Background: The cancer transcriptome is difficult to explore due to the heterogeneity of quantitative and qualitative changes in gene expression linked to the disease status. An increasing number of "unconventional" transcripts, such as novel isoforms, non-coding RNAs, somatic gene fusions and deletions have been associated with the tumoral state. Massively parallel sequencing techniques provide a framework for exploring the transcriptional complexity inherent to cancer with a limited laboratory and financial effort. We developed a deep sequencing and bioinformatics analysis protocol to investigate the molecular composition of a breast cancer poly(A) + transcriptome. This method utilizes a cDNA library normalization step to diminish the representation of highly expressed transcripts and biology-oriented bioinformatic analyses to facilitate detection of rare and novel transcripts.

A new ionization method named surface-activated chemical ionization (SACI) has been realized. In this invention a commercially available atmospheric pressure chemical ionization (APCI) chamber, employed without any corona discharge (no-discharge APCI), has been modified with the insertion of a gold surface, leading to a significant improvement in the ionization efficiency. The ionization of the sample takes place by both gas-phase and surface-activated processes. This new ionization source is able to generate ions with high molecular mass and low charge states, leading to improved sensitivity and reduced noise. The new device has been tested in the analysis of some peptides. A comparison between the performance with and without the presence of the surface, and the optimization of the operating conditions (nebulizing gas flow, sample solution flow, pH of solution, and surface area), are reported and discussed.

In previous studies, the production of ions in an APCI source without any corona discharge was observed, and the intensity of the ion signals showed significant increases on placing a metallic surface at 45 degrees inside an orthogonal ion source. This method was named surface-activated chemical ionization (SACI). The present study was performed to investigate the mechanisms of ion production with or without the presence of the metallic surface, by varying instrumental parameters and the geometrical configuration. Approximate calculations show that, in the absence of corona discharge and of any additional surfaces, ions cannot be produced by collisional phenomena, because of their low kinetic energy, in the 10(-2) to 10(-3) eV range. Two alternative possibilities have been considered: the first takes into account that ions may originate by collision of neutral clusters of polar solvent molecules with the APCI source surfaces through clusterelectric effect. The second takes into account that the water dissociation constant k(w) is temperature dependent, passing from 10(-14.1669) at 20 degrees C to 10(-12.4318) at 90 degrees C. It means that the [H(+)] varies from 8.3 x 10(-8) to 6.1 x 10(-7) M going from 20 to 90 degrees C. Hence, at the high temperatures experimented in the APCI vaporizer, H(+) becomes available in solution in molar quantities analogous to those of analyte, and the protonation of the analyte itself can consequently occur. The activation of further ionization processes in the presence of the metallic surface can be reasonably attributed to interactions between gas-phase analyte molecules and solvent molecules adsorbed on the surface. Experiments performed with a thin layer of deuterated glycerol on the surface led to unequivocal results, i.e. the production of [M + D](+) ions of the analyte.

I. Introduction 370 II. Techniques That Are Usually Employed in the Study of Bioorganic Macromolecules 371 A. Proteins and Peptides 371 B. Oligonucleotides 374 C. Oligosaccharides and Glycoconjugates 375 D. Various Complexes (DNA–Protein, Antigen–Antibody, Macromolecules–Metals) 377 III. Common Problems and Developments in the Analysis of Bioorganic Macromolecules by Mass Spectrometry 377 A.  Ionization Source Problems and Developments 377     1.  Sensitivity 377     2.  Problems with Buffers 379     3.  Multicharge Effect 381 B.  Mass Analyzer Problems and Developments 381     1.  Linear Dynamic Range 381     2.  Tandem Mass Spectrometry 382     3.  Sensitivity 382     4.  Resolution 383     5.  Mass Accuracy 383 IV. New Promising Technologies 384 A.  Interfaces and Ionization Sources 384     1.  Improvements in the Coupling of Liquid‐Phase Separation Systems to Mass Spectrometry 384     2.  AP‐MALDI 384     3.  Deprotonant Agents 385     4.  Sonic Spray Ionization 388     5.  APCI without Corona Discharge 391 B.  Mass Analyzers 393     1.  Linear Quadrupole Ion Trap 394     2.  TOF Analyzers with New Detectors 395     3.  Multiple Mass Analyzers 396  V. Software for Data Treatment 397  VI. Conclusions and Future Developments 399 Acknowledgments 400 References 400 In recent years, mass spectrometry has been increasingly used for the analysis of various macromolecules of biological, biomedical, and biochemical interest. This increase has been made possible by two key developments: the advent of electrospray ionization (ESI) and matrix‐assisted laser desorption ionization (MALDI) sources. The two new techniques produce a significant increase in mass range and in sensitivity that led to the development of new applications and of new analyzer designs, software, and robotics. This review, apart from the description of the status of mass spectrometry in the analysis of bioorganic macromolecules, is mainly devoted to the illustration of the more recent promising techniques and on their possible future evolution. © 2003 Wiley Periodicals, Inc., Mass Spec Rev 22:369–406, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mas.10062