1
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Guan X, Brownstein NC, Young NL, Marshall AG. Ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry and tandem mass spectrometry for peptide de novo amino acid sequencing for a seven-protein mixture by paired single-residue transposed Lys-N and Lys-C digestion. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:207-217. [PMID: 27813191 DOI: 10.1002/rcm.7783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/29/2016] [Accepted: 10/30/2016] [Indexed: 06/06/2023]
Abstract
RATIONALE Bottom-up tandem mass spectrometry (MS/MS) is regularly used in proteomics to identify proteins from a sequence database. De novo sequencing is also available for sequencing peptides with relatively short sequence lengths. We recently showed that paired Lys-C and Lys-N proteases produce peptides of identical mass and similar retention time, but different tandem mass spectra. Such parallel experiments provide complementary information, and allow for up to 100% MS/MS sequence coverage. METHODS Here, we report digestion by paired Lys-C and Lys-N proteases of a seven-protein mixture: human hemoglobin alpha, bovine carbonic anhydrase 2, horse skeletal muscle myoglobin, hen egg white lysozyme, bovine pancreatic ribonuclease, bovine rhodanese, and bovine serum albumin, followed by reversed-phase nanoflow liquid chromatography, collision-induced dissociation, and 14.5 T Fourier transform ion cyclotron resonance mass spectrometry. RESULTS Matched pairs of product peptide ions of equal precursor mass and similar retention times from each digestion are compared, leveraging single-residue transposed information with independent interferences to confidently identify fragment ion types, residues, and peptides. Selected pairs of product ion mass spectra for de novo sequenced protein segments from each member of the mixture are presented. CONCLUSIONS Pairs of the transposed product ions as well as complementary information from the parallel experiments allow for both high MS/MS coverage for long peptide sequences and high confidence in the amino acid identification. Moreover, the parallel experiments in the de novo sequencing reduce false-positive matches of product ions from the single-residue transposed peptides from the same segment, and thereby further improve the confidence in protein identification. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Xiaoyan Guan
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
| | - Naomi C Brownstein
- Department of Behavioral Sciences and Social Medicine, College of Medicine, Florida State University, 1115 W. Call St., Tallahassee, FL, 32306, USA
- Department of Statistics, Florida State University, 117 N. Woodward Ave., Tallahassee, FL, 32306, USA
| | - Nicolas L Young
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, One Baylor Plaza, MS-125, Houston, TX, 77030-3411, USA
| | - Alan G Marshall
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32303, USA
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2
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Zubarev R. Protein primary structure using orthogonal fragmentation techniques in Fourier transform mass spectrometry. Expert Rev Proteomics 2014; 3:251-61. [PMID: 16608437 DOI: 10.1586/14789450.3.2.251] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Proteomics analysis using tandem mass spectrometry requires informative backbone fragmentation of peptide ions. Collision-activated dissociation (CAD) of cations alone is not sufficiently informative to satisfy all requirements. Thus, there is a need to supplement CAD with a complementary fragmentation technique. Electron capture dissociation (ECD) is complementary to collisional excitation in terms of the cleavage of a different bond (N-Calpha versus C-N bond) and other properties. CAD-ECD combination improves protein identification and enables high-throughput de novo sequencing of peptides. ECD and its variants are also useful in mapping labile post-translational modifications in proteins and isomer differentiation; for example, distinguishing Ile from Leu, iso-Asp from Asp and even D- from L-amino acid residues.
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Affiliation(s)
- Roman Zubarev
- Laboratory for Biological & Medical Mass Spectrometry, Uppsala University, Box 583, Uppsala S-751 23, Sweden.
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3
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Cristoni S, Bernardi LR. Bioinformatics in mass spectrometry data analysis for proteomics studies. Expert Rev Proteomics 2014; 1:469-83. [PMID: 15966842 DOI: 10.1586/14789450.1.4.469] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Mass spectrometry is a technique widely employed for the identification and characterization of proteins. The role of bioinformatics is fundamental for the elaboration of mass spectrometry data due to the amount of data that this technique can produce. To process data efficiently, new software packages and algorithms are continuously being developed to improve protein identification and characterization in terms of high-throughput and statistical accuracy. However, many limitations exist concerning bioinformatics spectral data elaboration. This review aims to critically cover the recent and future developments of new bioinformatics approaches in mass spectrometry data analysis for proteomics studies.
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Affiliation(s)
- Simone Cristoni
- Università degli Studi di Milano, Via Fratelli Cervi 93, 20090 Segrate, Milan, Italy.
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4
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Nagore LI, Nadeau RJ, Guo Q, Jadhav YLA, Jarrett HW, Haskins WE. Purification and characterization of transcription factors. MASS SPECTROMETRY REVIEWS 2013; 32:386-398. [PMID: 23832591 PMCID: PMC3758410 DOI: 10.1002/mas.21369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 11/19/2012] [Accepted: 11/19/2012] [Indexed: 06/02/2023]
Abstract
Transcription factors (TFs) are essential for the expression of all proteins, including those involved in human health and disease. However, TFs are resistant to proteomic characterization because they are frequently masked by more abundant proteins due to the limited dynamic range of capillary liquid chromatography-tandem mass spectrometry and protein database searching. Purification methods, particularly strategies that exploit the high affinity of TFs for DNA response elements (REs) on gene promoters, can enrich TFs prior to proteomic analysis to improve dynamic range and penetrance of the TF proteome. For example, trapping of TF complexes specific for particular REs has been achieved by recovering the element DNA-protein complex on solid supports. Additional methods for improving dynamic range include two- and three-dimensional gel electrophoresis incorporating electrophoretic mobility shift assays and Southwestern blotting for detection. Here we review methods for TF purification and characterization. We fully expect that future investigations will apply these and other methods to illuminate this important but challenging proteome.
