Clarify assay name uniqueness applies to all experiments including multiplexed

Co-authored-by: ypriverol <52113+ypriverol@users.noreply.github.com>

Author: Copilot

sdrf-proteomics/README.adoc

@@ -261,11 +261,11 @@ The connection between the Samples to the Data files is done by using a series o
 
 The order of the columns is important, _assay name_ SHOULD always be located before the comments. It is RECOMMENDED to put the last column as _comment[data file]_. The following properties MUST be provided for each data file (ms run) file:
 
-- **assay name**: Assay name is a unique identifier for the data file. All assay names within an SDRF file MUST be unique to ensure unambiguous identification of each MS run or data file, except in multiplexed experiments (TMT, iTRAQ, SILAC) where multiple samples are analyzed in a single MS run. Examples of assay names are: "sample1_run1", "run_fraction_1_2", "batch1_fraction2_rep3".
+- **assay name**: Assay name is a unique identifier for the data file. All assay names within an SDRF file MUST be unique to ensure unambiguous identification of each MS run or data file. Each assay name must correspond uniquely to a specific data file name and its properties. Examples of assay names are: "sample1_run1", "run_fraction_1_2", "batch1_fraction2_rep3".
 
 TIP: To ensure assay name uniqueness when multiple samples have similar experimental conditions, consider incorporating sample-specific information (e.g., sample ID, biological replicate number) or sequential numbering across all runs in the assay name. For example, use "sample1_run1", "sample1_run2", "sample2_run1", "sample2_run2" instead of repeating generic names for each sample.
 
-NOTE: An exception to the uniqueness requirement applies to multiplexed experiments (TMT, iTRAQ, SILAC) where multiple samples are analyzed together in a single MS run. In such cases, multiple rows may share the same assay name when they represent different samples or channels within the same multiplexed analysis. This is the only scenario where assay name duplication is acceptable.
+NOTE: In multiplexed experiments (TMT, iTRAQ, SILAC) where multiple samples are analyzed together in a single MS run, the assay name is still unique to the data file. What occurs in these cases is that multiple rows in the SDRF file may reference the same unique assay name, with each row representing a different sample or channel within that multiplexed analysis. The combination of source name (sample identifier) and assay name creates the unique relationship between samples and data files.
 
 - **technology type**: The technology type is used to describe the technology used to capture the data. It is RECOMMENDED to use the technology type column immediately after the assay name column in the SDRF file.
 - **comment[fraction identifier]**: The fraction identifier allows recording the number of a given fraction. The fraction identifier corresponds to this ontology term. It MUST start from 1, and if the experiment is not fractionated, 1 MUST be used for each MSRun (assay).