Abstract：
:Shotgun proteomics produces collections of tandem mass spectra that contain all the data needed to identify mutated peptides from clinical samples. Identifying these sequence variations, however, has not been feasible with conventional database search strategies, which require exact matches between observed and expected sequences. Searching for mutations as mass shifts on specified residues through database search can incur significant performance penalties and generate substantial false positive rates. Here we describe TagRecon, an algorithm that leverages inferred sequence tags to identify unanticipated mutations in clinical proteomic data sets. TagRecon identifies unmodified peptides as sensitively as the related MyriMatch database search engine. In both LTQ and Orbitrap data sets, TagRecon outperformed state of the art software in recognizing sequence mismatches from data sets with known variants. We developed guidelines for filtering putative mutations from clinical samples, and we applied them in an analysis of cancer cell lines and an examination of colon tissue. Mutations were found in up to 6% of identified peptides, and only a small fraction corresponded to dbSNP entries. The RKO cell line, which is DNA mismatch repair deficient, yielded more mutant peptides than the mismatch repair proficient SW480 line. Analysis of colon cancer tumor and adjacent tissue revealed hydroxyproline modifications associated with extracellular matrix degradation. These results demonstrate the value of using sequence tagging algorithms to fully interrogate clinical proteomic data sets.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Dasari S,Chambers MC,Slebos RJ,Zimmerman LJ,Ham AJ,Tabb DLdoi
10.1021/pr900850msubject
Has Abstractpub_date
2010-04-05 00:00:00pages
1716-26issue
4eissn
1535-3893issn
1535-3907journal_volume
9pub_type
杂志文章abstract：:Peptide amidination labeling using S-methyl thioacetimidate (SMTA) is investigated in an attempt to increase the number and types of peptides that can be detected in a bottom-up proteomics experiment. This derivatization method affects the basicity of lysine residues and is shown here to significantly impact the idios...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00468
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journal_title：Journal of proteome research
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journal_title：Journal of proteome research
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journal_title：Journal of proteome research
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doi：10.1021/pr800865d
更新日期：2009-03-01 00:00:00
abstract：:Histones are subjected to extensive post-translational modifications (PTMs) that are known to play key roles in many biological processes. In this study, we report a fast, efficient, highly reproducible, and easily automated method involving ultra-high performance liquid chromatography (UHPLC) coupled to a high resolu...
journal_title：Journal of proteome research
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journal_title：Journal of proteome research
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journal_title：Journal of proteome research
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更新日期：2008-01-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
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更新日期：2008-04-01 00:00:00
abstract：:The protein expression pattern in the cytosol fraction of the adriamycin resistant MCF-7 cell line (MCF-7/ADR) was compared to that of the parental MCF-7 cell line using two-dimensional gel electrophoresis and mass spectrometry. Twenty proteins with altered abundances were identified and studied in MCF-7/ADR. Both up ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0340577
更新日期：2004-05-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0601180
更新日期：2006-07-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00499
更新日期：2019-06-07 00:00:00
abstract：:Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomic methods have been widely used to identify lysine acylation proteins. However, these experimental approaches often fail to detect proteins that are in low abundance or absent in specific biological samples. To circumvent these problems, we develo...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00240
更新日期：2016-12-02 00:00:00
abstract：:Hepatocellular carcinoma (HCC) remains as the fifth most common cancer in the world and accounts for more than 700,000 deaths annually. Changes in serum glycosylation have long been associated with this cancer but the source of that material is unknown and direct glycan analysis of HCC tissues has been limited. Our la...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00323
更新日期：2018-10-05 00:00:00
abstract：:Human milk oligosaccharides (HMOs) perform a number of functions including serving as prebiotics to stimulate the growth of beneficial intestinal bacteria, as receptor analogues to inhibit binding of pathogens, and as substances that promote postnatal brain development. There is further evidence that HMOs participate ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100362f
更新日期：2010-08-06 00:00:00
abstract：:Pinus radiata is one of the most economically important forest tree species, with a worldwide production of around 370 million m (3) of wood per year. Current selection of elite trees to be used in conservation and breeding programes requires the physiological and molecular characterization of available populations. T...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr7006285
更新日期：2008-07-01 00:00:00
abstract：:A rate-limiting and costly step in many proteomics analyses is the cloning of all of the ORFs for an organism into technique-specific vectors. Here, we describe the generation of a Campylobacter jejuni expression clone set using a high-throughput cloning approach based on recombination in E. coli. The approach uses na...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0341134
更新日期：2004-05-01 00:00:00
abstract：:Antibody reagents have been remained as a standard approach to characterize blood group (BG) antigens in clinic. The specificity and cross-reactivity of these BG antibodies are routine detected using the gel microcolumn assay (GMA). However, the GMA is neither specific nor sensitive, thus increasing the risk of improp...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00370
更新日期：2018-09-07 00:00:00
abstract：:Lipolysis involves a number of components including signaling pathways, droplet-associated proteins, and lipases such as hormone-sensitive lipase (HSL). We used surface enhanced laser desorption/ionization time-of-flight mass spectroscopy to identify cellular proteins that might interact with HSL and potentially influ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900909t
更新日期：2010-04-05 00:00:00
abstract：:Recombinant virus-like particles (VLPs) have been shown to induce protective immunity. Despite their potential significance as promising vaccine candidates, the protein composition of VLPs produced in insect cells has not been well characterized. Here we report a proteomic analysis of influenza VLPs containing hemaggl...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200086v
更新日期：2011-08-05 00:00:00
abstract：:The bacterial ribosomal protein S12 contains a universally conserved D88 residue on a loop region thought to be critically involved in translation due to its proximal location to the A site of the 30S subunit. While D88 mutants are lethal this residue has been found to be post-translationally modified to β-methylthioa...
journal_title：Journal of proteome research
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更新日期：2013-03-01 00:00:00
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journal_title：Journal of proteome research
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doi：10.1021/pr400352n
更新日期：2013-07-05 00:00:00
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journal_title：Journal of proteome research
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doi：10.1021/pr060586+
更新日期：2007-05-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
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更新日期：2006-02-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070314m
更新日期：2007-11-01 00:00:00
abstract：:An alternative sieving matrix, replaceable cross-linked polyacrylamide (rCPA), was developed for sodium dodecyl sulfate capillary gel electrophoresis (SDS-CGE) separation of proteins. This rCPA could be conveniently pressurized into separation capillaries under a pressure of 80 psi. SDS-CGE separations using this matr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0500206
更新日期：2005-05-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr034081k
更新日期：2004-01-01 00:00:00
abstract：:In line with the aims of the Chromosome-based Human Proteome Project and the Biology/Disease-based Human Proteome Project, we have been studying differentially expressed transcripts and proteins in gliomas—the most prevalent primary brain tumors. Here, we present a perspective on important insights from this analysis ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00488
更新日期：2015-09-04 00:00:00
abstract：:Quantitative comparison of protein expression levels in 2D gels is complicated by the variables associated with protein separation and mass spectrometric responses. Metabolic labeling allows cells from different experiments to be mixed prior to analysis. This approach has been reported for prokaryotic cells. Here, we ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr025523f
更新日期：2002-07-01 00:00:00
abstract：:Untargeted GC-TOF-MS analysis proved to be a suitable analytical platform to determine alterations in the metabolic profile. Several metabolic pathways were found to be altered in a first clinical study comparing smokers against nonsmokers. Subsequently, we conducted a clinical diet-controlled study to investigate alt...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00128
更新日期：2017-10-06 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
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更新日期：2010-01-01 00:00:00
