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      • Record: found
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      ⿿Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples

      research-article
      Author(s): a , b , 1 , b , 1 , c , c , d , b , a , e , 2 , b , ⿿ , 2
      Publication date (Electronic):
      Journal: EuPA Open Proteomics
      Publisher: Elsevier
      Keywords: CAN, acetonitrile, FA, formic acid, FDR, false discovery rate, DF, directly-frozen, FASP, filter-aided sample preparation, FFPE, formalin-fixed, HLA-A class I, histocompatibility antigen A-23 alpha chain, HLA-DRB1 class II, histocompatibility antigen DRB1-4 beta chain, LFQ, label-free quantification, iFFPE, immediately formalin-fixed, PCA, principle component analysis, PSM, peptide spectral match, PTM, post-translational modification, s, standard deviation, sFFPE, stored for 30 min prior to formalin-fixed, SDC, sodium deoxycholate, SDS, sodium dodecyl sulfate, TEAB, triethylammonium bicarbonate, Proteomics, RNAlater, Formalin-fixed, Paraffin-embedded, Human colon mucosa, Preservation, Mass spectrometry

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          Highlights

          • ⿢

            We evaluated proteome analyses of snap frozen, RNAlater, and FFPE preserved samples.

          • ⿢

            Reliable proteome studies can be conducted on RNAlater, and FFPE preserved samples.

          • ⿢

            RNAlater sample preservation is highly usable for proteomics studies.

          Abstract

          Large biobanks exist worldwide containing formalin-fixed, paraffin-embedded samples and samples stored in RNAlater. However, the impact of tissue preservation on the result of a quantative proteome analysis remains poorly described.

          Human colon mucosal biopsies were extracted from the sigmoideum and either immediately frozen, stabilized in RNAlater, or stabilized by formalin-fixation. In one set of biopsies, formalin stabilization was delayed for 30 min. The protein content of the samples was characterized by high throughput quantitative proteomics.

          We were able to identify a similar high number of proteins in the samples regardless of preservation method, with only minor differences in protein quantitation.

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          Most cited references37

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          The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

          Juan Antonio Vizcaíno, Richard Côté, Attila Csordas … (2012)
          The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in the PRIDE database and related tools. First, we provide up-to-date statistics in data content, splitting the figures by groups of organisms and species, including peptide and protein identifications, and post-translational modifications. We then describe the tools that are part of the PRIDE submission pipeline, especially the recently developed PRIDE Converter 2 (new submission tool) and PRIDE Inspector (visualization and analysis tool). We also give an update about the integration of PRIDE with other MS proteomics resources in the context of the ProteomeXchange consortium. Finally, we briefly review the quality control efforts that are ongoing at present and outline our future plans.
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            The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra.

            Ignat Shilov, Sean Seymour, Alpesh A Patel … (2007)
            The Paragon Algorithm, a novel database search engine for the identification of peptides from tandem mass spectrometry data, is presented. Sequence Temperature Values are computed using a sequence tag algorithm, allowing the degree of implication by an MS/MS spectrum of each region of a database to be determined on a continuum. Counter to conventional approaches, features such as modifications, substitutions, and cleavage events are modeled with probabilities rather than by discrete user-controlled settings to consider or not consider a feature. The use of feature probabilities in conjunction with Sequence Temperature Values allows for a very large increase in the effective search space with only a very small increase in the actual number of hypotheses that must be scored. The algorithm has a new kind of user interface that removes the user expertise requirement, presenting control settings in the language of the laboratory that are translated to optimal algorithmic settings. To validate this new algorithm, a comparison with Mascot is presented for a series of analogous searches to explore the relative impact of increasing search space probed with Mascot by relaxing the tryptic digestion conformance requirements from trypsin to semitrypsin to no enzyme and with the Paragon Algorithm using its Rapid mode and Thorough mode with and without tryptic specificity. Although they performed similarly for small search space, dramatic differences were observed in large search space. With the Paragon Algorithm, hundreds of biological and artifact modifications, all possible substitutions, and all levels of conformance to the expected digestion pattern can be searched in a single search step, yet the typical cost in search time is only 2-5 times that of conventional small search space. Despite this large increase in effective search space, there is no drastic loss of discrimination that typically accompanies the exploration of large search space.
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              Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins*

