reversed-phase protein captrap column Search Results


peptide captrap  (Michrom)
90
Michrom peptide captrap
Peptide Captrap, supplied by Michrom, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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reversed-phase protein captrap column  (Michrom)
90
Michrom reversed-phase protein captrap column
Reversed Phase Protein Captrap Column, supplied by Michrom, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 90 stars, based on 1 article reviews
reversed-phase protein captrap column - by Bioz Stars, 2026-02
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reverse phase peptide c18 captrap  (Bruker Corporation)
90
Bruker Corporation reverse phase peptide c18 captrap
Reverse Phase Peptide C18 Captrap, supplied by Bruker Corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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reverse phase peptide c18 trap bruker peptide captrap  (Bruker Corporation)
90
Bruker Corporation reverse phase peptide c18 trap bruker peptide captrap
Blood-based multi-analyte proteomic signature discovery workflow: a A total of 100 age- and sex-matched EDTA-plasma samples were procured [n = 20 per stage I, II, III, IV, and n = 20 healthy controls (non-menopausal, non-smoking and no history of any cancers)]. b Plasma samples were collected as per ethics requirements. To create a plasma reference library, equal volumes of all patients and healthy plasmas were pooled. For the SWATH experiments, equal volumes of 20 plasma samples were combined to produce pools of each of the 4 CRC stages (I–IV) and healthy controls. c For library generation, HAPs depleted using MARS-14 column (Agilent) followed by tryptic digestion and peptide fractionation by SAX, SCX, SEC and HpH (independently), followed by IDA-MS analysis. d The stage pooled samples were processed through four different experiments (three, where the plasma HAP were depleted and one where it was not). The resulting proteins were digested and subjected to SWATH-MS. Lists of quantifiable proteins were extracted from the SWATH dataset using the peptide library generated in c . e Differentially expressed proteins were first identified using ANOVA/t-test (p-value < 0.05, fold change cut off ± 1.5), resulting in 37 proteins exhibited with differential expression across all CRC stages compared to healthy controls. These 37 proteins were further evaluated by unsupervised clustering method to increase discriminatory power. Differentially expressed proteins were subjected to validation pipeline where they were checked to identify evidence in the literature, followed by experimental validation (ELISA/Western blotting) of a subset that seemed most promising. Concurrently, the samples also underwent a supervised classification method which identified potential candidates which were then validated with an augmented dataset (with a SD 10 times the observed variance). This resulted in a subset of 5 candidate proteins that were able to classify the different stages of the disease. SAX strong anion exchange, SCX strong cation exchange, SEC size exclusion chromatography, HpH high pH reversed phased <t>c18,</t> SWATH sequential window acquisition of all theoretical mass spectra, IDA-MS information-dependent acquisition mass spectrometry, SD standard deviation, HAPs high abundant proteins
Reverse Phase Peptide C18 Trap Bruker Peptide Captrap, supplied by Bruker Corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/reverse phase peptide c18 trap bruker peptide captrap/product/Bruker Corporation
Average 90 stars, based on 1 article reviews
reverse phase peptide c18 trap bruker peptide captrap - by Bioz Stars, 2026-02
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sample trap captrap  (Michrom)
90
Michrom sample trap captrap
Blood-based multi-analyte proteomic signature discovery workflow: a A total of 100 age- and sex-matched EDTA-plasma samples were procured [n = 20 per stage I, II, III, IV, and n = 20 healthy controls (non-menopausal, non-smoking and no history of any cancers)]. b Plasma samples were collected as per ethics requirements. To create a plasma reference library, equal volumes of all patients and healthy plasmas were pooled. For the SWATH experiments, equal volumes of 20 plasma samples were combined to produce pools of each of the 4 CRC stages (I–IV) and healthy controls. c For library generation, HAPs depleted using MARS-14 column (Agilent) followed by tryptic digestion and peptide fractionation by SAX, SCX, SEC and HpH (independently), followed by IDA-MS analysis. d The stage pooled samples were processed through four different experiments (three, where the plasma HAP were depleted and one where it was not). The resulting proteins were digested and subjected to SWATH-MS. Lists of quantifiable proteins were extracted from the SWATH dataset using the peptide library generated in c . e Differentially expressed proteins were first identified using ANOVA/t-test (p-value < 0.05, fold change cut off ± 1.5), resulting in 37 proteins exhibited with