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Pathologists play an important role in the final diagnosis for the patient and help the clinician in appropriate treatment planning. Both clinicians and pathologists have a crucial role in the laboratory process and it should be monitored properly for accurate and timely reporting. There are many steps in the laboratory process, where errors can occur which can affect the final diagnosis and prognosis for the patient. Errors can be major or minor but it eventually affects the patient's outcome. The laboratory process is broadly classified into three categories- pre-analytic, analytic and post-analytic phases. The errors that could frequently occur in each phase and the troubleshooting methods are broadly discussed in this article. Errors that have occurred should be investigated properly by identifying the main source of error and preventive action should be taken to avoid it in the future. [ABSTRACT FROM AUTHOR]

The outbreak of the SARS-CoV-2 pandemic created an unprecedented requirement for diagnostic testing, challenging not only healthcare workers and laboratories, but also providers. Quantitative RT-PCR of various specimen types is considered the diagnostic gold standard for the detection of SARS-CoV-2, both in terms of sensitivity and specificity. The pre-analytical handling of patient specimens is a critical factor to ensure reliable and valid test results. Therefore, the effect of storage duration and temperature on SARS-CoV-2 RNA copy number stability was examined in various commercially available specimen collection, transport and storage devices for naso/oropharyngeal swabs and saliva. The swab specimen transport and storage devices tested showed no significant alteration of viral RNA copy numbers when stored at room temperature, except for one system when stored for up to 96 h. However, at 37 °C a significant reduction of detectable RNA was found in 3 out of 4 of the swab solutions tested. It was also found that detectability of viral RNA remained unchanged in all 7 saliva devices as well as in unstabilized saliva when stored for 96 h at room temperature, but one device showed marked RNA copy number loss at 37 °C. All tested saliva collection devices inhibited SARS-CoV-2 infectivity immediately, whereas SARS-CoV-2 remained infectious in the swab transport systems examined, which are designed to be used for viral or bacterial growth in cell culture systems. • Raised temperature has major impact on SARS-CoV-2 RNA stability in 3 of 4 swab systems and 1 of 7 saliva collection devices. • SARS-CoV-2 RNA stability should be tested in specimen collection/transport/storage devices at level close to detection limit. • Tested saliva collection devices inactivate SARS-CoV-2. • Tested swab systems do not inactivate SARS-CoV-2. [ABSTRACT FROM AUTHOR]

Background: The recommendation for coagulation blood samples is to centrifuge at 4000 revolutions per minute (rpm) for 15 min to produce platelet-poor plasma before analysis. Rapid centrifugation, defined as centrifuging samples at higher speeds for shorter durations, could potentially reduce turn-around times (TAT), provided sample integrity is maintained. Objective: This study assessed the impact of rapid centrifugation on routine coagulation assay results. Methods: Blood samples were collected from volunteers at Inkosi Albert Luthuli Central Hospital and King Edward VIII Hospital, Durban, KwaZulu-Natal, South Africa, from September to November 2021. Samples were centrifuged using Method A, the current standard (4000 rpm/15 min), Method B (4000 rpm/10 min), Method C (5000 rpm/10 min) and Method D (5000 rpm/5 min). Platelet count, prothrombin time, activated partial thromboplastin time, thrombin time (TT), fibrinogen and D-dimer levels were analysed and results from Methods B, C and D compared to reference Method A. Results: Platelet-poor plasma was obtained from all samples (n = 60) using Methods A and B, and from 33/60 (55%) samples using Methods C and D. Differences between Method A and Methods C and D for normal prothrombin time, normal D-dimer and abnormal TT results were statistically significant. Prothrombin time results correlated strongly across all methods, while TT and D-dimer results correlated poorly. Activated partial thromboplastin time and fibrinogen results showed no significant differences across all methods. Conclusion: Rapid centrifugation at 4000 rpm/10 min (Method B) showed results consistent with the reference method. This method could potentially reduce the overall TAT for routine coagulation assays.

