Affinity Depletion of Plasma and Serum for Mass Spectrometry-Based Proteome Analysis

Jaros, Julian A. J.; Guest, Paul C.; Bahn, Sabine; Martins-de-Souza, Daniel

doi:10.1007/978-1-62703-360-2_1

Cited by 35 publications

(30 citation statements)

References 23 publications

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“…Sera were processed in random order to avoid potential sequential biases and were depleted of the 14 most abundant proteins using MARS14 (Agilent, USA) on a ÄKTA™ purifier UPC 10 chromatography system (GE Healthcare, UK) using affinity chromatography as reported previously (Jaros et al, 2013). This was carried out to increase detection of a higher number of serum proteins, which are normally masked by the higher abundance proteins.…”

Section: Lc-ms E Analysismentioning

confidence: 99%

Proteomic changes in serum of first onset, antidepressant drug-naïve major depression patients

Stelzhammer

Haenisch

Chan

et al. 2014

Int. J. Neuropsychopharm.

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101

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Major depressive disorder (MDD) is a complex and multi-factorial disorder. Although genetic factors and other molecular aspects of MDD have been widely studied, the underlying pathological mechanisms are still mostly unknown. We sought to investigate the pathophysiology of MDD by identifying and characterising serum molecular differences and their correlation to symptom severity in first onset, antidepressant drug-naïve MDD patients. We performed an exploratory molecular profiling study on serum samples of MDD patients and controls using multiplex immunoassay and label-free liquid chromatography mass spectrometry in data independent mode (LC-MSE). We included two independent cohorts of first onset, antidepressant drug-naïve MDD patients (n = 23 and 15) and matched controls (n = 42 and 21) in our study in order to validate the results. The main outcome included the following list of circulatory molecules changing and/or correlating to symptom severity: angiotensin-converting enzyme, acute phase proteins (e.g. ferritin and serotransferrin), brain-derived neurotrophic factor, complement component C4-B, cortisol, cytokines (e.g. macrophage migration inhibitory factor and interleukin-16), extracellular newly identified receptor for advanced glycosylation end products-binding protein, growth hormone and superoxide dismutase-1. This study provides evidence of an increased pro-inflammatory and oxidative stress response, followed by a hyperactivation of the HPA-axis in the acute stages of first onset MDD, as well as a dysregulation in growth factor pathways. These findings help to elucidate MDD related pathways in more detail and further studies may lead to identification of novel drug targets, including components of the inflammatory and oxidative stress response.

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Section: Lc-ms E Analysismentioning

confidence: 99%

Proteomic changes in serum of first onset, antidepressant drug-naïve major depression patients

Stelzhammer

Haenisch

Chan

et al. 2014

Int. J. Neuropsychopharm.

Self Cite

101

View full text Add to dashboard Cite

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“…While the medium abundance (≈µg mL −1 ) proteins take one small portion (≈20%), high abundant (≈mg mL −1 ) proteins such of albumin and immunoglobulins make up the other most (≈65–80%) of total plasma proteins. By employing the immunoaffinity depletion of these high abundant proteins from urine and cerebrospinal fluid and plasma, the depth of proteomic analysis was increased . Although a few studies have tried, the depletion has not been fully explored in BALF of lung cancer proteomic analysis.…”

mentioning

confidence: 99%

In‐Depth Proteomic Analysis of Human Bronchoalveolar Lavage Fluid toward the Biomarker Discovery for Lung Cancers

Sim

Choi

Lee

et al. 2019

Proteomics Clinical Apps

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Purpose Lung cancer is among the most common cancers. Bronchoalveolar lavage fluid (BALF) can be easily obtained from patients with lung cancers. The aim is to develop a novel proteomic method of the molecule‐based sensitive detection of biomarkers from BALF. Experimental Design BALF samples are collected from segmental bronchus of 14 patients with lung cancers from Kyung Hee University Hospital. First, BALF proteome is depleted using a depletion column, and then peptides are prepared from the enriched low abundant proteins and fractionated by high pH reverse phase liquid chromatography prior to LC‐MS/MS. Data are available via ProteomeXchange with identifier PXD012645. Results A novel method is developed for in‐depth proteomic analysis of BALF by combining antibody‐based depletion of high abundant proteins from BALF with high pH peptide fractionation. Peptides are analyzed on a high resolution Orbitrap Fusion mass spectrometer. MaxQuant search result in the identification of 4615 protein groups mapped to 4534 genes. Conclusions and Clinical Relevance It is found that the method outperformed conventional BALF proteomic methods and it is believed that this method will facilitate the biomarker research for lung cancer. In addition, it is shown that BALF will be a great source of biomarkers of lung diseases.

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“…A traditional approach to this issue is to remove the high-abundance proteins (HAPs) and thereby enrich for low-abundance proteins (Jaros et al 2013). Immunoaffinity depletion of HAPs has become a routine sample preparation strategy (see Fig.…”

Section: Biomarker Development In Human Bloodmentioning

confidence: 99%

Mass Spectrometry for Biomarker Development

Wu¹,

Liu²,

Baker³

et al. 2015

Biomarkers in Disease: Methods, Discoveries and Applications

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Affinity Depletion of Plasma and Serum for Mass Spectrometry-Based Proteome Analysis

Cited by 35 publications

References 23 publications

Proteomic changes in serum of first onset, antidepressant drug-naïve major depression patients

Proteomic changes in serum of first onset, antidepressant drug-naïve major depression patients

In‐Depth Proteomic Analysis of Human Bronchoalveolar Lavage Fluid toward the Biomarker Discovery for Lung Cancers

Mass Spectrometry for Biomarker Development

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