differential expression across all CRC stages compared to healthy controls. These 37 proteins were further evaluated by unsupervised clustering method to increase discriminatory power. Differentially expressed proteins were subjected to validation pipeline where they were checked to identify evidence in the literature, followed by experimental validation (ELISA/Western blotting) of a subset that seemed most promising. Concurrently, the samples also underwent a supervised classification method which identified potential candidates which were then validated with an augmented dataset (with a SD 10 times the observed variance). This resulted in a subset of 5 candidate proteins that were able to classify the different stages of the disease. SAX strong anion exchange, SCX strong cation exchange, SEC size exclusion chromatography, HpH high pH reversed phased <t>c18,</t> SWATH sequential window acquisition of all theoretical mass spectra, IDA-MS information-dependent acquisition mass spectrometry, SD standard deviation, HAPs high abundant proteins
Sample Trap Captrap, supplied by Michrom, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 90 stars, based on 1 article reviews
sample trap captrap - by Bioz Stars, 2026-02
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q-tof 2 mass spectrometer  (Micromass UK Limited)
90
Micromass UK Limited q-tof 2 mass spectrometer
Blood-based multi-analyte proteomic signature discovery workflow: a A total of 100 age- and sex-matched EDTA-plasma samples were procured [n = 20 per stage I, II, III, IV, and n = 20 healthy controls (non-menopausal, non-smoking and no history of any cancers)]. b Plasma samples were collected as per ethics requirements. To create a plasma reference library, equal volumes of all patients and healthy plasmas were pooled. For the SWATH experiments, equal volumes of 20 plasma samples were combined to produce pools of each of the 4 CRC stages (I–IV) and healthy controls. c For library generation, HAPs depleted using MARS-14 column (Agilent) followed by tryptic digestion and peptide fractionation by SAX, SCX, SEC and HpH (independently), followed by IDA-MS analysis. d The stage pooled samples were processed through four different experiments (three, where the plasma HAP were depleted and one where it was not). The resulting proteins were digested and subjected to SWATH-MS. Lists of quantifiable proteins were extracted from the SWATH dataset using the peptide library generated in c . e Differentially expressed proteins were first identified using ANOVA/t-test (p-value < 0.05, fold change cut off ± 1.5), resulting in 37 proteins exhibited with differential expression across all CRC stages compared to healthy controls. These 37 proteins were further evaluated by unsupervised clustering method to increase discriminatory power. Differentially expressed proteins were subjected to validation pipeline where they were checked to identify evidence in the literature, followed by experimental validation (ELISA/Western blotting) of a subset that seemed most promising. Concurrently, the samples also underwent a supervised classification method which identified potential candidates which were then validated with an augmented dataset (with a SD 10 times the observed variance). This resulted in a subset of 5 candidate proteins that were able to classify the different stages of the disease. SAX strong anion exchange, SCX strong cation exchange, SEC size exclusion chromatography, HpH high pH reversed phased <t>c18,</t> SWATH sequential window acquisition of all theoretical mass spectra, IDA-MS information-dependent acquisition mass spectrometry, SD standard deviation, HAPs high abundant proteins
Q Tof 2 Mass Spectrometer, supplied by Micromass UK Limited, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/q-tof 2 mass spectrometer/product/Micromass UK Limited
Average 90 stars, based on 1 article reviews
q-tof 2 mass spectrometer - by Bioz Stars, 2026-02
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endurance autosampler  (Spark Holland)
90
Spark Holland endurance autosampler
Blood-based multi-analyte proteomic signature discovery workflow: a A total of 100 age- and sex-matched EDTA-plasma samples were procured [n = 20 per stage I, II, III, IV, and n = 20 healthy controls (non-menopausal, non-smoking and no history of any cancers)]. b Plasma samples were collected as per ethics requirements. To create a plasma reference library, equal volumes of all patients and healthy plasmas were pooled. For the SWATH experiments, equal volumes of 20 plasma samples were combined to produce pools of each of the 4 CRC stages (I–IV) and healthy controls. c For library generation, HAPs depleted using MARS-14 column (Agilent) followed by tryptic digestion and peptide fractionation by SAX, SCX, SEC and HpH (independently), followed by IDA-MS analysis. d The stage pooled samples were processed through four different experiments (three, where the plasma HAP were depleted and one where it was not). The resulting proteins were digested and subjected