              Tamar Geiger, Anja Wehner, Christoph Schaab … (2012)
              Deep proteomic analysis of mammalian cell lines would yield an inventory of the building blocks of the most commonly used systems in biological research. Mass spectrometry-based proteomics can identify and quantify proteins in a global and unbiased manner and can highlight the cellular processes that are altered between such systems. We analyzed 11 human cell lines using an LTQ-Orbitrap family mass spectrometer with a “high field” Orbitrap mass analyzer with improved resolution and sequencing speed. We identified a total of 11,731 proteins, and on average 10,361 ± 120 proteins in each cell line. This very high proteome coverage enabled analysis of a broad range of processes and functions. Despite the distinct origins of the cell lines, our quantitative results showed surprisingly high similarity in terms of expressed proteins. Nevertheless, this global similarity of the proteomes did not imply equal expression levels of individual proteins across the 11 cell lines, as we found significant differences in expression levels for an estimated two-third of them. The variability in cellular expression levels was similar for low and high abundance proteins, and even many of the most highly expressed proteins with household roles showed significant differences between cells. Metabolic pathways, which have high redundancy, exhibited variable expression, whereas basic cellular functions such as the basal transcription machinery varied much less. We harness knowledge of these cell line proteomes for the construction of a broad coverage “super-SILAC” quantification standard. Together with the accompanying paper (Schaab, C. MCP 2012, PMID: 22301388) (17) these data can be used to obtain reference expression profiles for proteins of interest both within and across cell line proteomes.
              Article 0 comments Cited 235 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Allan Stensballe
                Journal
                Journal ID (nlm-ta): EuPA Open Proteom
                Journal ID (iso-abbrev): EuPA Open Proteom
                Title: EuPA Open Proteomics
                Publisher: Elsevier
                ISSN (Electronic): 2212-9685
                Publication date PMC-release: 02 November 2015
                Publication date Collection: March 2016
                Publication date (Electronic): 02 November 2015
                Volume: 10
                Pages: 9-18
                Affiliations
                [a ]Research Unit for Molecular Diagnostic and Clinical Research, Hospital of Southern Jutland, Aabenraa, Denmark
                [b ]Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
                [c ]Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Aalborg, Denmark,
                [d ]Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
                [e ]Institute of Regional Health Research-Center Soenderjylland, University of Southern Denmark, Odense, Denmark
                Author notes
                [⿿ ]Corresponding author. Department of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 3B, 9220 Aalborg, Denmark. Fax: +45 9815 4008. as@ 123456hst.aau.dk
                [1]

                Contributed equally to the manuscript.

                [2]

                Shared last authors.

                Article
                Publisher ID: S2212-9685(15)30022-2
                DOI: 10.1016/j.euprot.2015.10.001
                PMC ID: 5988570
                PubMed ID: 29900094
                SO-VID: d7c3c28d-593d-4a86-9121-9df99ea1979e
                Copyright © © 2015 The Authors
                License:

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                Date received : 24 June 2015
                Date revision received : 19 August 2015
                Date accepted : 25 October 2015
                Categories
                Subject: Regular Article

                Keywords: can, acetonitrile,fa, formic acid,fdr, false discovery rate,df, directly-frozen,fasp, filter-aided sample preparation,ffpe, formalin-fixed,hla-a class i, histocompatibility antigen a-23 alpha chain,hla-drb1 class ii, histocompatibility antigen drb1-4 beta chain,lfq, label-free quantification,iffpe, immediately formalin-fixed,pca, principle component analysis,psm, peptide spectral match,ptm, post-translational modification,s, standard deviation,sffpe, stored for 30 min prior to formalin-fixed,sdc, sodium deoxycholate,sds, sodium dodecyl sulfate,teab, triethylammonium bicarbonate,proteomics,rnalater,formalin-fixed,paraffin-embedded,human colon mucosa,preservation,mass spectrometry
                Data availability:
                Keywords: can, acetonitrile, fa, formic acid, fdr, false discovery rate, df, directly-frozen, fasp, filter-aided sample preparation, ffpe, formalin-fixed, hla-a class i, histocompatibility antigen a-23 alpha chain, hla-drb1 class ii, histocompatibility antigen drb1-4 beta chain, lfq, label-free quantification, iffpe, immediately formalin-fixed, pca, principle component analysis, psm, peptide spectral match, ptm, post-translational modification, s, standard deviation, sffpe, stored for 30 min prior to formalin-fixed, sdc, sodium deoxycholate, sds, sodium dodecyl sulfate, teab, triethylammonium bicarbonate, proteomics, rnalater, formalin-fixed, paraffin-embedded, human colon mucosa, preservation, mass spectrometry

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