• Glucose concentration drops quickly before centrifugation in tubes containing only sodium fluoride (NaF). • Placing samples at 4 °C reduces only partially glucose decrease. • Citrate-containing tubes stabilize glucose concentrations for at least 24 h. • Mean bias between both tubes peaked between two- and four-hours following blood collection and reached 8.59%. • The use of citrate-containing tubes increased IFG, DM and GDM prevalences by 84.0%, 36.7% and 150%, respectively. Since 2023, guidelines of the AACC/ADA recommend the use of citrate buffer-containing tubes as a first option for glucose measurement. This study aims to assess the pre-analytical stability of glucose under various conditions (room temperature (RT) or at 4 °C) and the potential real-world impact of introducing these tubes on (gestational) diabetes and IFG prevalence. 25 healthy volunteers were sampled to assess glucose stability across time, at 4 °C and at RT, before and following centrifugation. 701 patients undergoing fasting plasma glucose analysis and 109 women having OGTT were collected according to current procedures (NaFl K 2 C 2 O 4 (NaFl) tubes) as well as with citrate-containing tubes (FC Mix). The mean glucose concentration bias between FC Mix and NaFl tubes when centrifugation occurred within 5 min was 0.53 % and this difference raised slowly to reach 2.3 %, six-hours post-centrifugation. When centrifugation was delayed, a rapid decrease in glucose concentrations was observed for NaFl tubes (4.9 % at 30 min) and this trend was only partially reduced by placing samples at 4 °C (3.1 %). The decrease reached 10.8 % (RT) and 7.8 % (4 °C) at 2 h, before reaching a plateau. Samples collected on citrate remained stable during 24 h. In real-life conditions, the mean bias between FC Mix and NaFl tubes increased progressively over time and reached 8.59 % for samples centrifuged between two- and four-hours following sampling. Compared to widespread practices, the use of citrate-containing tubes increased IFG, DM and GDM prevalences by 84.0 %, 36.7 % and 150 %, respectively. Glucose concentrations rapidly decrease in NaFl tubes following collection and placing samples at 4 °C reduces only marginally the decay. Citrate-containing tubes offer a valuable solution for direct and long-lasting glucose stabilization but, before wider adoption, large epidemiologic studies should confirm or redefine current diabetes diagnostic thresholds. [ABSTRACT FROM AUTHOR]

Background: Studies have shown that most errors in laboratory medicine occur in the pre-analytic phase of the test cycle. Specimen registration, a component of the pre-analytic phase, is reliant on an accompanying correctly completed requisition form containing mandatory information as stipulated by the receiving laboratory. Objective: This study was conducted to assess the completeness of requisition forms submitted to a histopathology laboratory. Method: This retrospective study was conducted at the National Health Laboratory Services (NHLS) histopathology laboratory at the Chris Hani Baragwanath Academic Hospital, Johannesburg, South Africa. Every tenth archived, original requisition form submitted between 1 January and 31 December 2019 was examined for completeness of information. Results: In total, 1 603 cases were included in the cohort. The following information was supplied in more than 95% of the cases: patient name, gender, hospital number, ward, clinician name, medical practitioner number, clinical history and biopsy site. Of the remaining variables, date of birth was missing in 64.3%, clinician contact number in 88.3% and time of collection in 73.2% of the cases. Although it is not mandatory, patient stickers were not attached in most (94.6%) forms and 82% did not have a doctor's stamp. Discussion: While most details were completed on the selected requisition forms, clinicians' contact numbers were absent on most requisition forms. These numbers should be provided in order to facilitate communication. Although doctors' stamps and hospitalgenerated patient stickers were sparingly used, these could limit typographical registration errors which impact on traceability and linking of patient records. The requisition form should be viewed as a referral letter to the pathologist. Conlusion: Clinicians and laboratory personnel should appreciate the importance of completing each mandatory field. Clinical meetings, electronic ordering systems and written guidelines may be useful to decrease some pre-analytic errors. [ABSTRACT FROM AUTHOR]