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Affiliation(s)
- LI Nagore
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
| | - RJ Nadeau
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
| | - Q Guo
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
| | - YLA Jadhav
- Pediatric Biochemistry Laboratory, University of Texas at San Antonio, San Antonio, TX, 78249
- RCMI Proteomics, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
| | - HW Jarrett
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
| | - WE Haskins
- Pediatric Biochemistry Laboratory, University of Texas at San Antonio, San Antonio, TX, 78249
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249
- Departments of Biology, University of Texas at San Antonio, San Antonio, TX, 78249
- RCMI Proteomics, University of Texas at San Antonio, San Antonio, TX, 78249
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Interdisciplinary Health Research, University of Texas at San Antonio, San Antonio, TX, 78249
- Center for Research & Training in the Sciences, University of Texas at San Antonio, San Antonio, TX, 78249
- Departments of Medicine, Division of Hematology & Medical Oncology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229
- Cancer Therapy & Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229
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5
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Van Riper SK, de Jong EP, Carlis JV, Griffin TJ. Mass Spectrometry-Based Proteomics: Basic Principles and Emerging Technologies and Directions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 990:1-35. [DOI: 10.1007/978-94-007-5896-4_1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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6
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Guthals A, Bandeira N. Peptide identification by tandem mass spectrometry with alternate fragmentation modes. Mol Cell Proteomics 2012; 11:550-7. [PMID: 22595789 PMCID: PMC3434779 DOI: 10.1074/mcp.r112.018556] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 05/04/2012] [Indexed: 11/06/2022] Open
Abstract
The high-throughput nature of proteomics mass spectrometry is enabled by a productive combination of data acquisition protocols and the computational tools used to interpret the resulting spectra. One of the key components in mainstream protocols is the generation of tandem mass (MS/MS) spectra by peptide fragmentation using collision induced dissociation, the approach currently used in the large majority of proteomics experiments to routinely identify hundreds to thousands of proteins from single mass spectrometry runs. Complementary to these, alternative peptide fragmentation methods such as electron capture/transfer dissociation and higher-energy collision dissociation have consistently achieved significant improvements in the identification of certain classes of peptides, proteins, and post-translational modifications. Recognizing these advantages, mass spectrometry instruments now conveniently support fine-tuned methods that automatically alternate between peptide fragmentation modes for either different types of peptides or for acquisition of multiple MS/MS spectra from each peptide. But although these developments have the potential to substantially improve peptide identification, their routine application requires corresponding adjustments to the software tools and procedures used for automated downstream processing. This review discusses the computational implications of alternative and alternate modes of MS/MS peptide fragmentation and addresses some practical aspects of using such protocols for identification of peptides and post-translational modifications.
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Affiliation(s)
- Adrian Guthals
- Department of Computer Science and Engineering, University of California, San Diego, California, USA
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7
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Mohimani H, Yang YL, Liu WT, Hsieh PW, Dorrestein PC, Pevzner PA. Sequencing cyclic peptides by multistage mass spectrometry. Proteomics 2011; 11:3642-50. [PMID: 21751357 DOI: 10.1002/pmic.201000697] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Revised: 05/16/2011] [Accepted: 06/09/2011] [Indexed: 11/08/2022]
Abstract
Some of the most effective antibiotics (e.g. Vancomycin and Daptomycin) are cyclic peptides produced by non-ribosomal biosynthetic pathways. While hundreds of biomedically important cyclic peptides have been sequenced, the computational techniques for sequencing cyclic peptides are still in their infancy. Previous methods for sequencing peptide antibiotics and other cyclic peptides are based on Nuclear Magnetic Resonance spectroscopy, and require large amount (miligrams) of purified materials that, for most compounds, are not possible to obtain. Recently, development of MS-based methods has provided some hope for accurate sequencing of cyclic peptides using picograms of materials. In this paper we develop a method for sequencing of cyclic peptides by multistage MS, and show its advantages over single-stage MS. The method is tested on known and new cyclic peptides from Bacillus brevis, Dianthus superbus and Streptomyces griseus, as well as a new family of cyclic peptides produced by marine bacteria.
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Affiliation(s)
- Hosein Mohimani
- Department of Electrical and Computer Engineering, UC San Diego, CA, USA
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8
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SUN HC, ZHANG JY, LIU H, ZHANG W, XU CM, MA HB, ZHU YP, XIE HW. Algorithm Development of de novo Peptide Sequencing Via Tandem Mass Spectrometry. PROG BIOCHEM BIOPHYS 2011. [DOI: 10.3724/sp.j.1206.2010.00226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Ahrné E, Müller M, Lisacek F. Unrestricted identification of modified proteins using MS/MS. Proteomics 2010; 10:671-86. [PMID: 20029840 DOI: 10.1002/pmic.200900502] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Proteins undergo PTM, which modulates their structure and regulates their function. Estimates of the PTM occurrence vary but it is safe to assume that there is an important gap between what is currently known and what remains to be discovered. The highest throughput and most comprehensive efforts to catalogue protein mixtures have so far been using MS-based shotgun proteomics. The standard approach to analyse MS/MS data is to use Peptide Fragment Fingerprinting tools such as Sequest, MASCOT or Phenyx. These tools commonly identify 5-30% of the spectra in an MS/MS data set while only a limited list of predefined protein modifications can be screened. An important part of the unidentified spectra is likely to be spectra of peptides carrying modifications not considered in the search. Bioinformatics for PTM discovery is an active area of research. In this review we focus on software solutions developed for unrestricted identification of modifications in MS/MS data, here referred to as open modification search tools. We give an overview of the conceptually different algorithmic solutions to evaluate the large number of candidate peptides per spectrum when accounting for modifications of unrestricted size and demonstrate the value of results of large-scale open modification search studies. Efficient and easy-to-use tools for protein modification discovery should prove valuable in the quest for mapping the dynamics of proteomes.
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Affiliation(s)
- Erik Ahrné
- Swiss Institute of Bioinformatics, Proteome Informatics Group, Geneva, Switzerland.
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10
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Nikoulina SE, Andon NL, McCowen KM, Hendricks MD, Lowe C, Taylor SW. A primary colonic crypt model enriched in enteroendocrine cells facilitates a peptidomic survey of regulated hormone secretion. Mol Cell Proteomics 2010; 9:728-41. [PMID: 20081152 DOI: 10.1074/mcp.m900529-mcp200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
To enable the first physiologically relevant peptidomic survey of gastrointestinal tissue, we have developed a primary mouse colonic crypt model enriched for enteroendocrine L-cells. The cells in this model were phenotypically profiled using PCR-based techniques and showed peptide hormone and secretory and processing marker expression at mRNA levels that were increased relative to the parent tissue. Co-localization of glucagon-like peptide-1 and peptide YY, a characteristic feature of L-cells, was demonstrated by double label immunocytochemistry. The L-cells displayed regulated hormone secretion in response to physiological and pharmacological stimuli as measured by immunoassay. Using a high resolution mass spectrometry-based platform, more than 50 endogenous peptides (<16 kDa), including all known major hormones, were identified a priori. The influence of culture conditions on peptide relative abundance and post-translational modification was characterized. The relative abundance of secreted peptides in the presence/absence of the stimulant forskolin was measured by label-free quantification. All peptides exhibiting a statistically significant increase in relative concentration in the culture media were derived from prohormones, consistent with a cAMP-coupled response. The only peptides that exhibited a statistically significant decrease in secretion on forskolin stimulation were derived from annexin A1 and calcyclin. Biophysical interactions between annexin A1 and calcyclin have been reported very recently and may have functional consequences. This work represents the first step in characterizing physiologically relevant peptidomic secretion of gastrointestinally derived primary cells and will aid in elucidating new endocrine function.
