Improved proteome coverage by using high efficiency cysteinyl peptide enrichment: The human mammary epithelial cell proteome

Liu, Tao; Qian, Weijun; Chen, Wan Nan U; Jacobs, Jon; Moore, Ronald J.; Anderson, David J.; Gritsenko, Marina; Monroe, Matthew E.; Thrall, Brian D.; Camp, David G.; Smith, Richard D.

doi:10.1002/pmic.200401055

Cited by 63 publications

(88 citation statements)

References 42 publications

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“…In addition, a fourth system comprised of the combined proteins identified from 436 SEQUEST analyses of LC-MS/MS analyses of human mammary epithelial cells (HMEC) was used to represent an observed subset of human proteins (described in an appendix at the end of this paper). This HMEC dataset represents a set of proteins that have been observed in the proteome for this human cell line [28,29].…”

Section: Databasesmentioning

confidence: 99%

The Utility of Accurate Mass and LC Elution Time Information in the Analysis of Complex Proteomes

Norbeck

Monroe

Adkins

et al. 2005

J. Am. Soc. Mass Spectrom.

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The combination of mass and normalized elution time (NET) of a peptide identified by liquid chromatography-mass spectrometry (LC-MS) measurements can serve as a unique signature for that peptide. However, the specificity of an LC-MS measurement depends upon the complexity of the proteome (i.e., the number of possible peptides) and the accuracy of the LC-MS measurements. In this work, theoretical tryptic digests of all predicted proteins from the genomes of three organisms of varying complexity were evaluated for specificity. Accuracy of the LC-MS measurement of mass-NET pairs (on a 0 to 1.0 NET scale) was described by bivariate normal sampling distributions centered on the peptide signatures. Measurement accuracy (i.e., mass and NET standard deviations of Ϯ0.1, 1, 5, and 10 ppm, and Ϯ0.01 and 0.05, respectively) was varied to evaluate improvements in process quality. The spatially localized confidence score, a conditional probability of peptide uniqueness, formed the basis for the peptide identification. Application of this approach to organisms with comparatively small proteomes, such as Deinococcus radiodurans, shows that modest mass and elution time accuracies are generally adequate for confidently identifying most peptides. For more complex proteomes, more accurate measurements are required. However, the study suggests that the majority of proteins for even the human proteome should be identifiable with reasonable confidence by using LC-MS measurements with mass accuracies within Ϯ1 ppm and high efficiency separations having elution time measurements within Ϯ0.01

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Section: Databasesmentioning

confidence: 99%

The Utility of Accurate Mass and LC Elution Time Information in the Analysis of Complex Proteomes

Norbeck

Monroe

Adkins

et al. 2005

J. Am. Soc. Mass Spectrom.

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“…The resulting peptides are then fractionated by SCX, the peptide fractions analyzed by LC-MS/MS, and the spectra analyzed by SEQUEST. Prior to SCX fractionation, cysteine-containing peptides in the tryptic digest of cellular lysates can be specifically enriched using high efficiency Cys-peptide enrichment to further improve the proteome coverage (Liu, et al, 2005). To date, several mammalian proteomes have been profiled, including HMEC , Liu, et al, 2005, hepatocyte HCV replicon model system Huh-7.5 cells , and human blood plasma (Qian, et al, 2005a.…”

Section: Mammalian Proteomesmentioning

confidence: 99%

“…Prior to SCX fractionation, cysteine-containing peptides in the tryptic digest of cellular lysates can be specifically enriched using high efficiency Cys-peptide enrichment to further improve the proteome coverage (Liu, et al, 2005). To date, several mammalian proteomes have been profiled, including HMEC , Liu, et al, 2005, hepatocyte HCV replicon model system Huh-7.5 cells , and human blood plasma (Qian, et al, 2005a. For the HMEC proteome, a combination of Cys-peptide enrichment and global approaches enabled confident identification of >25,000 unique peptides that corresponded to >6,700 distinct proteins, which is ∼17% coverage of the human proteome.…”

Section: Mammalian Proteomesmentioning

confidence: 99%

Advances in proteomics data analysis and display using an accurate mass and time tag approach

Zimmer

Monroe

Qian

et al. 2006

Mass Spectrometry Reviews

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360

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Proteomics has recently demonstrated utility in understanding cellular processes on the molecular level as a component of systems biology approaches and for identifying potential biomarkers of various disease states. The large amount of data generated by utilizing high efficiency (e.g., chromatographic) separations coupled to high mass accuracy mass spectrometry for high-throughput proteomics analyses presents challenges related to data processing, analysis, and display. This review focuses on recent advances in nanoLC-FTICR-MS-based proteomics approaches and the accompanying data processing tools that have been developed to display and interpret the large volumes of data being produced.