Background: The recommendation for coagulation blood samples is to centrifuge at 4000 revolutions per minute (rpm) for 15 min to produce platelet-poor plasma before analysis. Rapid centrifugation, defined as centrifuging samples at higher speeds for shorter durations, could potentially reduce turn-around times (TAT), provided sample integrity is maintained. Objective: This study assessed the impact of rapid centrifugation on routine coagulation assay results. Methods: Blood samples were collected from volunteers at Inkosi Albert Luthuli Central Hospital and King Edward VIII Hospital, Durban, KwaZulu-Natal, South Africa, from September to November 2021. Samples were centrifuged using Method A, the current standard (4000 rpm/15 min), Method B (4000 rpm/10 min), Method C (5000 rpm/10 min) and Method D (5000 rpm/5 min). Platelet count, prothrombin time, activated partial thromboplastin time, thrombin time (TT), fibrinogen and D-dimer levels were analysed and results from Methods B, C and D compared to reference Method A. Results: Platelet-poor plasma was obtained from all samples (n = 60) using Methods A and B, and from 33/60 (55%) samples using Methods C and D. Differences between Method A and Methods C and D for normal prothrombin time, normal D-dimer and abnormal TT results were statistically significant. Prothrombin time results correlated strongly across all methods, while TT and D-dimer results correlated poorly. Activated partial thromboplastin time and fibrinogen results showed no significant differences across all methods. Conclusion: Rapid centrifugation at 4000 rpm/10 min (Method B) showed results consistent with the reference method. This method could potentially reduce the overall TAT for routine coagulation assays. [ABSTRACT FROM AUTHOR]

Objective: Digital pathology is an opportunity to revise the routine and old artisanal workflow, moving to standard operating procedures, quality control and reproducibility. Here the results of a survey promoted by the Coordinamento della Medicina di Laboratorio (CRC Med Lab) of the Lombardy region in Italy are reported to shed light on the current situation of digital adoption in the country., Methods: The survey composed of 58 questions was sent to 60 pathology laboratories. The results were collected and most significant answers were reported and discussed., Results: Answers were received from 57 (95%) laboratories, a minority organized in spoke-hub networks (16%) with a centralized processing phase (11%). Hybrid manual/computer-assisted traceability was prevalent (36%), with QR/barcode labeling starting within the pathology lab (23%). Different laboratory information systems (LIS) were employed, mostly with alert functions and/or multimedial file attachments (56% and 46%, respectively). The majority opted for a semi-automated tracking management (44, 77%) and 18 centers (32%) were partly digitizing the routine (¾ scanning < 25% of slides). Whole slide images were retained for 3.7 years in average; in-house blocks/slides archiving was still preferred (30, 53%), with 1838 (±1551) and 1798 (±1950) days (5 years) internal permanence for blocks and slides that are stored in out-source (mean turnaround time for return on-demand 3.7±2.1, range 1-10 days)., Conclusions: The advantages of digital pathology must be balanced against the challenges faced in the structural revision of the pathology workflow. This regional scouting can represent the foundation to build an efficient and connected digital pathology system in the territory., (Copyright © 2024 Società Italiana di Anatomia Patologica e Citopatologia Diagnostica, Divisione Italiana della International Academy of Pathology.)

The stability of lipids and other metabolites in human body fluids ranges from very stable over several days to very unstable within minutes after sample collection. Since the high-resolution analytics of metabolomics and lipidomics approaches comprise all these compounds, the handling of body fluid samples, and thus the pre-analytical phase, is of utmost importance to obtain valid profiling data. This phase consists of two parts, sample collection in the hospital ("bedside") and sample processing in the laboratory ("bench"). For sample quality, the apparently simple steps in the hospital are much more critical than the "bench" side handling, where (bio)analytical chemists focus on highly standardized processing for high-resolution analysis under well-controlled conditions. This review discusses the most critical pre-analytical steps for sample quality from patient preparation; collection of body fluids (blood, urine, cerebrospinal fluid) to sample handling, transport, and storage in freezers; and subsequent thawing using current literature, as well as own investigations and practical experiences in the hospital. Furthermore, it provides guidance for (bio)analytical chemists to detect and prevent potential pre-analytical pitfalls at the "bedside," and how to assess the quality of already collected body fluid samples. A knowledge base is provided allowing one to decide whether or not the sample quality is acceptable for its intended use in distinct profiling approaches and to select the most suitable samples for high-resolution metabolomics and lipidomics investigations. [ABSTRACT FROM AUTHOR]