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11
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Datta R, Bern M. Spectrum fusion: using multiple mass spectra for de novo Peptide sequencing. J Comput Biol 2009; 16:1169-82. [PMID: 19645594 DOI: 10.1089/cmb.2009.0122] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
We report on a new algorithm for combining the information from several mass spectra of the same peptide. The algorithm automatically learns peptide fragmentation patterns, so that it can handle spectra from any instrument and fragmentation technique. We demonstrate the utility of the algorithm, and the power of multiple spectra, by showing that combining pairs of spectra (one CID and one ETD) greatly improves de novo sequencing success rates.
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Affiliation(s)
- Ritendra Datta
- Computing Science Lab, Palo Alto Research Center (PARC) , Palo Alto, California, USA.
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12
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Shenar N, Sommerer N, Martinez J, Enjalbal C. Comparison of LID versus CID activation modes in tandem mass spectrometry of peptides. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:621-632. [PMID: 19097045 DOI: 10.1002/jms.1535] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We report our contribution to the systematic investigation of peptide fragmentations performed on high-performance Tof equipment, operating in MS and MS/MS modes, such as ESI-QqTof and MALDI-Tof/Tof instruments that are commonly available today in proteomic laboratories. Whereas the former analyzer's configuration provides low-energy collision-induced dissociations (CID), the latter allows tunable activation methods of the selected parent ion to induce either metastable laser-induced dissociations (LID) or high-energy CID ('gas on spectra LID'). Fragmentation of the monoprotonated ion of 53 peptides (FW 807-2853 g/mol) was undertaken upon low-energy CID on an ESI-QTof mass spectrometer (Waters) as well as high-energy CID and LID conditions on a MALDI Ultraflex mass spectrometer (Bruker). Systematic comparison of MS/MS spectra provided useful information on the performance of each piece of equipment for efficient peptide sequencing and also insights into the observed fragmentation behaviors.
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Affiliation(s)
- Nawar Shenar
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS-Universités Montpellier 1 et 2, Bâtiment Chimie (17), Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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13
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Bandeira N, Olsen JV, Mann JV, Mann M, Pevzner PA. Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. Bioinformatics 2008; 24:i416-23. [PMID: 18785330 PMCID: PMC2718660 DOI: 10.1093/bioinformatics/btn184] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Despite a recent surge of interest in database-independent peptide identifications, accurate de novo peptide sequencing remains an elusive goal. While the recently introduced spectral network approach resulted in accurate peptide sequencing in low-complexity samples, its success depends on the chance of presence of spectra from overlapping peptides. On the other hand, while multistage mass spectrometry (collecting multiple MS 3 spectra from each MS 2 spectrum) can be applied to all spectra in a complex sample, there are currently no software tools for de novo peptide sequencing by multistage mass spectrometry. We describe a rigorous probabilistic framework for analyzing spectra of overlapping peptides and show how to apply it for multistage mass spectrometry. Our software results in both accurate de novo peptide sequencing from multistage mass spectra (despite the inferior quality of MS 3 spectra) and improved interpretation of spectral networks. We further study the problem of de novo peptide sequencing with accurate parent mass (but inaccurate fragment masses), the protocol that may soon become the dominant mode of spectral acquisition. Most existing peptide sequencing algorithms (based on the spectrum graph approach) do not track the accurate parent mass and are thus not equipped for solving this problem. We describe a de novo peptide sequencing algorithm aimed at this experimental protocol and show that it improves the sequencing accuracy on both tandem and multistage mass spectrometry. Availability: The open-source implementation of our software is available at http://proteomics.bioprojects.org. Contact:bandeira@ucsd.edu Supplementary information:: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, USA.
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14
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Wan Y, Cripps D, Thomas S, Campbell P, Ambulos N, Chen T, Yang A. PhosphoScan: a probability-based method for phosphorylation site prediction using MS2/MS3 pair information. J Proteome Res 2008; 7:2803-11. [PMID: 18549264 DOI: 10.1021/pr700773p] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phosphopeptide identification and phosphorylation site localization are crucial aspects of many biological studies. Furthermore, multiple phosphorylations of peptides make site localization even more difficult. We developed a probability-based method to unambiguously determine phosphorylation sites within phosphopeptides using MS2/3 pair information. A comparison test was performed with SEQUEST and MASCOT predictions using a spectral data set from a synthetic doubly phosphorylated peptide, and the results showed that PhosphoScan analysis yielded a 63% phosphopeptide localization improvement compared with SEQUEST and a 57% improvement compared with MASCOT.
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Affiliation(s)
- Yunhu Wan
- Greenebaum Cancer Center, University of Maryland, Baltimore, Maryland 21201, USA.
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15
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Ulintz PJ, Bodenmiller B, Andrews PC, Aebersold R, Nesvizhskii AI. Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence. Mol Cell Proteomics 2007; 7:71-87. [PMID: 17872894 DOI: 10.1074/mcp.m700128-mcp200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Improvements in ion trap instrumentation have made n-dimensional mass spectrometry more practical. The overall goal of the study was to describe a model for making use of MS(2) and MS(3) information in mass spectrometry experiments. We present a statistical model for adjusting peptide identification probabilities based on the combined information obtained by coupling peptide assignments of consecutive MS(2) and MS(3) spectra. Using two data sets, a mixture of known proteins and a complex phosphopeptide-enriched sample, we demonstrate an increase in discriminating power of the adjusted probabilities compared with models using MS(2) or MS(3) data only. This work also addresses the overall value of generating MS(3) data as compared with an MS(2)-only approach with a focus on the analysis of phosphopeptide data.
