Abstract：
:Top-down proteomics (TDP) has great potential for high throughput proteoform characterization. With significant advances in mass spectrometry (MS) instrumentation permitting tandem MS of large intact proteins, a limitation to the widespread adoption of TDP still resides on front-end sample preparation protocols (e.g. fractionation, purification) that are amenable to MS analysis of intact proteins. Chromatographic strategies are improving but pose higher risk of sample loss. Gel-based separations (e.g. GELFrEE) may alleviate this concern but at the expense of requiring sodium dodecyl sulfate (SDS). While this surfactant maintains protein solubility during fractionation, the advantage is short-lived, as the detergent must ultimately be depleted to avoid MS signal suppression. To do so requires overcoming strong interactions between SDS and protein. Adding to the challenge, one must now consider upholding the solubility of purified protein(s) in the absence of SDS. This review explores uses of SDS in TDP workflows, addressing front-end strategies that reduce matrix interferences while maximizing recovery of intact proteins in MS-compatible formats. SIGNIFICANCE:The benefits of employing SDS in a TPD workflow can easily outweigh the disadvantages. Several SDS depletion strategies are available, though not all are equally amenable to TDP. This review provides a comprehensive and critical accounting of SDS in TDP, demonstrating methods that are suited to MS analysis of intact proteins.
journal_name
J Proteomicsjournal_title
Journal of proteomicsauthors
Kachuk C,Doucette AAdoi
10.1016/j.jprot.2017.03.002subject
Has Abstractpub_date
2018-03-20 00:00:00pages
75-86eissn
1874-3919issn
1876-7737pii
S1874-3919(17)30076-3journal_volume
175pub_type
杂志文章,评审abstract：:In the development of ischemia/reperfusion (I/R) injury, the role of the myosin light chain (MLC) phosphorylation has been given increased consideration. ML-7, a MLC kinase inhibitor, has been shown to protect cardiac function from I/R, however the exact mechanism remains unclear. Isolated rat hearts were perfused und...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2012.06.016
更新日期：2012-09-18 00:00:00
abstract：:Protein phosphorylation plays a pivotal role in the regulation of many cellular events; increasing evidences indicate that this post-translational modification is involved in plant response to various abiotic and biotic stresses. Since phosphorylated proteins may be present at low abundance, enrichment methods are gen...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2011.05.016
更新日期：2011-09-06 00:00:00
abstract：:Numerous surveys have highlighted the natural co-occurrence of deoxynivalenol (DON) and zearalenone (ZEA) mycotoxins in food and feed. Nevertheless, data regarding cellular mechanisms involved in response to their individual and simultaneous exposures are lacking. In this study, in order to analyze how low mycotoxin d...
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doi：10.1016/j.jprot.2017.11.025
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abstract：:The field of cancer immunotherapy has expanded rapidly in the past few years, with many new approaches entering the clinic for T cell mediated killing of tumors. Several of these clinical approaches involve the exploitation of a CD8 + T cell response against MHC I presented tumor antigens. Here, we describe the types ...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2018.04.021
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abstract：UNLABELLED:Clostridium difficile spores are considered the morphotype of infection, transmission and persistence of C. difficile infections. There is a lack of information on the composition of the outermost exosporium layer of C. difficile spores. Using recently developed exosporium removal methods combined with MS/MS...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2015.03.035
更新日期：2015-06-18 00:00:00
abstract：:Plasma membrane intrinsic proteins (PIPs) are one subfamily of aquaporins that mediate the transmembrane transport of water. To reveal their function in poplar, we generated transgenic poplar plants in which the translation of PIP genes was downregulated by RNA interference investigated these plants with a comprehensi...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2015.07.029
更新日期：2015-10-14 00:00:00
abstract：:Recently it was discovered that thioproline, an unnatural analog of proline, can arise in vivo from the reaction of cysteine and formaldehyde in cells under oxidative stress. Sequence-specific bioincorporation of thioproline into proteins was studied via shotgun proteomics of Escherichia coli (E. coli) cells. In a str...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2019.103541
更新日期：2020-01-06 00:00:00
abstract：:Ubiquitylation is an elaborate post-translational modification involved in all biological processes. Its pleotropic effect is driven by the ability to form complex polyubiquitin chain architectures that can influence biological functions. In this study, we optimised sample preparation and chromatographic separation of...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2020.103963
更新日期：2020-10-30 00:00:00
abstract：UNLABELLED:Marine bioadhesives have unmatched performances in wet environments, being an inspiration for biomedical applications. In sea urchins specialized adhesive organs, tube feet, mediate reversible adhesion, being composed by a disc, producing adhesive and de-adhesive secretions, and a motile stem. After tube foo...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2016.02.026
更新日期：2016-04-14 00:00:00
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journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2011.03.025
更新日期：2011-08-12 00:00:00
abstract：:In this study, we performed an integrated physiological and chloroplast proteome analysis of wheat seedling leaves under salt and osmotic stresses by label-free based quantitative proteomic approach. Both salt and osmotic stresses significantly increased the levels of abscisic acid and methyl jasmonate and led to dama...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2020.104097
更新日期：2021-03-15 00:00:00
abstract：:High-throughput technologies were used to identify venom gland toxin expression and to characterize the venom proteomes of two rear-fanged snakes, Ahaetulla prasina (Asian Green Vine Snake) and Borikenophis portoricensis (Puerto Rican Racer). Sixty-nine complete toxin-coding transcripts from 12 venom protein superfami...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2018.08.004
更新日期：2018-09-15 00:00:00
abstract：:Hyperaccumulators are distinguished from non-hyperaccumulators on the basis of their capacity to extract heavy metal ions from the soil, their more efficient root-to-shoot translocation of these ions and their greater ability to detoxify and sequester heavy metals in the shoot. The understanding of the mechanisms unde...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2012.12.006
更新日期：2013-02-21 00:00:00
abstract：:Drug resistance and relapse after treatment of visceral leishmaniasis (VL) with the chemotherapeutic drugs has impeded the VL elimination programme especially, in the endemic region of Bihar, India. Currently, Antimonials (Sbv) have been rendered obsolete (Bihar) as frequent treatment failure and relapse in Sbv treate...