Abstract Background Hemoglobin (Hb) is a hemeprotein with two linked pairs of globin chains. Each chain is connected to a heme residue in its center. Hemoglobinopathies are divided into quantitative and qualitative defects in globin synthesis. Hemolysis is a pre-analytical problem that reduces quality of sample for measurement of many analytes. Methods Blood samples from 311 female and 189 male subjects with normal and abnormal Hb electrophoresis patterns were studied. Three milliliters of whole blood was obtained from all subjects and transferred into EDTA tubes. To analyze hemolysis, 1.5 ml of blood from each tube was aliquoted and frozen, and the remaining blood was stored at 4 °C for 24 h. Hemoglobin was measured in both hemolyzed and non-hemolyzed samples by capillary electrophoresis. Results and discussion Data was analyzed with linear regression. The results were linear for the lower limit of detection of 9, 0.5, and 0.1% up to at least 99.5, 6.6, and 99.4% for HbA, HbA2, and HbF, respectively. Method comparison demonstrated good agreement between non-hemolyzed and hemolyzed conditions for hemoglobin measurement. Conclusion Use of hemolyzed samples had no effected on hemoglobin measurements.

Histamine is known to be stable in the plasma obtained after centrifugation up to 4 days at RT for patients and controls.9 According to these results, we suggest that whole blood samples can be stored at +4°C up to 72 hours for histamine and 7 days for tryptase when the laboratory is not available immediately. Tryptase release is considered a robust marker of mast cell degranulation but is not informative in mild reactions and often normal during food-induced allergic reactions.1 Histamine is released at the early beginning of the reaction and may be useful when tryptase levels are normal or not informative. Keywords: histamine; pre-analytic; tryptase; whole blood EN histamine pre-analytic tryptase whole blood 1579 1583 5 05/17/21 20210501 NES 210501 Immediate hypersensitivity reactions are related to mast cell and/or basophil activation. Increased tryptase is defined as >=1.2 × basal value + 2 µg.L SP -1 sp .4 In our hands, tryptase uncertainties of measurement for low and high concentrations (9 µg.L SP -1 sp and 38.2 µg.L SP -1 sp ) are 17% and 16%, respectively, in accordance with published results.5 Plasma histamine concentrations were measured by a radioimmunoassay (Beckman Coulter, ImmunoTech). [Extracted from the article]

A patient may have two contemporary hemoglobin test results; one received from a hematology analyzer and the other from a blood gas analyzer. Such results may pose a dilemma if validated without investigation. A 27-year-old female patient presented to the emergency department because of worsening dyspnea and hemoptysis. Her hemogram revealed Hb 4.5 g/dL; Hct 16.1% while blood gas analysis showed Hb 8.1 g/dL; Hct 25.3%. The results were evaluated to be suspicious. All results were rejected and new requests were made. Hb 9.8 g/dL; Hct 31.9% were seen in repeated hemogram while blood gas analysis showed Hb 10.2 g/dL; Hct 31.5%. It was understood that the nurse used the vein with an intravenous fluid for sampling the first hemogram. A multitude of factors affect the accuracy of hemoglobin concentration measurements. Literature suggests that hemoglobin values of hematology analyzers and blood gas analyzers should be in harmony. Any discordance must be an alarm to stop and review the test results before validation. [ABSTRACT FROM AUTHOR]