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Affiliation(s)
- Peter J Ulintz
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48103, USA
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16
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Affiliation(s)
- Tao Liu
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Mikhail E. Belov
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Navdeep Jaitly
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Richard D. Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
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17
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Granvogl B, Plöscher M, Eichacker LA. Sample preparation by in-gel digestion for mass spectrometry-based proteomics. Anal Bioanal Chem 2007; 389:991-1002. [PMID: 17639354 DOI: 10.1007/s00216-007-1451-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Revised: 06/14/2007] [Accepted: 06/20/2007] [Indexed: 10/23/2022]
Abstract
The proteomic characterization of proteins and protein complexes from cells and cell organelles is the next challenge for investigation of the cell. After isolation of the cell compartment, three steps have to be performed in the laboratory to yield information about the proteins present. The protein mixtures must be separated into single species, broken down into peptides, and, finally, identified by mass spectrometry. Most scientists engaged in proteomics separate proteins by electrophoresis. For characterization and identification of proteomes, mass spectrometry of peptides is the method of choice. To combine electrophoresis and mass spectrometry, sample preparation by "in-gel digestion" has been developed. Many procedures are available for in-gel digestion, which inspired us to review in-gel digestion approaches.
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Affiliation(s)
- Bernhard Granvogl
- Department für Biologie I, Ludwig-Maximilians-Universität, Menzinger Strasse 67, 80638, München, Germany
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18
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Qiu H, Wang Y. Probing adenosine nucleotide-binding proteins with an affinity-labeled nucleotide probe and mass spectrometry. Anal Chem 2007; 79:5547-56. [PMID: 17602667 PMCID: PMC2637870 DOI: 10.1021/ac0622375] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mass spectrometry combined with chemical labeling strategies has become very important in biological analysis. Herein, we described the application of a biotin-conjugated acyl nucleotide for probing adenosine nucleotide-binding proteins. We demonstrated that the probe reacted specifically with the lysine residue at the nucleotide-binding site of two purified adenosine nucleotide-binding proteins, Escherichia coli recombinase A (RecA) and Saccharomyces cerevisiae alcohol dehydrogenase-I (YADH-I). A single conjugate peptide with a specifically labeled lysine residue was identified, by using LC-MS/MS, from the tryptic digestion mixture of the reaction products of the nucleotide analogue with RecA or YADH-I. The strategy, which involved labeling reaction, enzymatic digestion, affinity purification, and LC-MS/MS analysis, was relatively simple, fast, and straightforward. The method should be generally applicable for the identification of lysine residues at the nucleotide-binding site of other proteins. The biotin-conjugated acyl nucleotide probe also allowed for the enrichment and identification of nucleotide-binding proteins from complex protein mixtures; we showed that more than 50 adenosine nucleotide-binding proteins could be identified from the whole-cell lysates of HeLa-S3 and WM-266-4 cells.
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Affiliation(s)
- Haibo Qiu
- Department of Chemistry-027, University of California, Riverside, California 92521-0403, USA
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19
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Bandeira N, Tsur D, Frank A, Pevzner PA. Protein identification by spectral networks analysis. Proc Natl Acad Sci U S A 2007; 104:6140-5. [PMID: 17404225 PMCID: PMC1851064 DOI: 10.1073/pnas.0701130104] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Advances in tandem mass spectrometry (MS/MS) steadily increase the rate of generation of MS/MS spectra. As a result, the existing approaches that compare spectra against databases are already facing a bottleneck, particularly when interpreting spectra of modified peptides. Here we explore a concept that allows one to perform an MS/MS database search without ever comparing a spectrum against a database. We propose to take advantage of spectral pairs, which are pairs of spectra obtained from overlapping (often nontryptic) peptides or from unmodified and modified versions of the same peptide. Having a spectrum of a modified peptide paired with a spectrum of an unmodified peptide allows one to separate the prefix and suffix ladders, to greatly reduce the number of noise peaks, and to generate a small number of peptide reconstructions that are likely to contain the correct one. The MS/MS database search is thus reduced to extremely fast pattern-matching (rather than time-consuming matching of spectra against databases). In addition to speed, our approach provides a unique paradigm for identifying posttranslational modifications by means of spectral networks analysis.
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Affiliation(s)
- Nuno Bandeira
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA.
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Poster Session C. Mol Cell Proteomics 2007. [DOI: 10.1016/s1535-9476(20)32190-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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21
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Frank AM, Savitski MM, Nielsen MN, Zubarev RA, Pevzner PA. De novo peptide sequencing and identification with precision mass spectrometry. J Proteome Res 2007; 6:114-23. [PMID: 17203955 PMCID: PMC2538556 DOI: 10.1021/pr060271u] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The recent proliferation of novel mass spectrometers such as Fourier transform, QTOF, and OrbiTrap marks a transition into the era of precision mass spectrometry, providing a 2 orders of magnitude boost to the mass resolution, as compared to low-precision ion-trap detectors. We investigate peptide de novo sequencing by precision mass spectrometry and explore some of the differences when compared to analysis of low-precision data. We demonstrate how the dramatically improved performance of de novo sequencing with precision mass spectrometry paves the way for novel approaches to peptide identification that are based on direct sequence lookups, rather than comparisons of spectra to a database. With the direct sequence lookup, it is not only possible to search a database very efficiently, but also to use the database in novel ways, such as searching for products of alternative splicing or products of fusion proteins in cancer. Our de novo sequencing software is available for download at http://peptide.ucsd.edu/.
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Affiliation(s)
- Ari M. Frank
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, California 92093-0404
| | - Mikhail M. Savitski
- Laboratory for Biological and Medical Mass Spectrometry, Uppsala University, Uppsala, Sweden
| | - Michael N. Nielsen
- Laboratory for Biological and Medical Mass Spectrometry, Uppsala University, Uppsala, Sweden
| | - Roman A. Zubarev
- Laboratory for Biological and Medical Mass Spectrometry, Uppsala University, Uppsala, Sweden
| | - Pavel A. Pevzner
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, California 92093-0404
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22
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Nordhoff E, Lehrach H. Identification and characterization of DNA-binding proteins by mass spectrometry. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2006; 104:111-95. [PMID: 17290821 DOI: 10.1007/10_2006_037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mass spectrometry is the most sensitive and specific analytical technique available for protein identification and quantification. Over the past 10 years, by the use of mass spectrometric techniques hundreds of previously unknown proteins have been identified as DNA-binding proteins that are involved in the regulation of gene expression, replication, or DNA repair. Beyond this task, the applications of mass spectrometry cover all aspects from sequence and modification analysis to protein structure, dynamics, and interactions. In particular, two new, complementary ionization techniques have made this possible: matrix-assisted laser desorption/ionization and electrospray ionization. Their combination with different mass-over-charge analyzers and ion fragmentation techniques, as well as specific enzymatic or chemical reactions and other analytical techniques, has led to the development of a broad repertoire of mass spectrometric methods that are now available for the identification and detailed characterization of DNA-binding proteins. These techniques, how they work, what their requirements and limitations are, and selected examples that document their performance are described and discussed in this chapter.