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“…To overcome these challenges, different complexity reduction strategies are used. In a first strategy, affinity depletion removes the most abundant serum proteins such as albumin (111)(112)(113)(114) and detects low-abundance proteins, which are more informative as tumorspecific biomarkers but unfortunately are obscured by highabundance proteins. Depletion procedures are limited by absence of standardization and problems of reproducibility.…”

Section: Strategies To Address the Complexity Of The Proteomementioning

confidence: 99%

Mass Spectrometry-based Proteomic Profiling of Lung Cancer

Ocak¹,

Chaurand²,

Massion³

2009

Proceedings of the American Thoracic Society

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In an effort to further our understanding of lung cancer biology and to identify new candidate biomarkers to be used in the management of lung cancer, we need to probe these tissues and biological fluids with tools that address the biology of lung cancer directly at the protein level. Proteins are responsible of the function and phenotype of cells. Cancer cells express proteins that distinguish them from normal cells. Proteomics is defined as the study of the proteome, the complete set of proteins produced by a species, using the technologies of large-scale protein separation and identification. As a result, new technologies are being developed to allow the rapid and systematic analysis of thousands of proteins. The analytical advantages of mass spectrometry (MS), including sensitivity and highthroughput, promise to make it a mainstay of novel biomarker discovery to differentiate cancer from normal cells and to predict individuals likely to develop or recur with lung cancer. In this review, we summarize the progress made in clinical proteomics as it applies to the management of lung cancer. We will focus our discussion on how MS approaches may advance the areas of early detection, response to therapy, and prognostic evaluation.Keywords: proteome; translational research; biomarkers Lung cancer is the leading cause of cancer-related death worldwide among both males and females, with more than 1 million deaths annually (1). Non-small cell lung cancer (NSCLC) accounts for about 80% of all lung cancers. Although advances have been made in diagnosis and treatment strategies in the last decade, the prognosis of NSCLC patients is poor, with a 5-year overall survival of 15 to 20% (2). This is mainly due to a lack of early diagnosis tools, with more than 60% of the patients diagnosed with advanced or metastatic disease (3) and therefore not eligible for a curative surgical resection. Lung cancer is often suspected on the basis of abnormal chest imaging and/or nonspecific symptoms. Bronchoscopy, with cytopathologic examination of bronchoalveolar lavage, endobronchial brushings and biopsies obtained from the suspect area, is in general used as an initial diagnostic tool. However, while this procedure is 100% specific for lung cancer, the sensitivity is low and ranges from 30% for small peripheral lesions to 80% for central endobronchial tumors (4). More invasive and expensive diagnostic tests are often required, delaying the diagnosis and the subsequent treatment initiation. Surgical resection offers the best chance for cure. For patients undergoing surgery, the longterm prognosis remains disappointing, with a 5-year overall survival of 50% only (5). Recent studies showed that survival of surgically resected patients with NSCLC might be improved by systemic platinum-based adjuvant chemotherapy (6, 7), but which patients might benefit from this treatment cannot be determined accurately.To improve lung cancer management and survival, there is a great need to develop screening and early diagnosis strategies that are sensitive,...

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Improved proteome coverage by using high efficiency cysteinyl peptide enrichment: The human mammary epithelial cell proteome

Cited by 63 publications

References 42 publications

The Utility of Accurate Mass and LC Elution Time Information in the Analysis of Complex Proteomes

The Utility of Accurate Mass and LC Elution Time Information in the Analysis of Complex Proteomes

Advances in proteomics data analysis and display using an accurate mass and time tag approach

Mass Spectrometry-based Proteomic Profiling of Lung Cancer

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