While Global Studies has been pursued for research and teaching purposes for a few decades, there is little agreement on what substantiates the field. The Framing the Global project tackles this question by arguing for a renewed engagement with the empirical. It asks global scholars to step back from the analytic, to return to a space where pre-conceived methods, theories, and disciplines do not guide our findings. In this way, scholars must engage in a pre-analytic un-framing before they can define the particularities of their global. Each author in this forum enters into the global through an entry point, a point of specific empirical significance – whether a diaspora, a classroom, a biennale circuit, the AIDS regime, or plastic buckets and masks – that guides the way they trace what is global. In addition to exploring the need for un-framing Global Studies, Kahn and Gille also explain how un-framing and re-framing might help us understand global pedagogies and pandemics, by demonstrating how critical an engagement with the empirical is for contemporary global challenges that require us to excavate our understandings and shatter concepts that predominate rather than engage. [ABSTRACT FROM AUTHOR]

Background: The selection and rejection of non-conforming coagulation specimens is essential in safeguarding quality management in hemostasis laboratories that provide routine testing for bleeding and thrombotic disorders. In order to increase quality, it is important to reduce pre-analytical errors that generally account for 60 - 70% of total laboratory failure. The accidental presence of clots in vitro, in the pre-analytical phase of the coagulation, is a reason for coagulation specimen rejection, given that the reliability of test results can be adversely compromised. This study aimed to ascertain the effect of clots identified in the post-analytical phase within the blood sample sediments upon standard laboratory tests such as PT (prothrombin time) and APTT (activated partial thromboplastin time). Methods: From a total of 24,670 coagulation specimens gathered and prospectively collected and analyzed at the Haematology Laboratory of the 'f. Spiridon' Emergency County Hospital Iasi, Romania, during four months, 671 were identified with clot. Of the coagulated samples, 153 (22.80%) were considered for this study, including those specimens pinpointed with sediment clot through a post-analytical new reverification procedure. Results: The comparative study of the PT and APTT results obtained based on the samples identified with sediment clots in relation to the actual results recorded after the repetition of the sampling, pointed out 43.93% false results for PT1 test, with a significant difference between the variances of the values at the two evaluated moments (t = 2.961, p = 0.0037). The pattern was congruent in the case of the APTT test as well, exhibiting 69.04% false results, for which the variances of values at the two evaluated moments displayed significant differences (t = 2.208, p = 0.0306). In both of the cases significantly lower mean values were noted in the second determination of PT (PT1: 33.1 ± 39.6 vs. PT2: 25.8 ± 30.5) and APTT (APTT1: 42.8 ± 42.7 vs. APTT2: 38.1 ± 26.1. Results are important as they highlight the actual interference between the clot in the erythrocyte sediment and the evaluation of the patient's hemostasis. Conclusions: Our results confirm that the presence of clots in the erythrocyte sediment, with no identification prior to centrifugation, significantly affect the PT and APTT analysis, their accurate results being critical for the proper diagnosis and monitoring of anticoagulant therapy. [ABSTRACT FROM AUTHOR]

Highlights • Complement testing is resurgent. • Methods and need has expanded. • It is important to understand the difference and limitations. Abstract Complement immunobiology, and with it complement analysis, has undergone a renaissance in the past decade. Classically, complement analysis was limited number of testing C3, C4 in a routine laboratory with the possible addition of CH50 with all other analysis being performed at only few highly esoteric laboratories. This diagnostics expanding beyond specialized laboratories is the result of the growing recognition of the role played by complement dysfunction in many more diseases and disorders and the concomitant increase in interest in complement targeting therapeutics. In response, laboratories specializing in complement analysis have joined with the International Complement Society and the IUIS to coordinate efforts to standardize and improve complement testing, ongoing efforts that have already borne fruit. A recognition of the power of complement analysis has brought forward new testing but also realization of the importance of post-draw specimen handling to limit ex vivo activation, as well as the sometimes large difference between testing laboratory results. The increased usefulness of complement analysis and efforts to standardize and expand it means the future is strong for complement analysis. [ABSTRACT FROM AUTHOR]