to SWATH-MS. Lists of quantifiable proteins were extracted from the SWATH dataset using the peptide library generated in c . e Differentially expressed proteins were first identified using ANOVA/t-test (p-value < 0.05, fold change cut off ± 1.5), resulting in 37 proteins exhibited with differential expression across all CRC stages compared to healthy controls. These 37 proteins were further evaluated by unsupervised clustering method to increase discriminatory power. Differentially expressed proteins were subjected to validation pipeline where they were checked to identify evidence in the literature, followed by experimental validation (ELISA/Western blotting) of a subset that seemed most promising. Concurrently, the samples also underwent a supervised classification method which identified potential candidates which were then validated with an augmented dataset (with a SD 10 times the observed variance). This resulted in a subset of 5 candidate proteins that were able to classify the different stages of the disease. SAX strong anion exchange, SCX strong cation exchange, SEC size exclusion chromatography, HpH high pH reversed phased <t>c18,</t> SWATH sequential window acquisition of all theoretical mass spectra, IDA-MS information-dependent acquisition mass spectrometry, SD standard deviation, HAPs high abundant proteins
Endurance Autosampler, supplied by Spark Holland, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 90 stars, based on 1 article reviews
endurance autosampler - by Bioz Stars, 2026-02
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spark holland endurance autosampler  (Spark Holland)
90
Spark Holland spark holland endurance autosampler
Blood-based multi-analyte proteomic signature discovery workflow: a A total of 100 age- and sex-matched EDTA-plasma samples were procured [n = 20 per stage I, II, III, IV, and n = 20 healthy controls (non-menopausal, non-smoking and no history of any cancers)]. b Plasma samples were collected as per ethics requirements. To create a plasma reference library, equal volumes of all patients and healthy plasmas were pooled. For the SWATH experiments, equal volumes of 20 plasma samples were combined to produce pools of each of the 4 CRC stages (I–IV) and healthy controls. c For library generation, HAPs depleted using MARS-14 column (Agilent) followed by tryptic digestion and peptide fractionation by SAX, SCX, SEC and HpH (independently), followed by IDA-MS analysis. d The stage pooled samples were processed through four different experiments (three, where the plasma HAP were depleted and one where it was not). The resulting proteins were digested and subjected to SWATH-MS. Lists of quantifiable proteins were extracted from the SWATH dataset using the peptide library generated in c . e Differentially expressed proteins were first identified using ANOVA/t-test (p-value < 0.05, fold change cut off ± 1.5), resulting in 37 proteins exhibited with differential expression across all CRC stages compared to healthy controls. These 37 proteins were further evaluated by unsupervised clustering method to increase discriminatory power. Differentially expressed proteins were subjected to validation pipeline where they were checked to identify evidence in the literature, followed by experimental validation (ELISA/Western blotting) of a subset that seemed most promising. Concurrently, the samples also underwent a supervised classification method which identified potential candidates which were then validated with an augmented dataset (with a SD 10 times the observed variance). This resulted in a subset of 5 candidate proteins that were able to classify the different stages of the disease. SAX strong anion exchange, SCX strong cation exchange, SEC size exclusion chromatography, HpH high pH reversed phased <t>c18,</t> SWATH sequential window acquisition of all theoretical mass spectra, IDA-MS information-dependent acquisition mass spectrometry, SD standard deviation, HAPs high abundant proteins
Spark Holland Endurance Autosampler, supplied by Spark Holland, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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spark holland endurance autosampler - by Bioz Stars, 2026-02
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nanolc ⋆ 1d  (Eksigent Technologies LLC)
90
Eksigent Technologies LLC nanolc ⋆ 1d
