A novel quantitative proteomics workflow by isobaric terminal labeling

Yang, Shujun; Nie, Aiying; Zhang, Lei; Yan, Guoquan; Yao, Jun; Xie, Lili; Lu, Haojie; Yang, Pengyuan

doi:10.1016/j.jprot.2012.07.011

Cited by 27 publications

(61 citation statements)

References 36 publications

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“…The ratios of each protein were averaged and delivered to Perseus (version 1.3.0.4) for analysis, 28 of which 128 proteins were detected as differentially expressed at the p value threshold of 0.01 (Significant A, both sides), with 41 proteins up-regulated in human-HCC-H and 87 protein down-regulated in human-HCC-H. The "D" labeled peptide and the "H" labeled peptide represent the peptide dimethylated using d(2), 13 C-formaldehyde and d(0), 12 C-formaldehyde, respectively. Among these differently regulated proteins, most of them were related to tumorigenesis and tumor metastasis.…”

Section: Application In Quantitative Proteome Analysis Of Human-hcc-h/lmentioning

confidence: 99%

“…[4][5][6][7][8][9] A modified approach for IPTL with pseudo-isobaric labeling was introduced relying on the mass defects of atoms and their isotopes. 12 Multiple quantification points per spectrum are definitely beneficial for the accuracy of quantification. 12 Multiple quantification points per spectrum are definitely beneficial for the accuracy of quantification.…”

Section: Introductionmentioning

confidence: 99%

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Pseudo isobaric peptide termini labelling for relative proteome quantification by SWATH MS acquisition

Zhang

Chen

Shan

et al. 2016

Analyst

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The pseudo isobaric peptide termini labeling (IPTL) method is a remarkable strategy in quantitative proteomics, and has been efficiently applied in biological studies due to its high quantitative accuracy. However, irreproducible precursor ion selection caused by data dependent acquisition and the chromatographic shift caused by isotope effects limit the wide application of this method. Herein, we expand the use of pseudo IPTL to SWATH MS application and develop a novel quantitative strategy, termed SWATH-pseudo-IPTL, by which the relative quantification could be achieved by comparing the "complete" extracted ion chromatogram (XIC) intensity of MS/MS scan instead of a single intensity measurement in DDA-pseudo-IPTL which only reflected the peptide abundances at that given time. The quantitative analysis of various proportions of mixed HeLa samples revealed the strong accuracy and precision of our SWATH-pseudo-IPTL method, both of which were better than that of the DDA-pseudo-IPTL strategy. SWATH-pseudo-IPTL was also applied to the quantitative profiling of the proteome from human hepatocellular carcinoma cell lines with high and low metastatic potential, and most of the differentially expressed proteins were related to tumorigenesis and tumor metastasis, demonstrating the feasibility of this methodology for biological applications.

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Section: Application In Quantitative Proteome Analysis Of Human-hcc-h/lmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Pseudo isobaric peptide termini labelling for relative proteome quantification by SWATH MS acquisition

Zhang

Chen

Shan

et al. 2016

Analyst

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“…22 After incubation for 24 h at 37°C, the two aliquots were boiled for 10 min at 100°C 22 After incubation for 24 h at 37°C, the two aliquots were boiled for 10 min at 100°C…”

Section: Offline Digestion and Labeling In Solutionmentioning

confidence: 99%

Integrated platform with a combination of online digestion and ¹⁸O labeling for proteome quantification via an immobilized trypsin microreactor

Zhang

Yuan

Zhao

et al. 2015

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A novel automated integrated platform for quantitative proteome analysis was established with a combination of online digestion of proteins and in situ(18)O labeling by an immobilized enzyme reactor (IMER); digests were captured and desalted by a C18 trap column, and peptides were analyzed by nanoRPLC-ESI-MS/MS. Bovine serum albumin (BSA) was used to evaluate the performance of the developed platform. Compared with traditional offline methods, not only the digestion and labeling time was shortened from 36 h to just 1 h, but also the labeling efficiency was improved from 95% to 99%. Furthermore, the back-exchange from (18)O to (16)O could also be efficiently avoided by the use of IMER. The platform was further evaluated by the quantitative analysis of 100 ng (18)O and (16)O online labeled yeast sample with a mixing ratio of 1 : 1, and the results showed significantly improved sensitivity and reproducibility, as well as improved quantitative accuracy than offline method. With these advantages, the integrated platform was finally applied to the quantitative profiling of 100 ng proteins extracted from two mouse hepatocarcinoma ascites syngeneic cell lines with high and low lymph node metastases rates, and ten differentially expressed proteins were successfully found, most of which were related to tumorigenesis and tumor metastasis. All these results demonstrate that the developed integrated platform can provide a new way for high efficiency (18)O labeling and the quantitative analysis of trace amounts of sample with high accuracy and high reproducibility.

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“…Of course, it can also be expected that new technological developments, like MS E (33); ion mobility (34) (a method where the ionized molecules are separated according to their mobility in a carrier gas instead of the separation according to their mass–charge ratio) and hybrid multi-dimensional ion-separation approaches combining both ion separation techiques; SWATH [a DIA (Data Independent Acquisition) method, where one has to specify a series of isolation windows called ‘swaths’); QITL (Quantitative Isobaric Terminal Labeling) (35), where the C termini of the peptides are labeled with 16 O or 18 O and the N-termini with normal or d(2)formaldehyde to allow the quantitation of the peptides; GeLC-MS, a combination of Gel-based and liquid chromatography-MS–based proteomics (36); or other upcoming methods will require the addition of new terms to the PSI-MS CV.…”

Section: Future Directionsmentioning

confidence: 99%

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary

Mayer¹,

Montecchi-Palazzi²,

Ovelleiro³

et al. 2013

Database

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Controlled vocabularies (CVs), i.e. a collection of predefined terms describing a modeling domain, used for the semantic annotation of data, and ontologies are used in structured data formats and databases to avoid inconsistencies in annotation, to have a unique (and preferably short) accession number and to give researchers and computer algorithms the possibility for more expressive semantic annotation of data. The Human Proteome Organization (HUPO)–Proteomics Standards Initiative (PSI) makes extensive use of ontologies/CVs in their data formats. The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS–related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. Owing to the range of topics covered by the CV, collaborative development across several PSI working groups, including proteomics research groups, instrument manufacturers and software vendors, was necessary. In this article, we describe the overall structure of the CV, the process by which it has been developed and is maintained and the dependencies on other ontologies.Database URL: http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo

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A novel quantitative proteomics workflow by isobaric terminal labeling

Cited by 27 publications

References 36 publications

Pseudo isobaric peptide termini labelling for relative proteome quantification by SWATH MS acquisition

Pseudo isobaric peptide termini labelling for relative proteome quantification by SWATH MS acquisition

Integrated platform with a combination of online digestion and ¹⁸O labeling for proteome quantification via an immobilized trypsin microreactor

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary

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A novel quantitative proteomics workflow by isobaric terminal labeling

Cited by 27 publications

References 36 publications

Pseudo isobaric peptide termini labelling for relative proteome quantification by SWATH MS acquisition

Pseudo isobaric peptide termini labelling for relative proteome quantification by SWATH MS acquisition

Integrated platform with a combination of online digestion and 18O labeling for proteome quantification via an immobilized trypsin microreactor

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary

Contact Info

Product

Resources

About

Integrated platform with a combination of online digestion and ¹⁸O labeling for proteome quantification via an immobilized trypsin microreactor