Ancillary testing in cytopathology has grown dramatically over the past decade, enhancing the clinical value of cytology specimens obtained via minimally invasive methods. However, a complex testing landscape brings with it new and emerging risks to patient safety. Recognition of complicated systems issues as well as shared responsibility in process ownership can help to minimize safety risks. Because pre‐analytic factors account for the majority of errors in pathology, attention to operational steps (test ordering, specimen collection, specimen transport, specimen accessioning, and specimen processing) is critical for successful quality improvement programs. With increasing technical costs and complexity of many ancillary molecular tests, a growing trend toward send‐out testing to centralized reference laboratories poses additional patient safety risks. Given these new realities in cytopathology ancillary testing, a collaborative, team‐based approach with all process stakeholders is needed to improve pre‐analytic processes, reduce error risk, and enhance patient safety. [ABSTRACT FROM AUTHOR]

Background: The validity of laboratory results depends on pre-analytical variables not detected by conventional quality control. Recommendations are for post-centrifugation coagulation samples to remain capped with cappiercing primary tube analysis. Total laboratory automation integrates analytical platforms with potential incompatibilities necessitating changes including pre-analytical uncapping of samples. Methods: Samples analyzed for Prothrombin Time (PT), activated Partial Thromboplastin Time (aPTT), D-dimers, Antithrombin and Fibrinogen at baseline, and after 60 and 120 minutes were left at ambient temperature, either re-capped or uncapped, in order to simulate changes from baseline that could occur in uncapped samples on an automation track prior to analysis. Changes were compared to the maximal permissible bias. Results: Sample uncapping for up to 120 minutes at ambient temperature post-centrifugation did not result in clinically significant changes in routine coagulation parameters. Conclusions: Routine coagulation parameters will not change significantly if the primary citrate tubes are uncapped after centrifugation prior to analysis. [ABSTRACT FROM AUTHOR]

Background Multiple organizations produce guidance documents that provide opportunities to harmonize quality practices for diagnostic testing. The International Organization for Standardization ISO 15189 standard addresses requirements for quality in management and technical aspects of the clinical laboratory. One technical aspect addresses the complexities of the pre-examination phase prior to diagnostic testing. Methods The Committee for Molecular Diagnostics of the International Federation for Clinical Chemistry and Laboratory Medicine (also known as, IFCC C-MD) conducted a survey of international molecular laboratories and determined ISO 15189 to be the most referenced guidance document. In this review, the IFCC C-MD provides case-based examples illustrating the value of select pre-examination processes as these processes relate to molecular diagnostic testing. Case-based examples in infectious disease, oncology, inherited disease and pharmacogenomics address the utility of: 1) providing information to patients and users, 2) designing requisition forms, 3) obtaining informed consent and 4) maintaining sample integrity prior to testing. Conclusions The pre-examination phase requires extensive and consistent communication between the laboratory, the healthcare provider and the end user. The clinical vignettes presented in this paper illustrate the value of applying select ISO 15189 recommendations for general laboratory to the more specialized area of Molecular Diagnostics. [ABSTRACT FROM AUTHOR]

The introduction of molecular testing into cytopathology laboratory practice has expanded the types of samples considered feasible for identifying genetic alterations that play an essential role in cancer diagnosis and treatment. Reverse transcription-polymerase chain reaction (RT-PCR), a sensitive and specific technical approach for amplifying a defined segment of RNA after it has been reverse-transcribed into its DNA complement, is commonly used in clinical practice for the identification of recurrent or tumor-specific fusion gene events. Real-time RT-PCR (quantitative RT-PCR), a technical variation, also permits the quantitation of products generated during each cycle of the polymerase chain reaction process. This review addresses qualitative and quantitative pre-analytic and analytic considerations of RT-PCR as they relate to various cytologic specimens. An understanding of these aspects of genetic testing is central to attaining optimal results in the face of the challenges that cytology specimens may present. Cancer Cytopathol 2017;125:11-19. © 2016 American Cancer Society. [ABSTRACT FROM AUTHOR]