Blood-based multi-analyte proteomic signature discovery workflow: a A total of 100 age- and sex-matched EDTA-plasma samples were procured [n = 20 per stage I, II, III, IV, and n = 20 healthy controls (non-menopausal, non-smoking and no history of any cancers)]. b Plasma samples were collected as per ethics requirements. To create a plasma reference library, equal volumes of all patients and healthy plasmas were pooled. For the SWATH experiments, equal volumes of 20 plasma samples were combined to produce pools of each of the 4 CRC stages (I–IV) and healthy controls. c For library generation, HAPs depleted using MARS-14 column (Agilent) followed by tryptic digestion and peptide fractionation by SAX, SCX, SEC and HpH (independently), followed by IDA-MS analysis. d The stage pooled samples were processed through four different experiments (three, where the plasma HAP were depleted and one where it was not). The resulting proteins were digested and subjected to SWATH-MS. Lists of quantifiable proteins were extracted from the SWATH dataset using the peptide library generated in c . e Differentially expressed proteins were first identified using ANOVA/t-test (p-value < 0.05, fold change cut off ± 1.5), resulting in 37 proteins exhibited with differential expression across all CRC stages compared to healthy controls. These 37 proteins were further evaluated by unsupervised clustering method to increase discriminatory power. Differentially expressed proteins were subjected to validation pipeline where they were checked to identify evidence in the literature, followed by experimental validation (ELISA/Western blotting) of a subset that seemed most promising. Concurrently, the samples also underwent a supervised classification method which identified potential candidates which were then validated with an augmented dataset (with a SD 10 times the observed variance). This resulted in a subset of 5 candidate proteins that were able to classify the different stages of the disease. SAX strong anion exchange, SCX strong cation exchange, SEC size exclusion chromatography, HpH high pH reversed phased <t>c18,</t> SWATH sequential window acquisition of all theoretical mass spectra, IDA-MS information-dependent acquisition mass spectrometry, SD standard deviation, HAPs high abundant proteins
Nanolc ⋆ 1d, supplied by Eksigent Technologies LLC, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/nanolc ⋆ 1d/product/Eksigent Technologies LLC
Average 90 stars, based on 1 article reviews
nanolc ⋆ 1d - by Bioz Stars, 2026-02
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sample trap caprap  (Michrom)
90
Michrom sample trap caprap
Blood-based multi-analyte proteomic signature discovery workflow: a A total of 100 age- and sex-matched EDTA-plasma samples were procured [n = 20 per stage I, II, III, IV, and n = 20 healthy controls (non-menopausal, non-smoking and no history of any cancers)]. b Plasma samples were collected as per ethics requirements. To create a plasma reference library, equal volumes of all patients and healthy plasmas were pooled. For the SWATH experiments, equal volumes of 20 plasma samples were combined to produce pools of each of the 4 CRC stages (I–IV) and healthy controls. c For library generation, HAPs depleted using MARS-14 column (Agilent) followed by tryptic digestion and peptide fractionation by SAX, SCX, SEC and HpH (independently), followed by IDA-MS analysis. d The stage pooled samples were processed through four different experiments (three, where the plasma HAP were depleted and one where it was not). The resulting proteins were digested and subjected to SWATH-MS. Lists of quantifiable proteins were extracted from the SWATH dataset using the peptide library generated in c . e Differentially expressed proteins were first identified using ANOVA/t-test (p-value < 0.05, fold change cut off ± 1.5), resulting in 37 proteins exhibited with differential expression across all CRC stages compared to healthy controls. These 37 proteins were further evaluated by unsupervised clustering method to increase discriminatory power. Differentially expressed proteins were subjected to validation pipeline where they were checked to identify evidence in the literature, followed by experimental validation (ELISA/Western blotting) of a subset that seemed most promising. Concurrently, the samples also underwent a supervised classification method which identified potential candidates which were then validated with an augmented dataset (with a SD 10 times the observed variance). This resulted in a subset of 5 candidate proteins that were able to classify the different stages of the disease. SAX strong anion exchange, SCX strong cation exchange, SEC size exclusion chromatography, HpH high pH reversed phased <t>c18,</t> SWATH sequential window acquisition of all theoretical mass spectra, IDA-MS information-dependent acquisition mass spectrometry, SD standard deviation, HAPs high abundant proteins
Sample Trap Caprap, supplied by Michrom, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 90 stars, based on 1 article reviews
sample trap caprap - by Bioz Stars, 2026-02
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reversed-phase protein captrap michrom bioresources  (Michrom)
90
Michrom reversed-phase protein captrap michrom bioresources
