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Liu N, Chan W, Lee KC, Cai Z. A method to enhance a1 ions and application for peptide sequencing and protein identification. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1214-1223. [PMID: 19299168 DOI: 10.1016/j.jasms.2009.02.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Revised: 02/10/2009] [Accepted: 02/10/2009] [Indexed: 05/27/2023]
Abstract
A simple and effective method was developed for peptide sequencing and protein identification through the determination of its N-terminal residue. The method of N-terminal carbamidomethylation with iodoacetamide could specifically and remarkably enhance the intensity of a(1) ions in the tandem mass spectra of the peptide derivatives without significantly altering their fragmentation pattern, thus allowing determination of their N-terminal residues. The effectiveness and specificity of the method was demonstrated by confirming and extending sequence interpretation of several model peptides and proteins. The developed method was then applied in the LC-MS/MS analysis of the tryptic digests of myoglobin and a whole protein extract from rat heart tissues. The results from database searches were well validated with the enhancement of a(1) ions in tandem mass spectra and the specificity of protein identification was obtained when the information of N-terminal residues was included in the database search.
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Affiliation(s)
- Ning Liu
- Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
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Proteomic analysis of seminal plasma from asthenozoospermia patients reveals proteins that affect oxidative stress responses and semen quality. Asian J Androl 2009; 11:484-91. [PMID: 19448646 DOI: 10.1038/aja.2009.26] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Asthenozoospermia (AS) is a common cause of human male infertility. In one study, more than 80% of the samples from infertile men had reduced sperm motility. Seminal plasma is a mixture of secretions from the testis, epididymis and several male accessory glands, including the prostate, seminal vesicles and Cowper's gland. Studies have shown that seminal plasma contains proteins that are important for sperm motility. To further explore the pathophysiological character of AS, we separated the seminal plasma proteins from AS patients and healthy donors using sodium dodecyl sulfate polyacrylamide gel electrophoresis and in-gel digestion, and then subjected the proteins to liquid chromatography-mass spectrometry (LC-MS/MS) analysis. A total of 741 proteins were identified in the seminal plasma, with a false discovery rate of 3.3%. Using spectral counting, we found that 45 proteins were threefold upregulated and 56 proteins were threefold downregulated in the AS group when compared with the control. Most of these proteins originated from the epididymis and prostate. This study identified a rich source of biomarker candidates for male infertility and indicates that functional abnormalities of the epididymis and prostate can contribute to AS. We identified DJ-1-a protein that has been shown elsewhere to be involved in the control of oxidative stress (OS)-as a downregulated protein in AS seminal plasma. The levels of DJ-1 in AS seminal plasma were about half of those in the control samples. In addition, the levels of reactive oxygen species were 3.3-fold higher in the AS samples than in the controls. Taken together, these data suggest that downregulation of DJ-1 is involved in OS in semen, and therefore affects the quality of the semen.
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Häkkinen J, Vincic G, Månsson O, Wårell K, Levander F. The Proteios Software Environment: An Extensible Multiuser Platform for Management and Analysis of Proteomics Data. J Proteome Res 2009; 8:3037-43. [DOI: 10.1021/pr900189c] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jari Häkkinen
- Department of Oncology, Clinical Sciences, Lund University, BMC C13, SE-221 84, Lund, Sweden, Department of Theoretical Physics, Lund University, Sölvegatan 14a, SE-223 62 Lund, Sweden, Department of Immunotechnology, Lund University, BMC D13, SE-221 84, Lund, Sweden, and CREATE Health Strategic Centre for Translational Cancer Research, Lund University, SE-22184 Lund, Sweden
| | - Gregory Vincic
- Department of Oncology, Clinical Sciences, Lund University, BMC C13, SE-221 84, Lund, Sweden, Department of Theoretical Physics, Lund University, Sölvegatan 14a, SE-223 62 Lund, Sweden, Department of Immunotechnology, Lund University, BMC D13, SE-221 84, Lund, Sweden, and CREATE Health Strategic Centre for Translational Cancer Research, Lund University, SE-22184 Lund, Sweden
| | - Olle Månsson
- Department of Oncology, Clinical Sciences, Lund University, BMC C13, SE-221 84, Lund, Sweden, Department of Theoretical Physics, Lund University, Sölvegatan 14a, SE-223 62 Lund, Sweden, Department of Immunotechnology, Lund University, BMC D13, SE-221 84, Lund, Sweden, and CREATE Health Strategic Centre for Translational Cancer Research, Lund University, SE-22184 Lund, Sweden
| | - Kristofer Wårell
- Department of Oncology, Clinical Sciences, Lund University, BMC C13, SE-221 84, Lund, Sweden, Department of Theoretical Physics, Lund University, Sölvegatan 14a, SE-223 62 Lund, Sweden, Department of Immunotechnology, Lund University, BMC D13, SE-221 84, Lund, Sweden, and CREATE Health Strategic Centre for Translational Cancer Research, Lund University, SE-22184 Lund, Sweden
| | - Fredrik Levander
- Department of Oncology, Clinical Sciences, Lund University, BMC C13, SE-221 84, Lund, Sweden, Department of Theoretical Physics, Lund University, Sölvegatan 14a, SE-223 62 Lund, Sweden, Department of Immunotechnology, Lund University, BMC D13, SE-221 84, Lund, Sweden, and CREATE Health Strategic Centre for Translational Cancer Research, Lund University, SE-22184 Lund, Sweden
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Li Q, Roxas BA. An assessment of false discovery rates and statistical significance in label-free quantitative proteomics with combined filters. BMC Bioinformatics 2009; 10:43. [PMID: 19187558 PMCID: PMC2645366 DOI: 10.1186/1471-2105-10-43] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Accepted: 02/02/2009] [Indexed: 11/25/2022] Open
Abstract
Background Many studies have provided algorithms or methods to assess a statistical significance in quantitative proteomics when multiple replicates for a protein sample and a LC/MS analysis are available. But, confidence is still lacking in using datasets for a biological interpretation without protein sample replicates. Although a fold-change is a conventional threshold that can be used when there are no sample replicates, it does not provide an assessment of statistical significance such as a false discovery rate (FDR) which is an important indicator of the reliability to identify differentially expressed proteins. In this work, we investigate whether differentially expressed proteins can be detected with a statistical significance from a pair of unlabeled protein samples without replicates and with only duplicate LC/MS injections per sample. A FDR is used to gauge the statistical significance of the differentially expressed proteins. Results We have experimented to operate on several parameters to control a FDR, including a fold-change, a statistical test, and a minimum number of permuted significant pairings. Although none of these parameters alone gives a satisfactory control of a FDR, we find that a combination of these parameters provides a very effective means to control a FDR without compromising the sensitivity. The results suggest that it is possible to perform a significance analysis without protein sample replicates. Only duplicate LC/MS injections per sample are needed. We illustrate that differentially expressed proteins can be detected with a FDR between 0 and 15% at a positive rate of 4–16%. The method is evaluated for its sensitivity and specificity by a ROC analysis, and is further validated with a [15N]-labeled internal-standard protein sample and additional unlabeled protein sample replicates. Conclusion We demonstrate that a statistical significance can be inferred without protein sample replicates in label-free quantitative proteomics. The approach described in this study would be useful in many exploratory experiments where a sample amount or instrument time is limited. Naturally, this method is also suitable for proteomics experiments where multiple sample replicates are available. It is simple, and is complementary to other more sophisticated algorithms that are not designed for dealing with a small number of sample replicates.
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Affiliation(s)
- Qingbo Li
- Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA.
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