We carried out a test sample study to try to identify errors leading to irreproducibility, including incompleteness of peptide sampling, in LC-MS-based proteomics. We distributed a test sample consisting of an equimolar mix of 20 highly purified recombinant human proteins, to 27 laboratories for identification. Each protein contained one or more unique tryptic peptides of 1250 Da to also test for ion selection and sampling in the mass spectrometer. Of the 27 labs, initially only 7 labs reported all 20 proteins correctly, and only 1 lab reported all the tryptic peptides of 1250 Da. Nevertheless, a subsequent centralized analysis of the raw data revealed that all 20 proteins and most of the 1250 Da peptides had in fact been detected by all 27 labs. The centralized analysis allowed us to determine sources of problems encountered in the study, which include missed identifications (false negatives), environmental contamination, database matching, and curation of protein identifications. Improved search engines and databases are likely to increase the fidelity of mass spectrometry-based proteomics.

Chinese hamster ovary cells (CHO) are the most common cell line used in the production of therapeutic proteins. Understanding the complex pattern of secreted host cell proteins (HCP) that are released by CHO cells will facilitate the development of new recombinant protein production processes. In this study, we have adapted the N-azido-galactosamine (GalNAz) metabolic labeling method to enable the mass spectrometry identification and quantification of secreted proteins in cell culture media. CHO DG44 and CHO-S cells were cultured in media containing GalNAz, which was metabolically incorporated into mucin-type O-linked glycans of secreted proteins. These proteins were effectively enriched using click-chemistry from the cell culture media, allowing for the analysis of secreted proteins across multiple days of cell growth. When compared to the standard method for secretome analysis, the GalNAz method not only increased the total number of proteins identified but dramatically improved the quality of data by decreasing the number of background proteins (cytosolic or nuclear) to essentially zero.

More than 50% of all major drug targets are membrane proteins, and their role in cell-cell interaction and signal transduction is a vital concern. By culturing normal and malignant breast cancer cells with light or heavy isotopes of amino acids (SILAC), followed by cell fractionation, 1D gel separation of crude membrane proteins, and analysis of the digests using nanoelectrospray LC-MS/MS, we have quantified 1600 gene products that group into 997 protein families with approximately 830 membrane or membrane-associated proteins; 100 unknown, unnamed, or hypothetical proteins; and 65 protein families classified as ribosomal, heat shock, or histone proteins. A number of proteins show increased expression levels in malignant breast cancer cells, such as autoantigen p542, osteoblast-specific factor 2 (OSF-2), 4F2 heavy chain antigen, 34 kDa nucleolar scleroderma antigen, and apoptosis inhibitor 5. The expression of other proteins, such as membrane alanine aminopeptidase (CD13), epididymal protein, macroglobulin alpha2, PZP_HUMAN, and transglutaminase C, decreased in malignant breast cancer cells, whereas the majority of proteins remained unchanged when compared to the corresponding nonmalignant samples. Downregulation of CD13 and upregulation of OSF-2 were confirmed by immunohistochemistry using human tissue arrays with breast carcinomas. Furthermore, at least half the gene products displaying an expression change of 5-fold or higher have been described previously in the literature as having an association with cancerous malignancy. These results indicate that SILAC is a powerful technique that can be extended to the discovery of membrane-bound antigens that may be used to phenotype diseased cells.

Protein phosphorylation regulates many aspects of cellular function, including cell proliferation, migration, and signal transduction. An efficient strategy to isolate phosphopeptides from a pool of unphosphorylated peptides is essential to global characterization using mass spectrometry. We describe an approach employing isotope tagging reagents for relative and absolute quantification (iTRAQ) labeling to compare quantitatively commercial and prototypal immobilized metal affinity chelate (IMAC) and metal oxide resins. Results indicate a prototype iron chelate resin coupled to magnetic beads outperforms either the Ga 3ϩ -coupled analog, Fe 3ϩ , or Ga 3ϩ -loaded, iminodiacetic acid (IDA)-coated magnetic particles, Ga 3ϩ -loaded Captivate beads, Fe 3ϩ -loaded Poros 20MC, or zirconium-coated ProteoExtract magnetic beads. For example, compared with Poros 20MC, the magnetic metal chelate (MMC) studied here improved phosphopeptide recovery by 20% and exhibited 60% less contamination from unphosphorylated peptides. With respect to efficiency and contamination, MMC performed as well as prototypal magnetic metal oxide-coated (TiO 2 ) beads (MMO) or TiO 2 chromatographic spheres, even if the latter were used with 2,5-dihydroxybenzoic acid (DHB) procedures. Thus far, the sensitivity of the new prototypes reaches 50 fmol, which is comparable to TiO 2 spheres. In an exploration of natural proteomes, tryptic (phospho)peptides captured from stable isotopic labeling with amino acids in cell culture (SILAC)-labeled immunocomplexes following EGF-treatment of 5 ϫ 10 7 HeLa cells were sufficient to quantify stimulated response of over 60 proteins and identify 20 specific phosphorylation sites. (J Am Soc Mass Spectrom 2007, 18, 1932-1944) © 2007 American Society for Mass Spectrometry C haracterization of protein phosphorylation status, especially following stimulated transduction events, can provide mechanistic insights into the biological basis of signaling, cell cycle progression, adhesion, migration, and numerous other functions. Nowadays, the identification of phosphorylation sites in a complex milieu is carried out mainly by mass spectrometry. However, the sensitivity of analysis is largely hindered by low stoichiometry of phosphorylation, the reversible nature of the modification, and relatively weak ionization of phosphopeptides. It has been noted that enrichment of phosphopeptides from a pool of unphosphorylated peptides dramatically improves the success frequency for characterization.Several methods for enriching phosphorylated peptides have been reported, including chemical derivatization of phospho-residues [1-5], antibody-based capture, immobilized metal affinity chromatography (IMAC) [6 -10], enrichment on metal oxide surfaces [11][12][13], strong cation exchange chromatography [14,15], and phosphoramidate chemistry [16,17]. For example, anti-phosphotyrosine antibodies have been used successfully to enrich tyrosine phosphorylated proteins and peptides [18 -22]. Some authors report hundreds of phosphopeptides are identi...

Phosphorylation by the constitutively activated BCR-ABL tyrosine kinase is associated with the pathogenesis of the human chronic myelogenous leukemia (CML). It is difficult to characterize kinase response to stimuli or drug treatment because regulatory phosphorylation events are largely transient changes affecting low abundance proteins. Stable isotope labeling with amino acids in cell culture (SILAC) has emerged as a pivotal technology for quantitative proteomics. By metabolically labeling proteins with light or heavy tyrosine, we are able to quantify the change in phosphorylation of BCR-ABL kinase and its substrates in response to drug treatment in human CML cells. In this study, we observed that BCR-ABL kinase is phosphorylated at tyrosines 393 and 644, and that SH2-domain containing inositol phosphatase (SHIP)-2 and downstream of kinase (Dok)-2 are phosphorylated at tyrosine 1135 and 299, respectively. Based on the relative intensity of isotopic peptide pairs, we demonstrate that the level of phosphorylation of BCR-ABL kinase as well as SHIP-2 and Dok-2 is reduced approximately 90% upon treatment with Imatinib, a specific inhibitor of BCR-ABL kinase. Furthermore, proteins, such as SHIP-1, SH2-containing protein (SHC) and Casitas B-lineage lymphoma proto-oncogene (CBL), are also regulated by Imatinib. These results demonstrate the simplicity and utility of SILAC as a method to quantify dynamic changes in phosphorylation at specific sites in response to stimuli or drug treatment in cell culture.