Blood-based multi-analyte proteomic signature discovery workflow: a A total of 100 age- and sex-matched EDTA-plasma samples were procured [n = 20 per stage I, II, III, IV, and n = 20 healthy controls (non-menopausal, non-smoking and no history of any cancers)]. b Plasma samples were collected as per ethics requirements. To create a plasma reference library, equal volumes of all patients and healthy plasmas were pooled. For the SWATH experiments, equal volumes of 20 plasma samples were combined to produce pools of each of the 4 CRC stages (I–IV) and healthy controls. c For library generation, HAPs depleted using MARS-14 column (Agilent) followed by tryptic digestion and peptide fractionation by SAX, SCX, SEC and HpH (independently), followed by IDA-MS analysis. d The stage pooled samples were processed through four different experiments (three, where the plasma HAP were depleted and one where it was not). The resulting proteins were digested and subjected to SWATH-MS. Lists of quantifiable proteins were extracted from the SWATH dataset using the peptide library generated in c . e Differentially expressed proteins were first identified using ANOVA/t-test (p-value < 0.05, fold change cut off ± 1.5), resulting in 37 proteins exhibited with differential expression across all CRC stages compared to healthy controls. These 37 proteins were further evaluated by unsupervised clustering method to increase discriminatory power. Differentially expressed proteins were subjected to validation pipeline where they were checked to identify evidence in the literature, followed by experimental validation (ELISA/Western blotting) of a subset that seemed most promising. Concurrently, the samples also underwent a supervised classification method which identified potential candidates which were then validated with an augmented dataset (with a SD 10 times the observed variance). This resulted in a subset of 5 candidate proteins that were able to classify the different stages of the disease. SAX strong anion exchange, SCX strong cation exchange, SEC size exclusion chromatography, HpH high pH reversed phased <t>c18,</t> SWATH sequential window acquisition of all theoretical mass spectra, IDA-MS information-dependent acquisition mass spectrometry, SD standard deviation, HAPs high abundant proteins
Reversed Phase Protein Captrap Michrom Bioresources, supplied by Michrom, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/reversed-phase protein captrap michrom bioresources/product/Michrom
Average 90 stars, based on 1 article reviews
reversed-phase protein captrap michrom bioresources - by Bioz Stars, 2026-02
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protein captrap (polymeric/reversed phase sorbent  (Microm International GmbH)
90
Microm International GmbH protein captrap (polymeric/reversed phase sorbent
Blood-based multi-analyte proteomic signature discovery workflow: a A total of 100 age- and sex-matched EDTA-plasma samples were procured [n = 20 per stage I, II, III, IV, and n = 20 healthy controls (non-menopausal, non-smoking and no history of any cancers)]. b Plasma samples were collected as per ethics requirements. To create a plasma reference library, equal volumes of all patients and healthy plasmas were pooled. For the SWATH experiments, equal volumes of 20 plasma samples were combined to produce pools of each of the 4 CRC stages (I–IV) and healthy controls. c For library generation, HAPs depleted using MARS-14 column (Agilent) followed by tryptic digestion and peptide fractionation by SAX, SCX, SEC and HpH (independently), followed by IDA-MS analysis. d The stage pooled samples were processed through four different experiments (three, where the plasma HAP were depleted and one where it was not). The resulting proteins were digested and subjected to SWATH-MS. Lists of quantifiable proteins were extracted from the SWATH dataset using the peptide library generated in c . e Differentially expressed proteins were first identified using ANOVA/t-test (p-value < 0.05, fold change cut off ± 1.5), resulting in 37 proteins exhibited with differential expression across all CRC stages compared to healthy controls. These 37 proteins were further evaluated by unsupervised clustering method to increase discriminatory power. Differentially expressed proteins were subjected to validation pipeline where they were checked to identify evidence in the literature, followed by experimental validation (ELISA/Western blotting) of a subset that seemed most promising. Concurrently, the samples also underwent a supervised classification method which identified potential candidates which were then validated with an augmented dataset (with a SD 10 times the observed variance). This resulted in a subset of 5 candidate proteins that were able to classify the different stages of the disease. SAX strong anion exchange, SCX strong cation exchange, SEC size exclusion chromatography, HpH high pH reversed phased <t>c18,</t> SWATH sequential window acquisition of all theoretical mass spectra, IDA-MS information-dependent acquisition mass spectrometry, SD standard deviation, HAPs high abundant proteins
Protein Captrap (Polymeric/Reversed Phase Sorbent, supplied by Microm International GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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protein captrap (polymeric/reversed phase sorbent - by Bioz Stars, 2026-02
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Image Search Results