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Affiliation(s)
- Eckhard Nordhoff
- Department Lehrach, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
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23
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Mujezinovic N, Raidl G, Hutchins JRA, Peters JM, Mechtler K, Eisenhaber F. Cleaning of raw peptide MS/MS spectra: Improved protein identification following deconvolution of multiply charged peaks, isotope clusters, and removal of background noise. Proteomics 2006; 6:5117-31. [PMID: 16955515 DOI: 10.1002/pmic.200500928] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The dominant ions in MS/MS spectra of peptides, which have been fragmented by low-energy CID, are often b-, y-ions and their derivatives resulting from the cleavage of the peptide bonds. However, MS/MS spectra typically contain many more peaks. These can result not only from isotope variants and multiply charged replicates of the peptide fragmentation products but also from unknown fragmentation pathways, sample-specific or systematic chemical contaminations or from noise generated by the electronic detection system. The presence of this background complicates spectrum interpretation. Besides dramatically prolonged computation time, it can lead to incorrect protein identification, especially in the case of de novo sequencing algorithms. Here, we present an algorithm for detection and transformation of multiply charged peaks into singly charged monoisotopic peaks, removal of heavy isotope replicates, and random noise. A quantitative criterion for the recognition of some noninterpretable spectra has been derived as a byproduct. The approach is based on numerical spectral analysis and signal detection methods. The algorithm has been implemented in a stand-alone computer program called MS Cleaner that can be obtained from the authors upon request.
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24
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Olson MT, Epstein JA, Yergey AL. De novo peptide sequencing using exhaustive enumeration of peptide composition. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:1041-1049. [PMID: 16735127 DOI: 10.1016/j.jasms.2006.03.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Revised: 03/09/2006] [Accepted: 03/13/2006] [Indexed: 05/09/2023]
Abstract
We introduce the use of a peptide composition lookup table indexed by residual mass and number of amino acids for de novo sequencing of polypeptides. Polypeptides of 1600 Daltons (Da) or more can be sequenced effectively through exhaustive compositional analysis of MS/MS spectra obtained by unimolecular decomposition (without CID) in a MALDI TOF/TOF despite a fragment mass accuracy of 50 mDa. Peaks are referenced against the lookup table to obtain a complete profile of amino acid combinations, and combinations are assembled into series of increasing length. Concatenating the differences between successive entries in compositional series yields peptide sequences that can be scored and ranked according to signal intensity. While the current work involves measurements acquired on MALDI TOF-TOF, such general treatment of the data anticipates extension to other types of mass analyzers.
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Affiliation(s)
- Matthew T Olson
- Laboratory of Cellular and Molecular Biophysics, NICHD, NIH, Bethesda, Maryland, USA
| | | | - Alfred L Yergey
- Laboratory of Cellular and Molecular Biophysics, NICHD, NIH, Bethesda, Maryland, USA.
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25
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Granvogl B, Reisinger V, Eichacker LA. Mapping the proteome of thylakoid membranes byde novo sequencing of intermembrane peptide domains. Proteomics 2006; 6:3681-95. [PMID: 16758444 DOI: 10.1002/pmic.200500924] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The proteome of a membrane compartment has been investigated by de novo sequence analysis after tryptic in gel digestion. Protein complexes and corresponding protein subunits were separated by a 2-D Blue Native (BN)/SDS-PAGE system. The transmembrane proteins of thylakoid membranes from a higher plant (Hordeum vulgare L.) were identified by the primary sequence of hydrophilic intermembrane peptide domains using nano ESI-MS/MS-analysis. Peptide analysis revealed that lysine residues of membrane proteins are primarily situated in the intermembrane domains. We concluded that esterification of lysine residues with fluorescent dyes may open the opportunity to label membrane proteins still localized in native protein complexes within the membrane phase. We demonstrate that covalent labelling of membrane proteins with the fluorescent dye Cy3 allows high sensitive visualization of protein complexes after 2-D BN/SDS-PAGE. We show that pre-electrophoretic labelling of protein subunits supplements detection of proteins by post-electrophoretic staining with silver and CBB and assists in completing the identification of the membrane proteome.
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Affiliation(s)
- Bernhard Granvogl
- Department für Biologie I, Ludwig-Maximilians-Universität, München, Germany
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26
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Meija J. Mathematical tools in analytical mass spectrometry. Anal Bioanal Chem 2006; 385:486-99. [PMID: 16514517 DOI: 10.1007/s00216-006-0298-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Revised: 12/14/2005] [Accepted: 01/05/2006] [Indexed: 10/25/2022]
Abstract
Over the last few decades, mass spectrometry has become a powerful tool for exploring various aspects of molecular processes occurring in biological systems. Such exploration is leading to a greater understanding of various complex life processes; unraveling these processes poses the greatest challenge to contemporary bioscience. With due respect to sample preparation, data analysis is rapidly becoming a major obstacle to the conversion of experimental knowledge into valid conclusions. It is interesting to note that many problems related to mass spectrometry can be solved using techniques from computer science, graph theory and discrete mathematics. The aim of this manuscript is to recollect several essays that demonstrate the power and the need to apply such skills to mass spectrometry data interpretation. Special attention is paid to situations where traditional chemical analysis reaches its limits but mathematical reasoning can still allow us to reach valid conclusions.
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Affiliation(s)
- Juris Meija
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221-0172, USA.
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27
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Hernandez P, Müller M, Appel RD. Automated protein identification by tandem mass spectrometry: issues and strategies. MASS SPECTROMETRY REVIEWS 2006; 25:235-54. [PMID: 16284939 DOI: 10.1002/mas.20068] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Protein identification by tandem mass spectrometry (MS/MS) is key to most proteomics projects and has been widely explored in bioinformatics research. Obtaining good and trustful identification results has important implications for biological and clinical work. Although well matured, automated software identification of proteins from MS/MS data still faces a number of obstacles due to the complexity of the proteome or procedural issues of mass spectrometry data acquisition. Expected or unexpected modifications of the peptide sequences, polymorphisms, errors in databases, missed or non-specific cleavages, unusual fragmentation patterns, and single MS/MS spectra of multiple peptides of the same m/z are so many pitfalls for identification algorithms. A lot of research work has been carried out in recent years that yielded new strategies to handle a number of these issues. Multiple MS/MS identification algorithms are now available or have been theoretically described. The difficulty resides in choosing the most adapted method for each type of spectra being identified. This review presents an overview of the state-of-the-art bioinformatics approaches to the identification of proteins by MS/MS to help the reader doing the spade work of finding the right tools among the many possibilities offered.
