Comparison of peptide and protein fractionation methods in proteomics

Mostovenko, Ekaterina; Hassan, Chopie; Rattke, Janine; Deelder, André M.; Veelen, Peter A. van; Palmblad, Magnus

doi:10.1016/j.euprot.2013.09.001

Cited by 50 publications

(48 citation statements)

References 32 publications

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“…Several proteomic studies have documented increased proteome depth by combining data from multiple workflows and/or instrumentation . Combining all our datasets yielded >8700 unique proteins.…”

Section: Resultsmentioning

confidence: 99%

Comparison of sample preparation techniques for large‐scale proteomics

et al. 2017

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Numerous workflows exist for large-scale bottom-up proteomics, many of which achieve exceptional proteome depth. Herein, we evaluated the performance of several commonly used sample preparation techniques for proteomic characterization of HeLa lysates [unfractionated in-solution digests, SDS-PAGE coupled with in-gel digestion, gel-eluted liquid fraction entrapment electrophoresis (GELFrEE) technology, SCX StageTips and high-/low-pH reversed phase fractionation (HpH)]. HpH fractionation was found to be superior in terms of proteome depth (>8400 proteins detected) and fractionation efficiency compared to other techniques. SCX StageTip fractionation required minimal sample handling and was also a substantial improvement over SDS-PAGE separation and GELFrEE technology. Sequence coverage of the HeLa proteome increased to 38% when combining all workflows, however, total proteins detected improved only slightly to 8710. In summary, HpH fractionation and SCX StageTips are robust techniques and highly suited for complex proteome analysis.

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Section: Resultsmentioning

confidence: 99%

Comparison of sample preparation techniques for large‐scale proteomics

et al. 2017

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“…The gel-free approaches include usually liquid chromatographic (LC) separation of proteins preceded in many cases by other off-line separation techniques such as solid-phase extraction or strong cation exchange [35,36]. In typical conditions the LC is coupled on-line with mass spectrometer and the proteins/peptides eluted from an analytical column are directly injected into the mass spectrometer for identification and/or quantification [37].…”

Section: Proteomic Methods Applied For Dr Diagnosismentioning

confidence: 99%

Diabetic retinopathy: Proteomic approaches to help the differential diagnosis and to understand the underlying molecular mechanisms

Csősz

Deák

Kalló

et al. 2017

Journal of Proteomics

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a b s t r a c t a r t i c l e i n f oDiabetic retinopathy is the most common diabetic eye disease and a leading cause of blindness among patients with diabetes. The appearance and the severity of the symptoms correlate with the duration of diabetes and poor blood glucose level management. Diabetic retinopathy is also categorized as a chronic low-level inflammatory disease; the high blood glucose level promotes the accumulation of the advanced glycation end products and leads to the stimulation of monocytes and macrophages. Examination of protein level alterations in tears using state-of the art proteomics techniques have identified several proteins as possible biomarkers for the different stages of the diabetic retinopathy. Some of the differentially expressed tear proteins have a role in the barrier function of tears linking the diabetic retinopathy with another eye complication of diabetes, namely the diabetic keratopathy resulting in impaired wound healing. Understanding the molecular events leading to the eye complications caused by hyperglycemia may help the identification of novel biomarkers as well as therapeutic targets in order to improve quality of life of diabetic patients. Biological significance: Diabetic retinopathy (DR), the leading cause of blindness among diabetic patients can develop without any serious symptoms therefore the early detection is crucial. Because of the increasing prevalence there is a high need for improved screening methods able to diagnose DR as soon as possible. The non-invasive collection and the relatively high protein concentration make the tear fluid a good source for biomarker discovery helping the early diagnosis. In this work we have reviewed the administration of advanced proteomics techniques used in tear biomarker studies and the identified biomarkers with potential to improve the already existing screening methods for DR detection.

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“…This reflects the fact that both structure and function of proteins are frequently recognized via their enzymatically generated peptide fragments. These peptide fragments are separated and identified by LC, 2DE, CE, and CEC methods with MS detection . This ”bottom‐up” or “shotgun” approach is one of the basic directions in the current proteome research .…”

Section: Introductionmentioning

confidence: 99%

Recent developments in capillary and microchip electroseparations of peptides (2013–middle 2015)

Kašička

2015

Electrophoresis

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The review brings a comprehensive survey of recent developments and applications of high performance capillary and microchip electroseparation methods (zone electrophoresis, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography) to analysis, micropreparation, purification, and physicochemical and biochemical characterization of peptides in the years 2013, 2014, and ca. up to the middle of 2015. Advances in the investigation of electromigration properties of peptides, in the methodology of their analysis, including sample preseparation, preconcentration and derivatization, adsorption suppression and EOF control, as well as in detection of peptides, are described. New developments in particular CE and CEC modes are presented and several types of their applications to peptide analysis are reported: conventional qualitative and quantitative analysis, determination in complex (bio)matrices, monitoring of chemical and enzymatical reactions and physical changes, amino acid, sequence, and chiral analysis, and peptide mapping of proteins. Some micropreparative peptide separations are shown and capabilities of CE and CEC techniques to provide important physicochemical characteristics of peptides are demonstrated.

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Comparison of peptide and protein fractionation methods in proteomics

Cited by 50 publications

References 32 publications

Comparison of sample preparation techniques for large‐scale proteomics

Comparison of sample preparation techniques for large‐scale proteomics

Diabetic retinopathy: Proteomic approaches to help the differential diagnosis and to understand the underlying molecular mechanisms

Recent developments in capillary and microchip electroseparations of peptides (2013–middle 2015)

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