Blood-based multi-analyte proteomic signature discovery workflow: a A total of 100 age- and sex-matched EDTA-plasma samples were procured [n = 20 per stage I, II, III, IV, and n = 20 healthy controls (non-menopausal, non-smoking and no history of any cancers)]. b Plasma samples were collected as per ethics requirements. To create a plasma reference library, equal volumes of all patients and healthy plasmas were pooled. For the SWATH experiments, equal volumes of 20 plasma samples were combined to produce pools of each of the 4 CRC stages (I–IV) and healthy controls. c For library generation, HAPs depleted using MARS-14 column (Agilent) followed by tryptic digestion and peptide fractionation by SAX, SCX, SEC and HpH (independently), followed by IDA-MS analysis. d The stage pooled samples were processed through four different experiments (three, where the plasma HAP were depleted and one where it was not). The resulting proteins were digested and subjected to SWATH-MS. Lists of quantifiable proteins were extracted from the SWATH dataset using the peptide library generated in c . e Differentially expressed proteins were first identified using ANOVA/t-test (p-value < 0.05, fold change cut off ± 1.5), resulting in 37 proteins exhibited with differential expression across all CRC stages compared to healthy controls. These 37 proteins were further evaluated by unsupervised clustering method to increase discriminatory power. Differentially expressed proteins were subjected to validation pipeline where they were checked to identify evidence in the literature, followed by experimental validation (ELISA/Western blotting) of a subset that seemed most promising. Concurrently, the samples also underwent a supervised classification method which identified potential candidates which were then validated with an augmented dataset (with a SD 10 times the observed variance). This resulted in a subset of 5 candidate proteins that were able to classify the different stages of the disease. SAX strong anion exchange, SCX strong cation exchange, SEC size exclusion chromatography, HpH high pH reversed phased c18, SWATH sequential window acquisition of all theoretical mass spectra, IDA-MS information-dependent acquisition mass spectrometry, SD standard deviation, HAPs high abundant proteins