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28
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Zhong H, Li L. An algorithm for interpretation of low-energy collision-induced dissociation product ion spectra for de novo sequencing of peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:1084-1096. [PMID: 15803512 DOI: 10.1002/rcm.1892] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
An algorithm for interpretation of product ion spectra of peptides generated from ion trap mass spectrometry is developed for de novo amino acid sequencing of peptides for the purpose of protein identification. It is based on a multi-pass analysis of product ion data using a rigorous data extraction and sequence interpretation protocol in the initial pass. The extraction/interpretation algorithm becomes more relaxed in subsequent passes, considering more of the fragment ions, and potentially more sequence candidates. The possible peptide sequences generated by the algorithm are scored according to those sequences which best explain the fragment ion spectrum. These sequences are searched against a protein database using a BLAST search engine to find likely protein candidates. The method is also suitable for locating and determining protein modifications, and can be applied to de novo interpretation of peptide fragment ions in the tandem mass (MS/MS) spectrum produced from a mixture of two peptides having similar nominal mass, but different sequences. Using a known protein, bovine serum albumin, as an example, it is illustrated that this method is rapid and efficient for MS/MS spectral interpretation. This method combined with BLAST programs is then applied to search homologies and to generate information on post-translational modifications of an unknown protein isolated from shark cartilage that does not have a complete genome or proteome database.
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Affiliation(s)
- Hongying Zhong
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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29
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Olsen JV, Mann M. Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc Natl Acad Sci U S A 2004; 101:13417-22. [PMID: 15347803 PMCID: PMC518757 DOI: 10.1073/pnas.0405549101] [Citation(s) in RCA: 247] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
MS-based proteomics usually involves the fragmentation of tryptic peptides (tandem MS or MS(2)) and their identification by searching protein sequence databases. In ion trap instruments fragments can be further fragmented and analyzed, a process termed MS/MS/MS or MS(3). Here, we report that efficient ion capture in a linear ion trap leads to MS(3) acquisition times and spectra quality similar to those for MS(2) experiments with conventional 3D ion traps. Fragmentation of N- or C-terminal ions resulted in informative and low-background spectra, even at subfemtomol levels of peptide. Typically C-terminal ions are chosen for further fragmentation, and the MS(3) spectrum greatly constrains the C-terminal amino acids of the peptide sequence. MS(3) spectra allow resolution of ambiguities in identification, a crucial problem in proteomics. Because of the sensitivity and rapid scan rates of the linear ion trap, several MS(3) spectra per peptide can be obtained even when sequencing very complex mixtures. We calculate the probability that an experimental MS(3) spectrum originates from fragmentation of a given N- or C-terminal ion of a peptide under consideration. This MS(3) identification score can be combined with the MS(2) scores of the precursor peptide from existing search engines. When MS(3) is performed on the linear ion trap-Fourier transform mass spectrometer combination, accurate peptide masses further increase confidence in peptide identification.
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Affiliation(s)
- Jesper V Olsen
- Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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30
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Wilke A, Rückert C, Bartels D, Dondrup M, Goesmann A, Hüser AT, Kespohl S, Linke B, Mahne M, McHardy A, Pühler A, Meyer F. Bioinformatics support for high-throughput proteomics. J Biotechnol 2004; 106:147-56. [PMID: 14651857 DOI: 10.1016/j.jbiotec.2003.08.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In the "post-genome" era, mass spectrometry (MS) has become an important method for the analysis of proteome data. The rapid advancement of this technique in combination with other methods used in proteomics results in an increasing number of high-throughput projects. This leads to an increasing amount of data that needs to be archived and analyzed. To cope with the need for automated data conversion, storage, and analysis in the field of proteomics, the open source system ProDB was developed. The system handles data conversion from different mass spectrometer software, automates data analysis, and allows the annotation of MS spectra (e.g. assign gene names, store data on protein modifications). The system is based on an extensible relational database to store the mass spectra together with the experimental setup. It also provides a graphical user interface (GUI) for managing the experimental steps which led to the MS data. Furthermore, it allows the integration of genome and proteome data. Data from an ongoing experiment was used to compare manual and automated analysis. First tests showed that the automation resulted in a significant saving of time. Furthermore, the quality and interpretability of the results was improved in all cases.
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Affiliation(s)
- Andreas Wilke
- Center for Genome Research, Bielefeld University, D-33594 Bielefeld, Germany.
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31
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Newton RP, Brenton AG, Smith CJ, Dudley E. Plant proteome analysis by mass spectrometry: principles, problems, pitfalls and recent developments. PHYTOCHEMISTRY 2004; 65:1449-1485. [PMID: 15276445 DOI: 10.1016/j.phytochem.2004.04.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2004] [Revised: 04/06/2004] [Indexed: 05/24/2023]
Abstract
The genome of several species has now been elucidated; these genomes indicate the proteomic potential of the cell. While identification of genomes has been, and continues to be, a technically and intellectually demanding process, the identification of the proteome contains inherently greater difficulties. The proteome of each living cell is dynamic, altering in response to the individual cell's metabolic state and reception of intracellular and extracellular signal molecules, and many of the proteins which are expressed will be post-translationally altered. Thus if the purpose of the proteome analysis is to aid the understanding of protein function and interaction, then it is identification of the proteins in their final state which is required: for this mass spectrometric identification of individual proteins, indicating site and nature of modifications, is essential. Here we review the principles of the methodologies involved in such analyses, give some indication of current achievements in plant proteomics, and indicate imminent and prospective technical developments.
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Affiliation(s)
- Russell P Newton
- School of Biological Sciences, University of Wales Swansea, Singleton Park, Swansea SA2 8PP, UK.
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32
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33
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Nisar S, Lane CS, Wilderspin AF, Welham KJ, Griffiths WJ, Patterson LH. A PROTEOMIC APPROACH TO THE IDENTIFICATION OF CYTOCHROME P450 ISOFORMS IN MALE AND FEMALE RAT LIVER BY NANOSCALE LIQUID CHROMATOGRAPHY-ELECTROSPRAY IONIZATION-TANDEM MASS SPECTROMETRY. Drug Metab Dispos 2004; 32:382-6. [PMID: 15039290 DOI: 10.1124/dmd.32.4.382] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Nanoscale reversed-phase liquid chromatography (LC) combined with electrospray ionization-tandem mass spectrometry (ESI-MS/MS) has been used as a method for the direct identification of multiple cytochrome P450 (P450) isoforms found in male and female rat liver. In this targeted proteomic approach, rat liver microsomes were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by in-gel tryptic digestion of the proteins present in the 48- to 62-kDa bands. The resultant peptides were extracted and analyzed by LC-ESI-MS/MS. P450 identifications were made by searching the MS/MS data against a rat protein database containing 21,576 entries including 47 P450s using Sequest software (Thermo Electron, Hemel Hempstead, UK). Twenty-four P450 isoforms from the subfamilies 1A, 2A, 2B, 2C, 2D, 2E, 3A, 4A, 4F, CYP17, and CYP19 were positively identified in rat liver.