journal_title：Journal of proteomics
pub_type： 已发布勘误
doi：10.1016/j.jprot.2020.104017
更新日期：2021-02-10 00:00:00
abstract：:Deposition of calcium oxalate (CaOx) crystals in renal interstitium is one of the key factors that cause progressive inflammation in kidney stone disease. Macrophages are responsible for elimination of these crystals but their roles to worsen inflammatory process remain under-investigated. This study thus aimed to def...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2018.06.015
更新日期：2018-08-15 00:00:00
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journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2016.07.029
更新日期：2017-01-16 00:00:00
abstract：:Plans for the European Proteomics Association (EuPA) were conceived and established during 2004 and 2005, and culminated in the formal inception of the organisation during the 4th HUPO World Congress held in Munich in 2005. The mission from the outset has been three-tiered and is to: i) strengthen the national Proteom...
journal_title：Journal of proteomics
pub_type： 历史文章,杂志文章
doi：10.1016/j.jprot.2008.03.004
更新日期：2008-04-30 00:00:00
abstract：:Calcium enhances salt stress tolerance of soybeans. Nevertheless, the molecular mechanism of calcium's involvement in resistance to salt stress is unclear. A comparative proteomic approach was used to investigate protein profiles in germinating soybeans under NaCl-CaCl2 and NaCl-LaCl3 treatments. A total of 80 protein...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2014.09.023
更新日期：2015-01-15 00:00:00
abstract：UNLABELLED:The reproductive stage of Paracentrotus lividus strongly influences product quality that, in turn, impacts significantly on the market price. Large, compact and sweet gonads are preferred, and sensory attributes are positively related to the ratio of nutritive phagocytes to gametes. Gonads at advanced matura...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2016.05.035
更新日期：2016-07-20 00:00:00
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journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2015.12.030
更新日期：2016-03-16 00:00:00
abstract：UNLABELLED:The composition and toxicological profile of the venom of the rattlesnake Crotalus simus in Mexico was analyzed at the subspecies and individual levels. Venoms of the subspecies C. s. simus, C. s. culminatus and C. s. tzabcan greatly differ in the expression of the heterodimeric neurotoxin complex 'crotoxin'...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2013.05.024
更新日期：2013-07-11 00:00:00
abstract：:Many scorpion accidents occur in the Brazilian Amazonian region and are frequently caused by Tityus obscurus. Approximately 5% of the crude venom of this species is composed of short linear, non-disulfide-bridged peptides, which have not been intensively investigated. As a consequence, only a few of these peptides hav...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2017.09.006
更新日期：2018-01-06 00:00:00
abstract：:For survival, parasite exerts several lines of defense of which drug neutralization is one of the major phenomena. Lack of phase I cytochrome P450 in some of the nematode render them depend on the phase II detoxification system involving GST as a major detoxifying enzymes. In present study, the antifilarial DEC, pheno...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2011.04.020
更新日期：2011-08-24 00:00:00
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journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2018.02.012
更新日期：2018-04-15 00:00:00
abstract：:The development of type 2 diabetes (T2D) is strongly associated with obesity. In humans, T2D increases the risk for end organ complications. Among these, heart disease has been ranked as the leading cause of death. We used a proteomic methodology to test the hypothesis that a pre-diabetic state generated by high-fat d...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2011.02.018
更新日期：2011-05-01 00:00:00
abstract：:In analysing the red blood cell cytoplasmic proteome, in search for low abundance proteins, 15 amino acid (AA; Arg, Asn, Asp, Gln, Gly, His, Ile, Lys, Phe, Pro, Ser, Thr, Trp, Tyr, and Val) probes, used individually, captured a total of 787 unique gene products. Of those, 76 were found to be the common catch of all AA...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2009.04.001
更新日期：2009-07-21 00:00:00
abstract：:The human papillomavirus type 16 (HPV-16) E6/E7 spliced transcripts are heterogeneously expressed in cervical carcinoma. The heterogeneity of the E6/E7 splicing profile might be in part due to the intrinsic variation of splicing factors in tumor cells. However, the splicing factors that bind the E6/E7 intron 1 (In-1) ...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2014.07.029
更新日期：2014-12-05 00:00:00
abstract：:We present a new module integrated into the widely adopted PatternLab for proteomics to enable analysis of isotope-labeled peptides produced using dimethyl or SILAC. The accurate quantitation of proteins lies within the heart of proteomics; dimethylation has shown to be reliable, inexpensive, and applicable to any sam...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2019.04.021
更新日期：2019-06-30 00:00:00
abstract：:No effective screening method is available for oral squamous cell carcinoma (OSCC) that is recognized to influence by environmental factors as well as human papillomavirus (HPV) and Epstein-Barr virus (EBV). Therefore, we sought to identify salivary biomarkers for screening of OSCC with or without HPV and/or EBV infec...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2017.11.022
更新日期：2018-02-20 00:00:00
abstract：UNLABELLED:We present a combined proteomic and bioinformatic investigation of mitochondrial proteins from the amoeboid protist Acanthamoeba castellanii, the first such comprehensive investigation in a free-living member of the supergroup Amoebozoa. This protist was chosen both for its phylogenetic position (as a sister...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2014.07.005
更新日期：2014-09-23 00:00:00