Journal: Clinical Proteomics

Article Title: Potential early clinical stage colorectal cancer diagnosis using a proteomics blood test panel

doi: 10.1186/s12014-019-9255-z

Figure Lengend Snippet: Blood-based multi-analyte proteomic signature discovery workflow: a A total of 100 age- and sex-matched EDTA-plasma samples were procured [n = 20 per stage I, II, III, IV, and n = 20 healthy controls (non-menopausal, non-smoking and no history of any cancers)]. b Plasma samples were collected as per ethics requirements. To create a plasma reference library, equal volumes of all patients and healthy plasmas were pooled. For the SWATH experiments, equal volumes of 20 plasma samples were combined to produce pools of each of the 4 CRC stages (I–IV) and healthy controls. c For library generation, HAPs depleted using MARS-14 column (Agilent) followed by tryptic digestion and peptide fractionation by SAX, SCX, SEC and HpH (independently), followed by IDA-MS analysis. d The stage pooled samples were processed through four different experiments (three, where the plasma HAP were depleted and one where it was not). The resulting proteins were digested and subjected to SWATH-MS. Lists of quantifiable proteins were extracted from the SWATH dataset using the peptide library generated in c . e Differentially expressed proteins were first identified using ANOVA/t-test (p-value < 0.05, fold change cut off ± 1.5), resulting in 37 proteins exhibited with differential expression across all CRC stages compared to healthy controls. These 37 proteins were further evaluated by unsupervised clustering method to increase discriminatory power. Differentially expressed proteins were subjected to validation pipeline where they were checked to identify evidence in the literature, followed by experimental validation (ELISA/Western blotting) of a subset that seemed most promising. Concurrently, the samples also underwent a supervised classification method which identified potential candidates which were then validated with an augmented dataset (with a SD 10 times the observed variance). This resulted in a subset of 5 candidate proteins that were able to classify the different stages of the disease. SAX strong anion exchange, SCX strong cation exchange, SEC size exclusion chromatography, HpH high pH reversed phased c18, SWATH sequential window acquisition of all theoretical mass spectra, IDA-MS information-dependent acquisition mass spectrometry, SD standard deviation, HAPs high abundant proteins

Article Snippet: Peptides were injected onto a reverse phase peptide C18 trap (Bruker peptide Captrap) for pre-concentration and desalted at a flow rate of 10 μl/min for 5 min with 0.1% formic acid (v/v) and 2% acetonitrile (v/v).

Techniques: Clinical Proteomics, Data-independent acquisition, Peptide Fractionation, Generated, Quantitative Proteomics, Biomarker Discovery, Enzyme-linked Immunosorbent Assay, Western Blot, Size-exclusion Chromatography, Mass Spectrometry, Standard Deviation

SWATH reference library with functional annotations; a Venn diagram comparing a number of common, unshared and shared proteins identified between four peptide fractionation methods used to compile a plasma SWATH library, with b “Anderson curve” superimposed with gene ontology information from plasma proteins identified in the study. The color code bar shown indicated on the right-hand side of b corresponds to various gene ontology characteristics applied to data points shown on the concentration curve. HpH high pH C18 reversed phase separation, SAX strong anion exchange, SEC size exclusion chromatography, SCX strong cation exchange

Journal: Clinical Proteomics

Article Title: Potential early clinical stage colorectal cancer diagnosis using a proteomics blood test panel

doi: 10.1186/s12014-019-9255-z

Figure Lengend Snippet: SWATH reference library with functional annotations; a Venn diagram comparing a number of common, unshared and shared proteins identified between four peptide fractionation methods used to compile a plasma SWATH library, with b “Anderson curve” superimposed with gene ontology information from plasma proteins identified in the study. The color code bar shown indicated on the right-hand side of b corresponds to various gene ontology characteristics applied to data points shown on the concentration curve. HpH high pH C18 reversed phase separation, SAX strong anion exchange, SEC size exclusion chromatography, SCX strong cation exchange

Article Snippet: Peptides were injected onto a reverse phase peptide C18 trap (Bruker peptide Captrap) for pre-concentration and desalted at a flow rate of 10 μl/min for 5 min with 0.1% formic acid (v/v) and 2% acetonitrile (v/v).

Techniques: Data-independent acquisition, Functional Assay, Peptide Fractionation, Clinical Proteomics, Concentration Assay, Size-exclusion Chromatography