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Affiliation(s)
- S Nisar
- Department of Pharmaceutical & Biological Chemistry, The School of Pharmacy, University of London, 29-39 Brunswick Square, London, United Kingdom
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34
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Zhang W, Krutchinsky AN, Chait BT. "De novo" peptide sequencing by MALDI-quadrupole-ion trap mass spectrometry: a preliminary study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2003; 14:1012-1021. [PMID: 12954169 DOI: 10.1016/s1044-0305(03)00346-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Collision-induced dissociation of singly charged peptide ions produced by resonant excitation in a matrix-assisted laser desorption/ionization (MALDI) ion trap mass spectrometer yields relatively low complexity MS/MS spectra that exhibit highly preferential fragmentation, typically occurring adjacent to aspartyl, glutamyl, and prolyl residues. Although these spectra have proven to be of considerable utility for database-driven protein identification, they have generally been considered to contain insufficient information to be useful for extensive de novo sequencing. Here, we report a procedure for de novo sequencing of peptides that uses MS/MS data generated by an in-house assembled MALDI-quadrupole-ion trap mass spectrometer (Krutchinsky, Kalkum, and Chait Anal. Chem. 2001, 73, 5066-5077). Peptide sequences of up 14 amino acid residues in length have been deduced from digests of proteins separated by SDS-PAGE. Key to the success of the current procedure is an ability to obtain MS/MS spectra with high signal-to-noise ratios and to efficiently detect relatively low abundance fragment ions that result from the less favorable fragmentation pathways. The high signal-to-noise ratio yields sufficiently accurate mass differences to allow unambiguous amino acid sequence assignments (with a few exceptions), and the efficient detection of low abundance fragment ions allows continuous reads through moderately long stretches of sequence. Finally, we show how the aforementioned preferential cleavage property of singly charged ions can be used to facilitate the de novo sequencing process.
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Affiliation(s)
- Wenzhu Zhang
- The Rockefeller University, New York, New York 10021, USA
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35
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Kuiper HA, Kok EJ, Engel KH. Exploitation of molecular profiling techniques for GM food safety assessment. Curr Opin Biotechnol 2003; 14:238-43. [PMID: 12732328 DOI: 10.1016/s0958-1669(03)00021-1] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Several strategies have been developed to identify unintended alterations in the composition of genetically modified (GM) food crops that may occur as a result of the genetic modification process. These include comparative chemical analysis of single compounds in GM food crops and their conventional non-GM counterparts, and profiling methods such as DNA/RNA microarray technologies, proteomics and metabolite profiling. The potential of profiling methods is obvious, but further exploration of specificity, sensitivity and validation is needed. Moreover, the successful application of profiling techniques to the safety evaluation of GM foods will require linked databases to be built that contain information on variations in profiles associated with differences in developmental stages and environmental conditions.
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Affiliation(s)
- Harry A Kuiper
- RIKILT, Institute of Food Safety, PO Box 230, 6700 AE, Wageningen, The Netherlands.
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36
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Gu S, Pan S, Bradbury EM, Chen X. Precise peptide sequencing and protein quantification in the human proteome through in vivo lysine-specific mass tagging. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2003; 14:1-7. [PMID: 12504328 DOI: 10.1016/s1044-0305(02)00799-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Proteomics studies demand new scalable and automatable MS-based methods with higher specificity and accuracy. Here we describe an accurate and efficient method for both precise quantification and comprehensive de novo identification of peptide sequences in complex mixtures. The unique feature of this method is based on the incorporation of deuterium-labeled (heavy) lysines into proteins through in vivo cell culturing, which introduces specific mass tags at the carboxyl termini of proteolytic peptides when cleaved by certain proteases. The mass shift between the unlabeled and the deuterated lysine (lys-d4) assigns a mass signature to all lysine-containing peptides in any pool of proteolytic peptides. Lys-d4 tags can also serve as internal markers in MS/MS fragment spectra when they are buried in some peptide sequences due to miscleavages. This signal specificity circumvents the mass accuracy limitations in determining particular amino acid residues for de novo sequencing. Further, this strategy of lysine-specific tagging was successfully implemented to measure the differential protein expression of human skin fibroblast cells in response to heat shock.
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Affiliation(s)
- Sheng Gu
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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37
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Garcia P, Popot MA, Fournier F, Bonnaire Y, Tabet JC. Gas-phase behaviour of negative ions produced from thiazidic diuretics under electrospray conditions. JOURNAL OF MASS SPECTROMETRY : JMS 2002; 37:940-953. [PMID: 12271437 DOI: 10.1002/jms.353] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A systematic mass spectrometric study of 10 thiazidic diuretics and related compounds was undertaken by mass spectrometry (MS) with electrospray ionization in the negative ion mode. Collisional dissociation 'in-source' (CID-MS) and in a low-pressure collision cell (CID-MS/MS) were compared in both excitation regions. Spectra obtained by CID-MS and by CID-MS/MS were matched. Using the two methods, loss of HCl and consecutive dissociations from 2HCl losses were exhibited from compounds such as methyclothiazide and trichlormethiazide but not from other thiazidic diuretics that contain chlorine substituents in the aromatic moiety. However, deprotonated dichlorphenamide gave rise to loss of HCl by CID-MS and CID-MS/MS. For other diuretics such as hydroflumethiazide and hydrochlorothiazide, the loss of HCN and [HCN + SO(2)] was relevant. Reaction mechanisms were checked by means of deuterium-hydrogen exchange, which showed that deprotonation took place regioselectively on the heterocyclic moiety. The cleavage pathways require molecular isomerization forming ion-dipole complexes prior to decompositions, allowing long-distance proton transfer for neutral elimination. Identifications of the most specific fragmentations presented in this paper were applied to the screening and unambiguous identification of diuretics for horse doping control.
