ELISA Kit
CN-02678M1 96T
EUR 439

Mouse Leukotriene C4,LT-C4 ELISA Kit
CN-02678M2 48T
EUR 290

Mouse APO-C4(Apolipoprotein C4) ELISA Kit
EM0845 96T
EUR 476.25
  • Detection range: 0.313-20 ng/ml
  • Uniprot ID: Q61268
  • Alias: Apo-C4(Apolipoprotein C4)/Apolipoprotein C-IV/APO-CIV/APOC-IV
Description: Method of detection: Double Antibody, Sandwich ELISA;Reacts with: Mus ;Sensitivity: 0.188 ng/ml

Human Leukotriene C4(LT-C4)ELISA Kit
GA-E1531HM-48T 48T
EUR 289

Human Leukotriene C4(LT-C4)ELISA Kit
GA-E1531HM-96T 96T
EUR 466

Mouse Leukotriene C4(LT-C4)ELISA Kit
GA-E0511MS-48T 48T
EUR 336

Mouse Leukotriene C4(LT-C4)ELISA Kit
GA-E0511MS-96T 96T
EUR 534

Rat Leukotriene C4(LT-C4)ELISA Kit
GA-E0148RT-48T 48T
EUR 317

Trying up a translation desk the place systematic names and the respective PDB residue codes are listed, each assignments are in contrast and inconsistencies are reported. Moreover, the reliability of reported and calculated connectivities for molecules listed inside the HETATOM information is checked and strange values are reported.