Background No study has explored the separate contributions of pre-analytical and analytical factors to hyperammonemia. Methods Laboratory information systems were queried for tests of ammonia concentrations over a 12 month period. Pre-analytic (collection to laboratory receipt) and analytic (laboratory receipt to result) elapsed times were determined. Results Under routine conditions for 3626 tests, normal and elevated results were similarly distributed if the time from venipuncture to result was < 120 min. Delays, during analysis performance and in transportation to the laboratory, potentially contributed to hyperammonemia in a small number of samples ( n = 96, 2.7%). Similar results were obtained from a second hospital with a separate laboratory. Conclusions Delays, in either transportation to the laboratory after collection or before completion of analysis, have the potential to elevate ammonia concentrations and may cause pseudo-hyperammonemia. Unexpectedly elevated ammonia concentrations need to be evaluated for errors in sampling handling. [ABSTRACT FROM AUTHOR]

Abstract: Introduction: We have recently described epitope detection in macrophages (EDIM) by flow cytometry. This is a promising tool for the diagnosis and follow-up of malignancies. However, biological and technical validation is warranted before clinical applicability can be explored. Methods: The pre-analytic and analytic phases were investigated. Five different aspects were assessed: blood sample stability, intra-individual variability in healthy persons, intra-assay variation, inter-assay variation and assay transferability. The post-analytic phase was already partly standardized and described in an earlier study. Results: The outcomes in the pre-analytic phase showed that samples are stable for 24h after venipuncture. Biological variation over time was similar to that of serum tumor marker assays; each patient has a baseline value. Intra-assay variation showed good reproducibility, while inter-assay variation showed reproducibility similar to that of to established serum tumor marker assays. Furthermore, the assay showed excellent transferability between analyzers. Conclusion: Under optimal analytic conditions the EDIM method is technically stable, reproducible and transferable. Biological variation over time needs further assessment in future work. [Copyright &y& Elsevier]

Metabolomics is the science of characterizing and quantifying small molecule metabolites in biological systems. These metabolites give organisms their biochemical characteristics, providing a link between genotype, environment, and phenotype. With these opportunities also come data challenges, such as compound annotation, missing values, and batch effects. We present the steps of a general pipeline to process untargeted mass spectrometry data to alleviate the latter two challenges. We assume to have a matrix with metabolite abundances, with metabolites in rows and samples in columns. The steps in the pipeline include summarizing technical replicates (if available), filtering, imputing, transforming, and normalizing the data. In each of these steps, a method and parameters should be chosen based on assumptions one is willing to make, the question of interest, and diagnostic tools. Besides giving a general pipeline that can be adapted by the reader, our goal is to review diagnostic tools and criteria that are helpful when making decisions in each step of the pipeline and assessing the effectiveness of normalization and batch correction. We conclude by giving a list of useful packages and discuss some alternative approaches that might be more appropriate for the reader's data.

Introduction: The pre-analytical step includes sample collection, preparation, transportation and storage in the pathology unit where the diagnosis is performed. The pathologist ensures that pre-analytical conditions are in line with expectations. The lack of standardization for handling cytological samples makes this pre-analytical step difficult to harmonize. Moreover, this step depends on the nature of the sample: fresh liquid or fixed material, air-dried smears, liquid-based cytology. The aim of the study was to review the different practices in French structures of pathology on the pre-analytical phase concerning cytological fluids such as broncho-alveolar lavage (BALF), serous fluids and urine., Methods: A survey was conducted on the basis of the pre-analytical chapter of the ISO 15189 and sent to 191 French pathological structures (105 public and 86 private)., Results: Fifty-six laboratories replied to the survey. Ninety-five per cent have a computerized management system and 70% a manual on sample handling. The general instructions requested for the patients and sample identification were highly correctly filled with a short time routing and additional tests prescription. By contrast, information are variable concerning the clinical information requested and the type of tubes for collecting fluids and the volumes required as well as the actions taken in case of non-conformity. For the specific items concerning BALF, serous fluids and urine, this survey has shown a great heterogeneity according to sample collection, fixation and of clinical information., Conclusion: This survey demonstrates that the pre-analytical quality for BALF, serous fluids and urine is not optimal and that some corrections of the practices are recommended with a standardization of numerous steps in order to increase the reproducibility of additional tests such as immunocytochemistry, cytogenetic and molecular biology. Some recommendations have been written., (Copyright © 2015 Elsevier Masson SAS. All rights reserved.)