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Affiliation(s)
- Patrice Garcia
- L.A.B./F.N.C.F., 169 Avenue de la Division Leclerc, 92290 Châtenay-Malabry, France
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38
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Yergey AL, Coorssen JR, Backlund PS, Blank PS, Humphrey GA, Zimmerberg J, Campbell JM, Vestal ML. De novo sequencing of peptides using MALDI/TOF-TOF. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2002; 13:784-791. [PMID: 12148803 DOI: 10.1016/s1044-0305(02)00393-8] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The recently developed MALDI TOF-TOF instrument yields relatively complex but interpretable fragmentation spectra. When coupled with a straightforward sequence extension algorithm, it is possible to develop complete peptide sequences de novo from the spectra. This approach has been applied to a set of peptides derived from typtic digestion of electrophoretically separated sea urchin egg membrane proteins. When directed to proteins that have been described previously, the results were in essential agreement with those obtained by conventional data base searching approaches, with certain important exceptions. The present method detected errors in published sequences and was able to develop sequences from peptides differing in mass by one dalton (Da). These results show both the power of the present approach and the need for using de novo methods more frequently than may be otherwise appreciated.
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Affiliation(s)
- Alfred L Yergey
- Laboratory of Cellular and Molecular Biophysics, National Institute of Child Health and Human Development, Bethesda, Maryland 20892, USA.
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39
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Petritis K, Brussaux S, Guenu S, Elfakire C, Dreux M. Ion-pair reversed-phase liquid chromatography-electrospray mass spectrometry for the analysis of underivatized small peptides. J Chromatogr A 2002; 957:173-85. [PMID: 12113341 DOI: 10.1016/s0021-9673(02)00372-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The single run analysis of 23 small peptides (principally glycyl and lysyl dipeptides) is performed by ion-pair reversed-phase liquid chromatography coupled with evaporative light scattering detection or electrospray (tandem) mass spectrometry. Several perfluorinated carboxylic acid homologues are evaluated with an octadecyl silica stationary phase (Supelcosil ABZ+ Plus). Among the perfluorocarboxylic acids tested the nonafluoropentanoic acid and the tridecafluoroheptanoic acid gave the best results. Special attention was paid to the separation of isomer/isobar dipeptides (e.g., Gly-Ile, Gly-Leu, Leu-Gly, as well as Gly-Gln, Gly-Lys, etc.) which is usually necessary in spite of the high specificity of mass spectrometry. Before LC-MS analysis, ion-spray fragmentation as well as optimization of MS parameters of the analysed peptides was investigated. The optimum collision energy of glysyl peptides, Ala-Gln, Asp-Asp and Asp-Asp-Asp (13-18 eV) was different from that of the lysyl peptides, Tyr-Glu and oxidised glutathione (25-32 eV). Limits of detection varied from 0.1 to 1.2 mg l(-1) for simple MS and 0.05 to 25 mg l(-1) for tandem MS.
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Affiliation(s)
- Konstantinos Petritis
- Institut de Chimie Organique et Analytique, CNRS UMR-6005, Université d'Orléans, France
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40
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Abstract
Recently, we reported the proteome analysis of a human hepatocellular carcinoma cell line, HCC-M (Electrophoresis 2000, 21, 1787-1813), using two-dimensional gel electrophoresis (2-DE) and matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS). From a total of 408 unique spots excised from the 2-DE gel, 301 spots yielded good MALDI spectra. Out of these, 272 spots had matches returned from the database search leading to the identification of these proteins. Here, we report the results on the identification of the remaining 29 spots using nanoelectrospray ionization-tandem mass spectrometry (nESI-MS/MS). First, "peptide tag sequencing" was performed to obtain partial amino acid sequences of the peptides to search the SWISS-PROTand NCBI nonredundant protein databases. Spots that were still not able to find any matches from the databases were subjected to de novo peptide sequencing. The tryptic peptide sequences were used to search for homologues in the protein and nucleotide databases with the NCBI Basic Local Alignment Search Tool (BLAST), which was essential for the characterization of novel or post-translationally modified proteins. Using this approach, all the 29 spots were unambiguously identified. Among them, phosphotyrosyl phosphatase activator (PTPA), RNA-binding protein regulatory subunit, replication protein A 32 kDa subunit (RP-A) and N-acetylneuraminic acid phosphate synthase were reported to be cancer-related proteins.
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Affiliation(s)
- K Ou
- Bioprocessing Technology Center, National University of Singapore.
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41
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Gilar M, Belenky A, Wang BH. High-throughput biopolymer desalting by solid-phase extraction prior to mass spectrometric analysis. J Chromatogr A 2001; 921:3-13. [PMID: 11461010 DOI: 10.1016/s0021-9673(01)00833-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In the last 10 years mass spectrometry (MS) has become an important method for analysis of peptides, proteins and DNA. It was recently utilized for accurate high-throughput protein identification, sequencing and DNA genotyping. The presence of non-volatile buffers compromises sensitivity and accuracy of MS biopolymer analysis; it is essential to remove sample contaminants prior to analysis. We have developed a fast and efficient method for desalting of DNA oligonucleotides and peptides using 96-well solid-phase extraction plates packed with 5 mg of Waters Oasis HLB sorbent (Waters, Milford, MA, USA). This reversed-phase sorbent retains the biopolymer analytes, while non-retained inorganic ions are washed out with pure deionized water. DNA oligonucleotides or peptides are eluted using a small amount (20-100 microl) of acetonitrile-water (70:30, v/v) solution. The SPE desalting performance meets the requirements for MS applications such as protein digest analysis and DNA genotyping.
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Affiliation(s)
- M Gilar
- Waters Corporation, Milford, MA 01757-3696, USA.
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42
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Fiehn O, Kloska S, Altmann T. Integrated studies on plant biology using multiparallel techniques. Curr Opin Biotechnol 2001; 12:82-6. [PMID: 11167078 DOI: 10.1016/s0958-1669(00)00165-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Plant biology, especially the fields of molecular genetics and molecular physiology, is currently undergoing a change in paradigm from 'vertical' analysis of the role(s) of one or a few genes to 'horizontal' holistic approaches, studying the function of many or even all of the genes of an organism simultaneously. This change is leading us beyond genomes to transcriptomes, proteomes and metabalomes, and to an understanding of life at an entirely new level. Profiling strategies are putting this change into effect through the generation of large amounts of data, requiring that current bioinformatic approaches adapt and grow in order to make the most of these data.
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Affiliation(s)
- O Fiehn
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm, Germany.
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43
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Affiliation(s)
- J Godovac-Zimmermann
- Center for Molecular Medicine, Department of Medicine, University College London, 5 University Street, London WC1E 6JJ, United Kingdom.
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44
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2000; 35:1228-1236. [PMID: 11110096 DOI: 10.1002/1096-9888(200010)35:10<1228::aid-jms983>3.0.co;2-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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